Setup a Tripal4 site with test data

README.md

The chado data as mapped to content types currently included in the database dump are:

• Gene: 50
• mRNA: 75
• Organism: 6
• Contact: 7
• Analysis: 7 (two are of type Genome Assembly and 2 are of type genome annotation)
• Project: 2 (both of type Genome Project)
• Publication: 4 (1 is the null pub)
• Protocol: 3
• Study: 3

1. Setup some variables to customize the following commands without copy/paste ;-)

export drupalVersion='10.1.x-dev'
export issueNum='1515'
export containerName="tripal$issueNum"

2. Build a fresh docker without chado installed using the branch in your current repo + then run a container.

docker build --tag=tripaldocker:tripal$issueNum --build-arg drupalversion=$drupalVersion --build-arg installchado=FALSE --file tripaldocker/Dockerfile-php8.2-pgsql13 ./
docker run --publish=80:80 --name=$containerName -tid --volume=$(pwd):/var/www/drupal/web/modules/contrib/tripal tripaldocker:tripal$issueNum
docker exec $containerName service postgresql restart

3. Download sampledataChadoDump.sql.txt then on the terminal from your downloads folder, use docker copy to get this file inside your new container.

docker cp ~/Downloads/sampledataChadoDump.sql.txt $containerName:/var/www/drupal/web

4. Use drush to apply this database dump to your current site.

docker exec -it $containerName drush sql:query --file sampledataChadoDump.sql.txt

5. Navigate to the chado schema listing in your browser: http://localhost/admin/tripal/storage/chado/manager. You should see an entry for "chado" and under "In Tripal" it says "No".
6. Click "Add to Tripal" and then click "Set as Default".
7. Prepare this schema (it's named chado in the dump)

docker exec $containerName drush trp-prep-chado --schema-name='chado'

8. Add content types in the general, genomic and germplasm collections.

docker exec -it $containerName drush tripal:trp-import-types --username=drupaladmin --collection_id=general_chado
docker exec -it $containerName drush tripal:trp-import-types --username=drupaladmin --collection_id=germplasm_chado
docker exec -it $containerName drush tripal:trp-import-types --username=drupaladmin --collection_id=genomic_chado

sampledataChadoDump.sql.txt

--
-- PostgreSQL database dump
--

-- Dumped from database version 13.13 (Debian 13.13-0+deb11u1)
-- Dumped by pg_dump version 13.13 (Debian 13.13-0+deb11u1)

SET statement_timeout = 0;
SET lock_timeout = 0;
SET idle_in_transaction_session_timeout = 0;
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SELECT pg_catalog.set_config('search_path', '', false);
SET check_function_bodies = false;
SET xmloption = content;
SET client_min_messages = warning;
SET row_security = off;

--
-- Name: chado; Type: SCHEMA; Schema: -; Owner: drupaladmin
--

CREATE SCHEMA chado;


ALTER SCHEMA chado OWNER TO drupaladmin;

--
-- Name: feature_by_fx_type; Type: TYPE; Schema: chado; Owner: drupaladmin
--

CREATE TYPE chado.feature_by_fx_type AS (
	feature_id bigint,
	depth integer
);


ALTER TYPE chado.feature_by_fx_type OWNER TO drupaladmin;

--
-- Name: soi_type; Type: TYPE; Schema: chado; Owner: drupaladmin
--

CREATE TYPE chado.soi_type AS (
	type_id bigint,
	subject_id bigint,
	object_id bigint
);


ALTER TYPE chado.soi_type OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4node(bigint, bigint, bigint, bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4node(bigint, bigint, bigint, bigint, integer) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    origin alias for $1;
    child_id alias for $2;
    cvid alias for $3;
    typeid alias for $4;
    depth alias for $5;
    cterm cvterm_relationship%ROWTYPE;
    exist_c int;

BEGIN

    --- RAISE NOTICE 'depth=% root=%', depth,child_id;
    --- not check type_id as it may be null and not very meaningful in cvtermpath when pathdistance > 1
    SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth;

    IF (exist_c = 0) THEN
        INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth);
    END IF;
    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP
        PERFORM _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1);
    END LOOP;
    RETURN 1;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4node(bigint, bigint, bigint, bigint, integer) OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4node2detect_cycle(bigint, bigint, bigint, bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4node2detect_cycle(bigint, bigint, bigint, bigint, integer) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    origin alias for $1;
    child_id alias for $2;
    cvid alias for $3;
    typeid alias for $4;
    depth alias for $5;
    cterm cvterm_relationship%ROWTYPE;
    exist_c int;
    ccount  int;
    ecount  int;
    rtn     bigint;
BEGIN

    EXECUTE 'SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id = '|| origin || ' AND p2.subject_id = ' || child_id || 'AND ' || depth || '> 0';
    GET DIAGNOSTICS ccount = ROW_COUNT;
    IF (ccount > 0) THEN
        --RAISE EXCEPTION 'FOUND CYCLE: node % on cycle path',origin;
        RETURN origin;
    END IF;

    EXECUTE 'SELECT * FROM tmpcvtermpath WHERE cv_id = ' || cvid || ' AND object_id = ' || origin || ' AND subject_id = ' || child_id || ' AND ' || origin || '<>' || child_id;
    GET DIAGNOSTICS ecount = ROW_COUNT;
    IF (ecount > 0) THEN
        --RAISE NOTICE 'FOUND TWICE (node), will check root obj % subj %',origin, child_id;
        SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(child_id, cvid);
        IF (rtn > 0) THEN
            RETURN rtn;
        END IF;
    END IF;

    EXECUTE 'SELECT * FROM tmpcvtermpath WHERE cv_id = ' || cvid || ' AND object_id = ' || origin || ' AND subject_id = ' || child_id || ' AND pathdistance = ' || depth;
    GET DIAGNOSTICS exist_c = ROW_COUNT;
    IF (exist_c = 0) THEN
        EXECUTE 'INSERT INTO tmpcvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(' || origin || ', ' || child_id || ', ' || cvid || ', ' || typeid || ', ' || depth || ')';
    END IF;

    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = child_id LOOP
        --RAISE NOTICE 'DOING for node, % %', origin, cterm.subject_id;
        SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(origin, cterm.subject_id, cvid, cterm.type_id, depth+1);
        IF (rtn > 0) THEN
            RETURN rtn;
        END IF;
    END LOOP;
    RETURN 0;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4node2detect_cycle(bigint, bigint, bigint, bigint, integer) OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4root(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4root(bigint, bigint) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    rootid alias for $1;
    cvid alias for $2;
    ttype bigint;
    cterm cvterm_relationship%ROWTYPE;
    child cvterm_relationship%ROWTYPE;

BEGIN

    SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = 'isa' OR name = 'is_a');
    PERFORM _fill_cvtermpath4node(rootid, rootid, cvid, ttype, 0);
    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP
        PERFORM _fill_cvtermpath4root(cterm.subject_id, cvid);
        -- RAISE NOTICE 'DONE for term, %', cterm.subject_id;
    END LOOP;
    RETURN 1;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4root(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4root2detect_cycle(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4root2detect_cycle(bigint, bigint) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    rootid alias for $1;
    cvid alias for $2;
    ttype bigint;
    ccount int;
    cterm cvterm_relationship%ROWTYPE;
    child cvterm_relationship%ROWTYPE;
    rtn     bigint;
BEGIN

    SELECT INTO ttype cvterm_id FROM cvterm WHERE (name = 'isa' OR name = 'is_a');
    SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, rootid, cvid, ttype, 0);
    IF (rtn > 0) THEN
        RETURN rtn;
    END IF;
    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = rootid LOOP
        EXECUTE 'SELECT * FROM tmpcvtermpath p1, tmpcvtermpath p2 WHERE p1.subject_id=p2.object_id AND p1.object_id=p2.subject_id AND p1.object_id=' || rootid || ' AND p1.subject_id=' || cterm.subject_id;
        GET DIAGNOSTICS ccount = ROW_COUNT;
        IF (ccount > 0) THEN
            --RAISE NOTICE 'FOUND TWICE (root), will check root obj % subj %',rootid,cterm.subject_id;
            SELECT INTO rtn _fill_cvtermpath4node2detect_cycle(rootid, cterm.subject_id, cvid, ttype, 0);
            IF (rtn > 0) THEN
                RETURN rtn;
            END IF;
        ELSE
            SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(cterm.subject_id, cvid);
            IF (rtn > 0) THEN
                RETURN rtn;
            END IF;
        END IF;
    END LOOP;
    RETURN 0;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4root2detect_cycle(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4soi(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4soi(bigint, bigint) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    rootid alias for $1;
    cvid alias for $2;
    ttype bigint;
    cterm soi_type%ROWTYPE;

BEGIN

    SELECT INTO ttype cvterm_id FROM cvterm WHERE name = 'isa';
    --RAISE NOTICE 'got ttype %',ttype;
    PERFORM _fill_cvtermpath4soinode(rootid, rootid, cvid, ttype, 0);
    FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = rootid LOOP
        PERFORM _fill_cvtermpath4soi(cterm.subject_id, cvid);
    END LOOP;
    RETURN 1;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4soi(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: _fill_cvtermpath4soinode(bigint, bigint, bigint, bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._fill_cvtermpath4soinode(bigint, bigint, bigint, bigint, integer) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    origin alias for $1;
    child_id alias for $2;
    cvid alias for $3;
    typeid alias for $4;
    depth alias for $5;
    cterm soi_type%ROWTYPE;
    exist_c int;

BEGIN

    --RAISE NOTICE 'depth=% o=%, root=%, cv=%, t=%', depth,origin,child_id,cvid,typeid;
    SELECT INTO exist_c count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth;
    --- longest path
    IF (exist_c > 0) THEN
        UPDATE cvtermpath SET pathdistance = depth WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id;
    ELSE
        INSERT INTO cvtermpath (object_id, subject_id, cv_id, type_id, pathdistance) VALUES(origin, child_id, cvid, typeid, depth);
    END IF;

    FOR cterm IN SELECT tmp_type AS type_id, subject_id FROM tmpcvtr WHERE object_id = child_id LOOP
        PERFORM _fill_cvtermpath4soinode(origin, cterm.subject_id, cvid, cterm.type_id, depth+1);
    END LOOP;
    RETURN 1;
END;
$_$;


ALTER FUNCTION chado._fill_cvtermpath4soinode(bigint, bigint, bigint, bigint, integer) OWNER TO drupaladmin;

SET default_tablespace = '';

SET default_table_access_method = heap;

--
-- Name: cvtermpath; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvtermpath (
    cvtermpath_id bigint NOT NULL,
    type_id bigint,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    cv_id bigint NOT NULL,
    pathdistance integer
);


ALTER TABLE chado.cvtermpath OWNER TO drupaladmin;

--
-- Name: TABLE cvtermpath; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvtermpath IS 'The reflexive transitive closure of
the cvterm_relationship relation.';


--
-- Name: COLUMN cvtermpath.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermpath.type_id IS 'The relationship type that
this is a closure over. If null, then this is a closure over ALL
relationship types. If non-null, then this references a relationship
cvterm - note that the closure will apply to both this relationship
AND the OBO_REL:is_a (subclass) relationship.';


--
-- Name: COLUMN cvtermpath.cv_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermpath.cv_id IS 'Closures will mostly be within
one cv. If the closure of a relationship traverses a cv, then this
refers to the cv of the object_id cvterm.';


--
-- Name: COLUMN cvtermpath.pathdistance; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermpath.pathdistance IS 'The number of steps
required to get from the subject cvterm to the object cvterm, counting
from zero (reflexive relationship).';


--
-- Name: _get_all_object_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._get_all_object_ids(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    leaf alias for $1;
    cterm cvtermpath%ROWTYPE;
    cterm2 cvtermpath%ROWTYPE;
BEGIN

    FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP
        RETURN NEXT cterm;
        FOR cterm2 IN SELECT * FROM _get_all_object_ids(cterm.object_id) LOOP
            RETURN NEXT cterm2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado._get_all_object_ids(bigint) OWNER TO drupaladmin;

--
-- Name: _get_all_subject_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado._get_all_subject_ids(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    root alias for $1;
    cterm cvtermpath%ROWTYPE;
    cterm2 cvtermpath%ROWTYPE;
BEGIN

    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP
        RETURN NEXT cterm;
        FOR cterm2 IN SELECT * FROM _get_all_subject_ids(cterm.subject_id) LOOP
            RETURN NEXT cterm2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado._get_all_subject_ids(bigint) OWNER TO drupaladmin;

--
-- Name: boxquery(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.boxquery(bigint, bigint) RETURNS box
    LANGUAGE sql IMMUTABLE
    AS $_$SELECT box (create_point($1, $2), create_point($1, $2))$_$;


ALTER FUNCTION chado.boxquery(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: boxquery(bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.boxquery(bigint, bigint, bigint) RETURNS box
    LANGUAGE sql IMMUTABLE
    AS $_$SELECT box (create_point($1, $2), create_point($1, $3))$_$;


ALTER FUNCTION chado.boxquery(bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: boxrange(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.boxrange(bigint, bigint) RETURNS box
    LANGUAGE sql IMMUTABLE
    AS $_$SELECT box (create_point(0, $1), create_point($2,500000000))$_$;


ALTER FUNCTION chado.boxrange(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: boxrange(bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.boxrange(bigint, bigint, bigint) RETURNS box
    LANGUAGE sql IMMUTABLE
    AS $_$SELECT box (create_point($1, $2), create_point($1,$3))$_$;


ALTER FUNCTION chado.boxrange(bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: complement_residues(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.complement_residues(text) RETURNS text
    LANGUAGE sql
    AS $_$SELECT (translate($1,
                   'acgtrymkswhbvdnxACGTRYMKSWHBVDNX',
                   'tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX'))$_$;


ALTER FUNCTION chado.complement_residues(text) OWNER TO drupaladmin;

--
-- Name: concat_pair(text, text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.concat_pair(text, text) RETURNS text
    LANGUAGE sql
    AS $_$SELECT $1 || $2$_$;


ALTER FUNCTION chado.concat_pair(text, text) OWNER TO drupaladmin;

--
-- Name: create_point(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.create_point(bigint, bigint) RETURNS point
    LANGUAGE sql
    AS $_$SELECT point ($1, $2)$_$;


ALTER FUNCTION chado.create_point(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: create_soi(); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.create_soi() RETURNS integer
    LANGUAGE plpgsql
    AS $$
DECLARE
    parent soi_type%ROWTYPE;
    isa_id cvterm.cvterm_id%TYPE;
    soi_term TEXT := 'soi';
    soi_def TEXT := 'ontology of SO feature instantiated in database';
    soi_cvid bigint;
    soiterm_id bigint;
    pcount INTEGER;
    count INTEGER := 0;
    cquery TEXT;
BEGIN

    SELECT INTO isa_id cvterm_id FROM cvterm WHERE name = 'isa';

    SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term;
    IF (soi_cvid > 0) THEN
        DELETE FROM cvtermpath WHERE cv_id = soi_cvid;
        DELETE FROM cvterm WHERE cv_id = soi_cvid;
    ELSE
        INSERT INTO cv (name, definition) VALUES(soi_term, soi_def);
    END IF;
    SELECT INTO soi_cvid cv_id FROM cv WHERE name = soi_term;
    INSERT INTO cvterm (name, cv_id) VALUES(soi_term, soi_cvid);
    SELECT INTO soiterm_id cvterm_id FROM cvterm WHERE name = soi_term;

    CREATE TEMP TABLE tmpcvtr (tmp_type BIGINT, type_id bigint, subject_id bigint, object_id bigint);
    CREATE UNIQUE INDEX u_tmpcvtr ON tmpcvtr(subject_id, object_id);

    INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id)
        SELECT DISTINCT isa_id, soiterm_id, f.type_id, soiterm_id FROM feature f, cvterm t
        WHERE f.type_id = t.cvterm_id AND f.type_id > 0;
    EXECUTE 'select * from tmpcvtr where type_id = ' || soiterm_id || ';';
    get diagnostics pcount = row_count;
    raise notice 'all types in feature %',pcount;
--- do it hard way, delete any child feature type from above (NOT IN clause did not work)
    FOR parent IN SELECT DISTINCT 0, t.cvterm_id, 0 FROM feature c, feature_relationship fr, cvterm t
            WHERE t.cvterm_id = c.type_id AND c.feature_id = fr.subject_id LOOP
        DELETE FROM tmpcvtr WHERE type_id = soiterm_id and object_id = soiterm_id
            AND subject_id = parent.subject_id;
    END LOOP;
    EXECUTE 'select * from tmpcvtr where type_id = ' || soiterm_id || ';';
    get diagnostics pcount = row_count;
    raise notice 'all types in feature after delete child %',pcount;

    --- create feature type relationship (store in tmpcvtr)
    CREATE TEMP TABLE tmproot (cv_id bigint not null, cvterm_id bigint not null, status INTEGER DEFAULT 0);
    cquery := 'SELECT * FROM tmproot tmp WHERE tmp.status = 0;';
    ---temp use tmpcvtr to hold instantiated SO relationship for speed
    ---use soterm_id as type_id, will delete from tmpcvtr
    ---us tmproot for this as well
    INSERT INTO tmproot (cv_id, cvterm_id, status) SELECT DISTINCT soi_cvid, c.subject_id, 0 FROM tmpcvtr c
        WHERE c.object_id = soiterm_id;
    EXECUTE cquery;
    GET DIAGNOSTICS pcount = ROW_COUNT;
    WHILE (pcount > 0) LOOP
        RAISE NOTICE 'num child temp (to be inserted) in tmpcvtr: %',pcount;
        INSERT INTO tmpcvtr (tmp_type, type_id, subject_id, object_id)
            SELECT DISTINCT fr.type_id, soiterm_id, c.type_id, p.cvterm_id FROM feature c, feature_relationship fr,
            tmproot p, feature pf, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = pf.feature_id
            AND p.cvterm_id = pf.type_id AND t.cvterm_id = c.type_id AND p.status = 0;
        UPDATE tmproot SET status = 1 WHERE status = 0;
        INSERT INTO tmproot (cv_id, cvterm_id, status)
            SELECT DISTINCT soi_cvid, c.type_id, 0 FROM feature c, feature_relationship fr,
            tmproot tmp, feature p, cvterm t WHERE c.feature_id = fr.subject_id AND fr.object_id = p.feature_id
            AND tmp.cvterm_id = p.type_id AND t.cvterm_id = c.type_id AND tmp.status = 1;
        UPDATE tmproot SET status = 2 WHERE status = 1;
        EXECUTE cquery;
        GET DIAGNOSTICS pcount = ROW_COUNT;
    END LOOP;
    DELETE FROM tmproot;

    ---get transitive closure for soi
    PERFORM _fill_cvtermpath4soi(soiterm_id, soi_cvid);

    DROP TABLE tmpcvtr;
    DROP TABLE tmproot;

    RETURN 1;
END;
$$;


ALTER FUNCTION chado.create_soi() OWNER TO drupaladmin;

--
-- Name: feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature (
    feature_id bigint NOT NULL,
    dbxref_id bigint,
    organism_id bigint NOT NULL,
    name character varying(255),
    uniquename text NOT NULL,
    residues text,
    seqlen bigint,
    md5checksum character(32),
    type_id bigint NOT NULL,
    is_analysis boolean DEFAULT false NOT NULL,
    is_obsolete boolean DEFAULT false NOT NULL,
    timeaccessioned timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL,
    timelastmodified timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL
);
ALTER TABLE ONLY chado.feature ALTER COLUMN residues SET STORAGE EXTERNAL;


ALTER TABLE chado.feature OWNER TO drupaladmin;

--
-- Name: TABLE feature; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature IS 'A feature is a biological sequence or a
section of a biological sequence, or a collection of such
sections. Examples include genes, exons, transcripts, regulatory
regions, polypeptides, protein domains, chromosome sequences, sequence
variations, cross-genome match regions such as hits and HSPs and so
on; see the Sequence Ontology for more. The combination of
organism_id, uniquename and type_id should be unique.';


--
-- Name: COLUMN feature.dbxref_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.dbxref_id IS 'An optional primary public stable
identifier for this feature. Secondary identifiers and external
dbxrefs go in the table feature_dbxref.';


--
-- Name: COLUMN feature.organism_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.organism_id IS 'The organism to which this feature
belongs. This column is mandatory.';


--
-- Name: COLUMN feature.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.name IS 'The optional human-readable common name for
a feature, for display purposes.';


--
-- Name: COLUMN feature.uniquename; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.uniquename IS 'The unique name for a feature; may
not be necessarily be particularly human-readable, although this is
preferred. This name must be unique for this type of feature within
this organism.';


--
-- Name: COLUMN feature.residues; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.residues IS 'A sequence of alphabetic characters
representing biological residues (nucleic acids, amino acids). This
column does not need to be manifested for all features; it is optional
for features such as exons where the residues can be derived from the
featureloc. It is recommended that the value for this column be
manifested for features which may may non-contiguous sublocations (e.g.
transcripts), since derivation at query time is non-trivial. For
expressed sequence, the DNA sequence should be used rather than the
RNA sequence. The default storage method for the residues column is
EXTERNAL, which will store it uncompressed to make substring operations
faster.';


--
-- Name: COLUMN feature.seqlen; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.seqlen IS 'The length of the residue feature. See
column:residues. This column is partially redundant with the residues
column, and also with featureloc. This column is required because the
location may be unknown and the residue sequence may not be
manifested, yet it may be desirable to store and query the length of
the feature. The seqlen should always be manifested where the length
of the sequence is known.';


--
-- Name: COLUMN feature.md5checksum; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.md5checksum IS 'The 32-character checksum of the sequence,
calculated using the MD5 algorithm. This is practically guaranteed to
be unique for any feature. This column thus acts as a unique
identifier on the mathematical sequence.';


--
-- Name: COLUMN feature.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.type_id IS 'A required reference to a table:cvterm
giving the feature type. This will typically be a Sequence Ontology
identifier. This column is thus used to subclass the feature table.';


--
-- Name: COLUMN feature.is_analysis; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.is_analysis IS 'Boolean indicating whether this
feature is annotated or the result of an automated analysis. Analysis
results also use the companalysis module. Note that the dividing line
between analysis and annotation may be fuzzy, this should be determined on
a per-project basis in a consistent manner. One requirement is that
there should only be one non-analysis version of each wild-type gene
feature in a genome, whereas the same gene feature can be predicted
multiple times in different analyses.';


--
-- Name: COLUMN feature.is_obsolete; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.is_obsolete IS 'Boolean indicating whether this
feature has been obsoleted. Some chado instances may choose to simply
remove the feature altogether, others may choose to keep an obsolete
row in the table.';


--
-- Name: COLUMN feature.timeaccessioned; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.timeaccessioned IS 'For handling object
accession or modification timestamps (as opposed to database auditing data,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado.';


--
-- Name: COLUMN feature.timelastmodified; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature.timelastmodified IS 'For handling object
accession or modification timestamps (as opposed to database auditing data,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado.';


--
-- Name: feature_disjoint_from(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.feature_disjoint_from(bigint) RETURNS SETOF chado.feature
    LANGUAGE sql
    AS $_$SELECT feature.*
  FROM feature
   INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
   INNER JOIN featureloc AS y ON (y.feature_id = $1)
  WHERE
   x.srcfeature_id = y.srcfeature_id            AND
   ( x.fmax < y.fmin OR x.fmin > y.fmax ) $_$;


ALTER FUNCTION chado.feature_disjoint_from(bigint) OWNER TO drupaladmin;

--
-- Name: feature_overlaps(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.feature_overlaps(bigint) RETURNS SETOF chado.feature
    LANGUAGE sql
    AS $_$SELECT feature.*
  FROM feature
   INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
   INNER JOIN featureloc AS y ON (y.feature_id = $1)
  WHERE
   x.srcfeature_id = y.srcfeature_id            AND
   ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) $_$;


ALTER FUNCTION chado.feature_overlaps(bigint) OWNER TO drupaladmin;

--
-- Name: featureloc; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featureloc (
    featureloc_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    srcfeature_id bigint,
    fmin bigint,
    is_fmin_partial boolean DEFAULT false NOT NULL,
    fmax bigint,
    is_fmax_partial boolean DEFAULT false NOT NULL,
    strand smallint,
    phase integer,
    residue_info text,
    locgroup integer DEFAULT 0 NOT NULL,
    rank integer DEFAULT 0 NOT NULL,
    CONSTRAINT featureloc_c2 CHECK ((fmin <= fmax))
);


ALTER TABLE chado.featureloc OWNER TO drupaladmin;

--
-- Name: TABLE featureloc; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featureloc IS 'The location of a feature relative to
another feature. Important: interbase coordinates are used. This is
vital as it allows us to represent zero-length features e.g. splice
sites, insertion points without an awkward fuzzy system. Features
typically have exactly ONE location, but this need not be the
case. Some features may not be localized (e.g. a gene that has been
characterized genetically but no sequence or molecular information is
available). Note on multiple locations: Each feature can have 0 or
more locations. Multiple locations do NOT indicate non-contiguous
locations (if a feature such as a transcript has a non-contiguous
location, then the subfeatures such as exons should always be
manifested). Instead, multiple featurelocs for a feature designate
alternate locations or grouped locations; for instance, a feature
designating a blast hit or hsp will have two locations, one on the
query feature, one on the subject feature. Features representing
sequence variation could have alternate locations instantiated on a
feature on the mutant strain. The column:rank is used to
differentiate these different locations. Reflexive locations should
never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.';


--
-- Name: COLUMN featureloc.feature_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.feature_id IS 'The feature that is being located. Any feature can have zero or more featurelocs.';


--
-- Name: COLUMN featureloc.srcfeature_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.srcfeature_id IS 'The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.';


--
-- Name: COLUMN featureloc.fmin; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.fmin IS 'The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.';


--
-- Name: COLUMN featureloc.is_fmin_partial; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.is_fmin_partial IS 'This is typically
false, but may be true if the value for column:fmin is inaccurate or
the leftmost part of the range is unknown/unbounded.';


--
-- Name: COLUMN featureloc.fmax; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.fmax IS 'The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).';


--
-- Name: COLUMN featureloc.is_fmax_partial; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.is_fmax_partial IS 'This is typically
false, but may be true if the value for column:fmax is inaccurate or
the rightmost part of the range is unknown/unbounded.';


--
-- Name: COLUMN featureloc.strand; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.strand IS 'The orientation/directionality of the
location. Should be 0, -1 or +1.';


--
-- Name: COLUMN featureloc.phase; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.phase IS 'Phase of translation with
respect to srcfeature_id.
Values are 0, 1, 2. It may not be possible to manifest this column for
some features such as exons, because the phase is dependant on the
spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.';


--
-- Name: COLUMN featureloc.residue_info; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.residue_info IS 'Alternative residues,
when these differ from feature.residues. For instance, a SNP feature
located on a wild and mutant protein would have different alternative residues.
for alignment/similarity features, the alternative residues is used to
represent the alignment string (CIGAR format). Note on variation
features; even if we do not want to instantiate a mutant
chromosome/contig feature, we can still represent a SNP etc with 2
locations, one (rank 0) on the genome, the other (rank 1) would have
most fields null, except for alternative residues.';


--
-- Name: COLUMN featureloc.locgroup; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.locgroup IS 'This is used to manifest redundant,
derivable extra locations for a feature. The default locgroup=0 is
used for the DIRECT location of a feature. Important: most Chado users may
never use featurelocs WITH logroup > 0. Transitively derived locations
are indicated with locgroup > 0. For example, the position of an exon on
a BAC and in global chromosome coordinates. This column is used to
differentiate these groupings of locations. The default locgroup 0
is used for the main or primary location, from which the others can be
derived via coordinate transformations. Another example of redundant
locations is storing ORF coordinates relative to both transcript and
genome. Redundant locations open the possibility of the database
getting into inconsistent states; this schema gives us the flexibility
of both warehouse instantiations with redundant locations (easier for
querying) and management instantiations with no redundant
locations. An example of using both locgroup and rank: imagine a
feature indicating a conserved region between the chromosomes of two
different species. We may want to keep redundant locations on both
contigs and chromosomes. We would thus have 4 locations for the single
conserved region feature - two distinct locgroups (contig level and
chromosome level) and two distinct ranks (for the two species).';


--
-- Name: COLUMN featureloc.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureloc.rank IS 'Used when a feature has >1
location, otherwise the default rank 0 is used. Some features (e.g.
blast hits and HSPs) have two locations - one on the query and one on
the subject. Rank is used to differentiate these. Rank=0 is always
used for the query, Rank=1 for the subject. For multiple alignments,
assignment of rank is arbitrary. Rank is also used for
sequence_variant features, such as SNPs. Rank=0 indicates the wildtype
(or baseline) feature, Rank=1 indicates the mutant (or compared) feature.';


--
-- Name: feature_subalignments(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.feature_subalignments(bigint) RETURNS SETOF chado.featureloc
    LANGUAGE plpgsql
    AS $_$
DECLARE
  return_data featureloc%ROWTYPE;
  f_id ALIAS FOR $1;
  feature_data feature%rowtype;
  featureloc_data featureloc%rowtype;

  s text;

  fmin bigint;
  slen bigint;
BEGIN
  --RAISE NOTICE 'feature_id is %', featureloc_data.feature_id;
  SELECT INTO feature_data * FROM feature WHERE feature_id = f_id;

  FOR featureloc_data IN SELECT * FROM featureloc WHERE feature_id = f_id LOOP

    --RAISE NOTICE 'fmin is %', featureloc_data.fmin;

    return_data.feature_id      = f_id;
    return_data.srcfeature_id   = featureloc_data.srcfeature_id;
    return_data.is_fmin_partial = featureloc_data.is_fmin_partial;
    return_data.is_fmax_partial = featureloc_data.is_fmax_partial;
    return_data.strand          = featureloc_data.strand;
    return_data.phase           = featureloc_data.phase;
    return_data.residue_info    = featureloc_data.residue_info;
    return_data.locgroup        = featureloc_data.locgroup;
    return_data.rank            = featureloc_data.rank;

    s = feature_data.residues;
    fmin = featureloc_data.fmin;
    slen = char_length(s);

    WHILE char_length(s) LOOP
      --RAISE NOTICE 'residues is %', s;

      --trim off leading match
      s = trim(leading '|ATCGNatcgn' from s);
      --if leading match detected
      IF slen > char_length(s) THEN
        return_data.fmin = fmin;
        return_data.fmax = featureloc_data.fmin + (slen - char_length(s));

        --if the string started with a match, return it,
        --otherwise, trim the gaps first (ie do not return this iteration)
        RETURN NEXT return_data;
      END IF;

      --trim off leading gap
      s = trim(leading '-' from s);

      fmin = featureloc_data.fmin + (slen - char_length(s));
    END LOOP;
  END LOOP;

  RETURN;

END;
$_$;


ALTER FUNCTION chado.feature_subalignments(bigint) OWNER TO drupaladmin;

--
-- Name: featureloc_slice(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.featureloc_slice(bigint, bigint) RETURNS SETOF chado.featureloc
    LANGUAGE sql
    AS $_$SELECT * from featureloc where boxquery($1, $2) <@ boxrange(fmin,fmax)$_$;


ALTER FUNCTION chado.featureloc_slice(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: featureloc_slice(bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.featureloc_slice(bigint, bigint, bigint) RETURNS SETOF chado.featureloc
    LANGUAGE sql
    AS $_$SELECT *
   FROM featureloc
   WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)$_$;


ALTER FUNCTION chado.featureloc_slice(bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: featureloc_slice(character varying, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.featureloc_slice(character varying, bigint, bigint) RETURNS SETOF chado.featureloc
    LANGUAGE sql
    AS $_$SELECT featureloc.*
   FROM featureloc
   INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id)
   WHERE boxquery($2, $3) <@ boxrange(fmin,fmax)
   AND srcf.name = $1 $_$;


ALTER FUNCTION chado.featureloc_slice(character varying, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: featureslice(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.featureslice(bigint, bigint) RETURNS SETOF chado.featureloc
    LANGUAGE sql
    AS $_$SELECT * from featureloc where boxquery($1, $2) <@ boxrange(fmin,fmax)$_$;


ALTER FUNCTION chado.featureslice(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: fill_cvtermpath(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.fill_cvtermpath(bigint) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvid alias for $1;
    root cvterm%ROWTYPE;

BEGIN

    DELETE FROM cvtermpath WHERE cv_id = cvid;

    FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP
        PERFORM _fill_cvtermpath4root(root.cvterm_id, root.cv_id);
    END LOOP;
    RETURN 1;
END;
$_$;


ALTER FUNCTION chado.fill_cvtermpath(bigint) OWNER TO drupaladmin;

--
-- Name: fill_cvtermpath(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.fill_cvtermpath(character varying) RETURNS integer
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvname alias for $1;
    cv_id   bigint;
    rtn     int;
BEGIN

    SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname;
    SELECT INTO rtn fill_cvtermpath(cv_id);
    RETURN rtn;
END;
$_$;


ALTER FUNCTION chado.fill_cvtermpath(character varying) OWNER TO drupaladmin;

--
-- Name: get_all_object_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_all_object_ids(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    leaf alias for $1;
    cterm cvtermpath%ROWTYPE;
    exist_c int;
BEGIN


    SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = leaf and pathdistance <= 0;
    IF (exist_c > 0) THEN
        FOR cterm IN SELECT * FROM cvtermpath WHERE subject_id = leaf AND pathdistance > 0 LOOP
            RETURN NEXT cterm;
        END LOOP;
    ELSE
        FOR cterm IN SELECT * FROM _get_all_object_ids(leaf) LOOP
            RETURN NEXT cterm;
        END LOOP;
    END IF;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_all_object_ids(bigint) OWNER TO drupaladmin;

--
-- Name: get_all_subject_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_all_subject_ids(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    root alias for $1;
    cterm cvtermpath%ROWTYPE;
    exist_c int;
BEGIN

    SELECT INTO exist_c count(*) FROM cvtermpath WHERE object_id = root and pathdistance <= 0;
    IF (exist_c > 0) THEN
        FOR cterm IN SELECT * FROM cvtermpath WHERE object_id = root and pathdistance > 0 LOOP
            RETURN NEXT cterm;
        END LOOP;
    ELSE
        FOR cterm IN SELECT * FROM _get_all_subject_ids(root) LOOP
            RETURN NEXT cterm;
        END LOOP;
    END IF;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_all_subject_ids(bigint) OWNER TO drupaladmin;

--
-- Name: get_cv_id_for_feature(); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cv_id_for_feature() RETURNS bigint
    LANGUAGE sql
    AS $$SELECT cv_id FROM cv WHERE name='sequence'$$;


ALTER FUNCTION chado.get_cv_id_for_feature() OWNER TO drupaladmin;

--
-- Name: get_cv_id_for_feature_relationsgip(); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cv_id_for_feature_relationsgip() RETURNS bigint
    LANGUAGE sql
    AS $$SELECT cv_id FROM cv WHERE name='relationship'$$;


ALTER FUNCTION chado.get_cv_id_for_feature_relationsgip() OWNER TO drupaladmin;

--
-- Name: get_cv_id_for_featureprop(); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cv_id_for_featureprop() RETURNS bigint
    LANGUAGE sql
    AS $$SELECT cv_id FROM cv WHERE name='feature_property'$$;


ALTER FUNCTION chado.get_cv_id_for_featureprop() OWNER TO drupaladmin;

--
-- Name: get_cycle_cvterm_id(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cycle_cvterm_id(bigint) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvid alias for $1;
    root cvterm%ROWTYPE;
    rtn     bigint;
BEGIN

    CREATE TEMP TABLE tmpcvtermpath(object_id bigint, subject_id bigint, cv_id bigint, type_id bigint, pathdistance int);
    CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id);

    FOR root IN SELECT DISTINCT t.* from cvterm t LEFT JOIN cvterm_relationship r ON (t.cvterm_id = r.subject_id) INNER JOIN cvterm_relationship r2 ON (t.cvterm_id = r2.object_id) WHERE t.cv_id = cvid AND r.subject_id is null LOOP
        SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(root.cvterm_id, root.cv_id);
        IF (rtn > 0) THEN
            DROP TABLE tmpcvtermpath;
            RETURN rtn;
        END IF;
    END LOOP;
    DROP TABLE tmpcvtermpath;
    RETURN 0;
END;
$_$;


ALTER FUNCTION chado.get_cycle_cvterm_id(bigint) OWNER TO drupaladmin;

--
-- Name: get_cycle_cvterm_id(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cycle_cvterm_id(character varying) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvname alias for $1;
    cv_id bigint;
    rtn bigint;
BEGIN

    SELECT INTO cv_id cv.cv_id from cv WHERE cv.name = cvname;
    SELECT INTO rtn  get_cycle_cvterm_id(cv_id);

    RETURN rtn;
END;
$_$;


ALTER FUNCTION chado.get_cycle_cvterm_id(character varying) OWNER TO drupaladmin;

--
-- Name: get_cycle_cvterm_id(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cycle_cvterm_id(bigint, bigint) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvid alias for $1;
    rootid alias for $2;
    rtn     bigint;
BEGIN

    CREATE TEMP TABLE tmpcvtermpath(object_id bigint, subject_id bigint, cv_id bigint, type_id bigint, pathdistance int);
    CREATE INDEX tmp_cvtpath1 ON tmpcvtermpath(object_id, subject_id);

    SELECT INTO rtn _fill_cvtermpath4root2detect_cycle(rootid, cvid);
    IF (rtn > 0) THEN
        DROP TABLE tmpcvtermpath;
        RETURN rtn;
    END IF;
    DROP TABLE tmpcvtermpath;
    RETURN 0;
END;
$_$;


ALTER FUNCTION chado.get_cycle_cvterm_id(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: get_cycle_cvterm_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_cycle_cvterm_ids(bigint) RETURNS SETOF bigint
    LANGUAGE plpgsql
    AS $_$
DECLARE
    cvid alias for $1;
    root cvterm%ROWTYPE;
    rtn     bigint;
BEGIN


    FOR root IN SELECT DISTINCT t.* from cvterm t WHERE cv_id = cvid LOOP
        SELECT INTO rtn get_cycle_cvterm_id(cvid,root.cvterm_id);
        IF (rtn > 0) THEN
            RETURN NEXT rtn;
        END IF;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_cycle_cvterm_ids(bigint) OWNER TO drupaladmin;

--
-- Name: get_feature_id(character varying, character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_id(character varying, character varying, character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
  SELECT feature_id
  FROM feature
  WHERE uniquename=$1
    AND type_id=get_feature_type_id($2)
    AND organism_id=get_organism_id($3)
 $_$;


ALTER FUNCTION chado.get_feature_id(character varying, character varying, character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_ids(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids(text) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    sql alias for $1;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;
    myrc3 feature_by_fx_type%ROWTYPE;

BEGIN

    FOR myrc IN EXECUTE sql LOOP
        RETURN NEXT myrc;
        FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc2;
        END LOOP;
        FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc3;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids(text) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_child_count(character varying, character varying, integer, character varying, character); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_child_count(character varying, character varying, integer, character varying, character) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    ptype alias for $1;
    ctype alias for $2;
    ccount alias for $3;
    operator alias for $4;
    is_an alias for $5;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type %ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT f.feature_id
        FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p
        INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr
        ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id)
        INNER join cvterm ct ON (c.type_id = ct.cvterm_id)
        WHERE pt.name = ' || quote_literal(ptype) || ' AND ct.name = ' || quote_literal(ctype)
        || ' AND p.is_analysis = ' || quote_literal(is_an) || ' group by p.feature_id) as cq
        ON (cq.feature_id = f.feature_id) WHERE cq.c ' || operator || ccount || ';';
    ---RAISE NOTICE '%', query;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_child_count(character varying, character varying, integer, character varying, character) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_ont(character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_ont(character varying, character varying) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    aspect alias for $1;
    term alias for $2;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT fcvt.feature_id
        FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND
        t.cvterm_id = fcvt.cvterm_id AND cv.name = ' || quote_literal(aspect) ||
        ' AND t.name = ' || quote_literal(term) || ';';
    IF (STRPOS(term, '%') > 0) THEN
        query := 'SELECT DISTINCT fcvt.feature_id
            FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND
            t.cvterm_id = fcvt.cvterm_id AND cv.name = ' || quote_literal(aspect) ||
            ' AND t.name like ' || quote_literal(term) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_ont(character varying, character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_ont_root(character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_ont_root(character varying, character varying) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    aspect alias for $1;
    term alias for $2;
    query TEXT;
    subquery TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    subquery := 'SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id
        AND cv.name = ' || quote_literal(aspect) || ' AND t.name = ' || quote_literal(term) || ';';
    IF (STRPOS(term, '%') > 0) THEN
        subquery := 'SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id
            AND cv.name = ' || quote_literal(aspect) || ' AND t.name like ' || quote_literal(term) || ';';
    END IF;
    query := 'SELECT DISTINCT fcvt.feature_id
        FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids(' || quote_literal(subquery) || ')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);';

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_ont_root(character varying, character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_property(character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_property(character varying, character varying) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    p_type alias for $1;
    p_val alias for $2;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT fprop.feature_id
        FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = ' ||
        quote_literal(p_type) || ' AND fprop.value = ' || quote_literal(p_val) || ';';
    IF (STRPOS(p_val, '%') > 0) THEN
        query := 'SELECT DISTINCT fprop.feature_id
            FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = ' ||
            quote_literal(p_type) || ' AND fprop.value like ' || quote_literal(p_val) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_property(character varying, character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_propval(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_propval(character varying) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    p_val alias for $1;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT fprop.feature_id
        FROM featureprop fprop WHERE fprop.value = ' || quote_literal(p_val) || ';';
    IF (STRPOS(p_val, '%') > 0) THEN
        query := 'SELECT DISTINCT fprop.feature_id
            FROM featureprop fprop WHERE fprop.value like ' || quote_literal(p_val) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_propval(character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_type(character varying, character); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_type(character varying, character) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    gtype alias for $1;
    is_an alias for $2;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT f.feature_id
        FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = ' || quote_literal(gtype) ||
        ' AND f.is_analysis = ' || quote_literal(is_an) || ';';
    IF (STRPOS(gtype, '%') > 0) THEN
        query := 'SELECT DISTINCT f.feature_id
            FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like '
            || quote_literal(gtype) || ' AND f.is_analysis = ' || quote_literal(is_an) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_type(character varying, character) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_type_name(character varying, text, character); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_type_name(character varying, text, character) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    gtype alias for $1;
    name alias for $2;
    is_an alias for $3;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT f.feature_id
        FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
        WHERE t.name = ' || quote_literal(gtype) || ' AND (f.uniquename = ' || quote_literal(name)
        || ' OR f.name = ' || quote_literal(name) || ') AND f.is_analysis = ' || quote_literal(is_an) || ';';

    IF (STRPOS(name, '%') > 0) THEN
        query := 'SELECT DISTINCT f.feature_id
            FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
            WHERE t.name = ' || quote_literal(gtype) || ' AND (f.uniquename like ' || quote_literal(name)
            || ' OR f.name like ' || quote_literal(name) || ') AND f.is_analysis = ' || quote_literal(is_an) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_type_name(character varying, text, character) OWNER TO drupaladmin;

--
-- Name: get_feature_ids_by_type_src(character varying, text, character); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_ids_by_type_src(character varying, text, character) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    gtype alias for $1;
    src alias for $2;
    is_an alias for $3;
    query TEXT;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT f.feature_id
        FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl
        ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
        WHERE t.name = ' || quote_literal(gtype) || ' AND src.uniquename = ' || quote_literal(src)
        || ' AND f.is_analysis = ' || quote_literal(is_an) || ';';

    IF (STRPOS(gtype, '%') > 0) THEN
        query := 'SELECT DISTINCT f.feature_id
            FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl
            ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
            WHERE t.name like ' || quote_literal(gtype) || ' AND src.uniquename = ' || quote_literal(src)
            || ' AND f.is_analysis = ' || quote_literal(is_an) || ';';
    END IF;

    FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_feature_ids_by_type_src(character varying, text, character) OWNER TO drupaladmin;

--
-- Name: get_feature_relationship_type_id(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_relationship_type_id(character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name='relationship'
 $_$;


ALTER FUNCTION chado.get_feature_relationship_type_id(character varying) OWNER TO drupaladmin;

--
-- Name: get_feature_type_id(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_feature_type_id(character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name='sequence'
 $_$;


ALTER FUNCTION chado.get_feature_type_id(character varying) OWNER TO drupaladmin;

--
-- Name: get_featureprop_type_id(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_featureprop_type_id(character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name='feature_property'
 $_$;


ALTER FUNCTION chado.get_featureprop_type_id(character varying) OWNER TO drupaladmin;

--
-- Name: get_graph_above(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_graph_above(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    leaf alias for $1;
    cterm cvtermpath%ROWTYPE;
    cterm2 cvtermpath%ROWTYPE;

BEGIN

    FOR cterm IN SELECT * FROM cvterm_relationship WHERE subject_id = leaf LOOP
        RETURN NEXT cterm;
        FOR cterm2 IN SELECT * FROM get_all_object_ids(cterm.object_id) LOOP
            RETURN NEXT cterm2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_graph_above(bigint) OWNER TO drupaladmin;

--
-- Name: get_graph_below(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_graph_below(bigint) RETURNS SETOF chado.cvtermpath
    LANGUAGE plpgsql
    AS $_$
DECLARE
    root alias for $1;
    cterm cvtermpath%ROWTYPE;
    cterm2 cvtermpath%ROWTYPE;

BEGIN

    FOR cterm IN SELECT * FROM cvterm_relationship WHERE object_id = root LOOP
        RETURN NEXT cterm;
        FOR cterm2 IN SELECT * FROM get_all_subject_ids(cterm.subject_id) LOOP
            RETURN NEXT cterm2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_graph_below(bigint) OWNER TO drupaladmin;

--
-- Name: cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvterm (
    cvterm_id bigint NOT NULL,
    cv_id bigint NOT NULL,
    name character varying(1024) NOT NULL,
    definition text,
    dbxref_id bigint NOT NULL,
    is_obsolete integer DEFAULT 0 NOT NULL,
    is_relationshiptype integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cvterm OWNER TO drupaladmin;

--
-- Name: TABLE cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvterm IS 'A term, class, universal or type within an
ontology or controlled vocabulary.  This table is also used for
relations and properties. cvterms constitute nodes in the graph
defined by the collection of cvterms and cvterm_relationships.';


--
-- Name: COLUMN cvterm.cv_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.cv_id IS 'The cv or ontology or namespace to which
this cvterm belongs.';


--
-- Name: COLUMN cvterm.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.name IS 'A concise human-readable name or
label for the cvterm. Uniquely identifies a cvterm within a cv.';


--
-- Name: COLUMN cvterm.definition; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.definition IS 'A human-readable text
definition.';


--
-- Name: COLUMN cvterm.dbxref_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.dbxref_id IS 'Primary identifier dbxref - The
unique global OBO identifier for this cvterm.  Note that a cvterm may
have multiple secondary dbxrefs - see also table: cvterm_dbxref.';


--
-- Name: COLUMN cvterm.is_obsolete; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.is_obsolete IS 'Boolean 0=false,1=true; see
GO documentation for details of obsoletion. Note that two terms with
different primary dbxrefs may exist if one is obsolete.';


--
-- Name: COLUMN cvterm.is_relationshiptype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm.is_relationshiptype IS 'Boolean
0=false,1=true relations or relationship types (also known as Typedefs
in OBO format, or as properties or slots) form a cv/ontology in
themselves. We use this flag to indicate whether this cvterm is an
actual term/class/universal or a relation. Relations may be drawn from
the OBO Relations ontology, but are not exclusively drawn from there.';


--
-- Name: get_it_sub_cvterm_ids(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_it_sub_cvterm_ids(text) RETURNS SETOF chado.cvterm
    LANGUAGE plpgsql
    AS $_$
DECLARE
    query alias for $1;
    cterm cvterm%ROWTYPE;
    cterm2 cvterm%ROWTYPE;
BEGIN
    FOR cterm IN EXECUTE query LOOP
        RETURN NEXT cterm;
        FOR cterm2 IN SELECT subject_id as cvterm_id FROM get_all_subject_ids(cterm.cvterm_id) LOOP
            RETURN NEXT cterm2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_it_sub_cvterm_ids(text) OWNER TO drupaladmin;

--
-- Name: get_organism_id(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_organism_id(character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
SELECT organism_id
  FROM organism
  WHERE genus=substring($1,1,position(' ' IN $1)-1)
    AND species=substring($1,position(' ' IN $1)+1)
 $_$;


ALTER FUNCTION chado.get_organism_id(character varying) OWNER TO drupaladmin;

--
-- Name: get_organism_id(character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_organism_id(character varying, character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
  SELECT organism_id
  FROM organism
  WHERE genus=$1
    AND species=$2
 $_$;


ALTER FUNCTION chado.get_organism_id(character varying, character varying) OWNER TO drupaladmin;

--
-- Name: get_organism_id_abbrev(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_organism_id_abbrev(character varying) RETURNS bigint
    LANGUAGE sql
    AS $_$
SELECT organism_id
  FROM organism
  WHERE substr(genus,1,1)=substring($1,1,1)
    AND species=substring($1,position(' ' IN $1)+1)
 $_$;


ALTER FUNCTION chado.get_organism_id_abbrev(character varying) OWNER TO drupaladmin;

--
-- Name: get_sub_feature_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_sub_feature_ids(bigint) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    root alias for $1;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN
    FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP
        RETURN NEXT myrc;
        FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_sub_feature_ids(bigint) OWNER TO drupaladmin;

--
-- Name: get_sub_feature_ids(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_sub_feature_ids(text) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    sql alias for $1;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN
    FOR myrc IN EXECUTE sql LOOP
        FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_sub_feature_ids(text) OWNER TO drupaladmin;

--
-- Name: get_sub_feature_ids(bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_sub_feature_ids(bigint, integer) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    root alias for $1;
    depth alias for $2;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN
    FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP
        RETURN NEXT myrc;
        FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_sub_feature_ids(bigint, integer) OWNER TO drupaladmin;

--
-- Name: get_sub_feature_ids_by_type_src(character varying, text, character); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_sub_feature_ids_by_type_src(character varying, text, character) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    gtype alias for $1;
    src alias for $2;
    is_an alias for $3;
    query text;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN

    query := 'SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
        INNER join featureloc fl
        ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
        WHERE t.name = ' || quote_literal(gtype) || ' AND src.uniquename = ' || quote_literal(src)
        || ' AND f.is_analysis = ' || quote_literal(is_an) || ';';

    IF (STRPOS(gtype, '%') > 0) THEN
        query := 'SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
             INNER join featureloc fl
            ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
            WHERE t.name like ' || quote_literal(gtype) || ' AND src.uniquename = ' || quote_literal(src)
            || ' AND f.is_analysis = ' || quote_literal(is_an) || ';';
    END IF;
    FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP
        RETURN NEXT myrc;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_sub_feature_ids_by_type_src(character varying, text, character) OWNER TO drupaladmin;

--
-- Name: get_up_feature_ids(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_up_feature_ids(bigint) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    leaf alias for $1;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
    FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP
        RETURN NEXT myrc;
        FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_up_feature_ids(bigint) OWNER TO drupaladmin;

--
-- Name: get_up_feature_ids(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_up_feature_ids(text) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    sql alias for $1;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;

BEGIN
    FOR myrc IN EXECUTE sql LOOP
        FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_up_feature_ids(text) OWNER TO drupaladmin;

--
-- Name: get_up_feature_ids(bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.get_up_feature_ids(bigint, integer) RETURNS SETOF chado.feature_by_fx_type
    LANGUAGE plpgsql
    AS $_$
DECLARE
    leaf alias for $1;
    depth alias for $2;
    myrc feature_by_fx_type%ROWTYPE;
    myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
    FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP
        RETURN NEXT myrc;
        FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP
            RETURN NEXT myrc2;
        END LOOP;
    END LOOP;
    RETURN;
END;
$_$;


ALTER FUNCTION chado.get_up_feature_ids(bigint, integer) OWNER TO drupaladmin;

--
-- Name: gffattstring(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.gffattstring(bigint) RETURNS character varying
    LANGUAGE plpgsql
    AS $_$DECLARE
  return_string      varchar;
  f_id               ALIAS FOR $1;
  atts_view          gffatts%ROWTYPE;
  feature_row        feature%ROWTYPE;
  name               varchar;
  uniquename         varchar;
  parent             varchar;
  escape_loc         bigint;
BEGIN
  --Get name from feature.name
  --Get ID from feature.uniquename

  SELECT INTO feature_row * FROM feature WHERE feature_id = f_id;
  name  = feature_row.name;
  return_string = 'ID=' || feature_row.uniquename;
  IF name IS NOT NULL AND name != ''
  THEN
    return_string = return_string ||';' || 'Name=' || name;
  END IF;

  --Get Parent from feature_relationship
  SELECT INTO feature_row * FROM feature f, feature_relationship fr
    WHERE fr.subject_id = f_id AND fr.object_id = f.feature_id;
  IF FOUND
  THEN
    return_string = return_string||';'||'Parent='||feature_row.uniquename;
  END IF;

  FOR atts_view IN SELECT * FROM gff3atts WHERE feature_id = f_id  LOOP
    escape_loc = position(';' in atts_view.attribute);
    IF escape_loc > 0 THEN
      atts_view.attribute = replace(atts_view.attribute, ';', '%3B');
    END IF;
    return_string = return_string || ';'
                     || atts_view.type || '='
                     || atts_view.attribute;
  END LOOP;

  RETURN return_string;
END;
$_$;


ALTER FUNCTION chado.gffattstring(bigint) OWNER TO drupaladmin;

--
-- Name: db; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.db (
    db_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    description character varying(255),
    urlprefix character varying(255),
    url character varying(255)
);


ALTER TABLE chado.db OWNER TO drupaladmin;

--
-- Name: TABLE db; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.db IS 'A database authority. Typical databases in
bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority
is generally known by this shortened form, which is unique within the
bioinformatics and biomedical realm.  To Do - add support for URIs,
URNs (e.g. LSIDs). We can do this by treating the URL as a URI -
however, some applications may expect this to be resolvable - to be
decided.';


--
-- Name: dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.dbxref (
    dbxref_id bigint NOT NULL,
    db_id bigint NOT NULL,
    accession character varying(1024) NOT NULL,
    version character varying(255) DEFAULT ''::character varying NOT NULL,
    description text
);


ALTER TABLE chado.dbxref OWNER TO drupaladmin;

--
-- Name: TABLE dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.dbxref IS 'A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>.';


--
-- Name: COLUMN dbxref.accession; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.dbxref.accession IS 'The local part of the identifier. Guaranteed by the db authority to be unique for that db.';


--
-- Name: feature_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_cvterm (
    feature_cvterm_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    is_not boolean DEFAULT false NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE feature_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.';


--
-- Name: COLUMN feature_cvterm.pub_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.';


--
-- Name: COLUMN feature_cvterm.is_not; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.';


--
-- Name: feature_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_dbxref (
    feature_dbxref_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.feature_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE feature_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_dbxref IS 'Links a feature to dbxrefs.';


--
-- Name: COLUMN feature_dbxref.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_dbxref.is_current IS 'True if this secondary dbxref is
the most up to date accession in the corresponding db. Retired accessions
should set this field to false';


--
-- Name: feature_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_pub (
    feature_pub_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.feature_pub OWNER TO drupaladmin;

--
-- Name: TABLE feature_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_pub IS 'Provenance. Linking table between features and publications that mention them.';


--
-- Name: feature_synonym; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_synonym (
    feature_synonym_id bigint NOT NULL,
    synonym_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    is_current boolean DEFAULT false NOT NULL,
    is_internal boolean DEFAULT false NOT NULL
);


ALTER TABLE chado.feature_synonym OWNER TO drupaladmin;

--
-- Name: TABLE feature_synonym; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_synonym IS 'Linking table between feature and synonym.';


--
-- Name: COLUMN feature_synonym.pub_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.';


--
-- Name: COLUMN feature_synonym.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the  current -official- symbol for the linked feature.';


--
-- Name: COLUMN feature_synonym.is_internal; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name.  If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.';


--
-- Name: featureprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featureprop (
    featureprop_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.featureprop OWNER TO drupaladmin;

--
-- Name: TABLE featureprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featureprop IS 'A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.';


--
-- Name: COLUMN featureprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. Certain property types will only apply to certain feature
types (e.g. the anticodon property will only apply to tRNA features) ;
the types here come from the sequence feature property ontology.';


--
-- Name: COLUMN featureprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.';


--
-- Name: COLUMN featureprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featureprop.rank IS 'Property-Value ordering. Any
feature can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used';


--
-- Name: pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pub (
    pub_id bigint NOT NULL,
    title text,
    volumetitle text,
    volume character varying(255),
    series_name character varying(255),
    issue character varying(255),
    pyear character varying(255),
    pages character varying(255),
    miniref character varying(255),
    uniquename text NOT NULL,
    type_id bigint NOT NULL,
    is_obsolete boolean DEFAULT false,
    publisher character varying(255),
    pubplace character varying(255)
);


ALTER TABLE chado.pub OWNER TO drupaladmin;

--
-- Name: TABLE pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pub IS 'A documented provenance artefact - publications,
documents, personal communication.';


--
-- Name: COLUMN pub.title; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pub.title IS 'Descriptive general heading.';


--
-- Name: COLUMN pub.volumetitle; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pub.volumetitle IS 'Title of part if one of a series.';


--
-- Name: COLUMN pub.series_name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pub.series_name IS 'Full name of (journal) series.';


--
-- Name: COLUMN pub.pages; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pub.pages IS 'Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.';


--
-- Name: COLUMN pub.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pub.type_id IS 'The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.';


--
-- Name: synonym; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.synonym (
    synonym_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    type_id bigint NOT NULL,
    synonym_sgml character varying(255) NOT NULL
);


ALTER TABLE chado.synonym OWNER TO drupaladmin;

--
-- Name: TABLE synonym; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.';


--
-- Name: COLUMN synonym.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.';


--
-- Name: COLUMN synonym.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.synonym.type_id IS 'Types would be symbol and fullname for now.';


--
-- Name: COLUMN synonym.synonym_sgml; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.';


--
-- Name: gffatts; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.gffatts AS
 SELECT fs.feature_id,
    'Ontology_term'::text AS type,
    s.name AS attribute
   FROM chado.cvterm s,
    chado.feature_cvterm fs
  WHERE (fs.cvterm_id = s.cvterm_id)
UNION ALL
 SELECT fs.feature_id,
    'Dbxref'::text AS type,
    (((d.name)::text || ':'::text) || (s.accession)::text) AS attribute
   FROM chado.dbxref s,
    chado.feature_dbxref fs,
    chado.db d
  WHERE ((fs.dbxref_id = s.dbxref_id) AND (s.db_id = d.db_id))
UNION ALL
 SELECT fs.feature_id,
    'Alias'::text AS type,
    s.name AS attribute
   FROM chado.synonym s,
    chado.feature_synonym fs
  WHERE (fs.synonym_id = s.synonym_id)
UNION ALL
 SELECT fp.feature_id,
    cv.name AS type,
    fp.value AS attribute
   FROM chado.featureprop fp,
    chado.cvterm cv
  WHERE (fp.type_id = cv.cvterm_id)
UNION ALL
 SELECT fs.feature_id,
    'pub'::text AS type,
    (((s.series_name)::text || ':'::text) || s.title) AS attribute
   FROM chado.pub s,
    chado.feature_pub fs
  WHERE (fs.pub_id = s.pub_id);


ALTER TABLE chado.gffatts OWNER TO drupaladmin;

--
-- Name: gfffeatureatts(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.gfffeatureatts(bigint) RETURNS SETOF chado.gffatts
    LANGUAGE sql
    AS $_$
SELECT feature_id, 'Ontology_term' AS type,  s.name AS attribute
FROM cvterm s, feature_cvterm fs
WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
UNION
SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute
FROM dbxref s, feature_dbxref fs, db d
WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id AND s.db_id = d.db_id
UNION
SELECT feature_id, 'Alias' AS type, s.name AS attribute
FROM synonym s, feature_synonym fs
WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
UNION
SELECT fp.feature_id,cv.name,fp.value
FROM featureprop fp, cvterm cv
WHERE fp.feature_id= $1 AND fp.type_id = cv.cvterm_id
UNION
SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute
FROM pub s, feature_pub fs
WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
$_$;


ALTER FUNCTION chado.gfffeatureatts(bigint) OWNER TO drupaladmin;

--
-- Name: order_exons(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.order_exons(bigint) RETURNS void
    LANGUAGE plpgsql
    AS $_$
  DECLARE
    parent_type      ALIAS FOR $1;
    exon_id          bigint;
    part_of          bigint;
    exon_type        bigint;
    strand           int;
    arow             RECORD;
    order_by         varchar;
    rowcount         int;
    exon_count       int;
    ordered_exons    int;
    transcript_id    bigint;
    transcript_row   feature%ROWTYPE;
  BEGIN
    SELECT INTO part_of cvterm_id FROM cvterm WHERE name='part_of'
      AND cv_id IN (SELECT cv_id FROM cv WHERE name='relationship');
    --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name='exon'
    --  AND cv_id IN (SELECT cv_id FROM cv WHERE name='sequence');

    --RAISE NOTICE 'part_of %, exon %',part_of,exon_type;

    FOR transcript_row IN
      SELECT * FROM feature WHERE type_id = parent_type
    LOOP
      transcript_id = transcript_row.feature_id;
      SELECT INTO rowcount count(*) FROM feature_relationship
        WHERE object_id = transcript_id
          AND rank = 0;

      --Dont modify this transcript if there are already numbered exons or
      --if there is only one exon
      IF rowcount = 1 THEN
        --RAISE NOTICE 'skipping transcript %, row count %',transcript_id,rowcount;
        CONTINUE;
      END IF;

      --need to reverse the order if the strand is negative
      SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id;
      IF strand > 0 THEN
          order_by = 'fl.fmin';
      ELSE
          order_by = 'fl.fmax desc';
      END IF;

      exon_count = 0;
      FOR arow IN EXECUTE
        'SELECT fr.*, fl.fmin, fl.fmax
          FROM feature_relationship fr, featureloc fl
          WHERE fr.object_id  = '||transcript_id||'
            AND fr.subject_id = fl.feature_id
            AND fr.type_id    = '||part_of||'
            ORDER BY '||order_by
      LOOP
        --number the exons for a given transcript
        UPDATE feature_relationship
          SET rank = exon_count
          WHERE feature_relationship_id = arow.feature_relationship_id;
        exon_count = exon_count + 1;
      END LOOP;

    END LOOP;

  END;
$_$;


ALTER FUNCTION chado.order_exons(bigint) OWNER TO drupaladmin;

--
-- Name: phylonode_depth(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.phylonode_depth(bigint) RETURNS double precision
    LANGUAGE plpgsql
    AS $_$DECLARE  id    ALIAS FOR $1;
  DECLARE  depth FLOAT := 0;
  DECLARE  curr_node phylonode%ROWTYPE;
  BEGIN
   SELECT INTO curr_node *
    FROM phylonode
    WHERE phylonode_id=id;
   depth = depth + curr_node.distance;
   IF curr_node.parent_phylonode_id IS NULL
    THEN RETURN depth;
    ELSE RETURN depth + phylonode_depth(curr_node.parent_phylonode_id);
   END IF;
 END
$_$;


ALTER FUNCTION chado.phylonode_depth(bigint) OWNER TO drupaladmin;

--
-- Name: phylonode_height(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.phylonode_height(bigint) RETURNS double precision
    LANGUAGE sql
    AS $_$
  SELECT coalesce(max(phylonode_height(phylonode_id) + distance), 0.0)
    FROM phylonode
    WHERE parent_phylonode_id = $1
$_$;


ALTER FUNCTION chado.phylonode_height(bigint) OWNER TO drupaladmin;

--
-- Name: project_featureloc_up(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.project_featureloc_up(bigint, bigint) RETURNS chado.featureloc
    LANGUAGE plpgsql
    AS $_$
DECLARE
    in_featureloc_id alias for $1;
    up_srcfeature_id alias for $2;
    in_featureloc featureloc%ROWTYPE;
    up_featureloc featureloc%ROWTYPE;
    nu_featureloc featureloc%ROWTYPE;
    nu_fmin BIGINT;
    nu_fmax BIGINT;
    nu_strand INT;
BEGIN
 SELECT INTO in_featureloc
   featureloc.*
  FROM featureloc
  WHERE featureloc_id = in_featureloc_id;

 SELECT INTO up_featureloc
   up_fl.*
  FROM featureloc AS in_fl
  INNER JOIN featureloc AS up_fl
    ON (in_fl.srcfeature_id = up_fl.feature_id)
  WHERE
   in_fl.featureloc_id = in_featureloc_id AND
   up_fl.srcfeature_id = up_srcfeature_id;

  IF up_featureloc.strand IS NULL
   THEN RETURN NULL;
  END IF;

  IF up_featureloc.strand < 0
  THEN
   nu_fmin = project_point_up(in_featureloc.fmax,
                              up_featureloc.fmin,up_featureloc.fmax,-1);
   nu_fmax = project_point_up(in_featureloc.fmin,
                              up_featureloc.fmin,up_featureloc.fmax,-1);
   nu_strand = -in_featureloc.strand;
  ELSE
   nu_fmin = project_point_up(in_featureloc.fmin,
                              up_featureloc.fmin,up_featureloc.fmax,1);
   nu_fmax = project_point_up(in_featureloc.fmax,
                              up_featureloc.fmin,up_featureloc.fmax,1);
   nu_strand = in_featureloc.strand;
  END IF;
  in_featureloc.fmin = nu_fmin;
  in_featureloc.fmax = nu_fmax;
  in_featureloc.strand = nu_strand;
  in_featureloc.srcfeature_id = up_featureloc.srcfeature_id;
  RETURN in_featureloc;
END
$_$;


ALTER FUNCTION chado.project_featureloc_up(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: project_point_down(bigint, bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.project_point_down(bigint, bigint, bigint, bigint) RETURNS bigint
    LANGUAGE sql
    AS $_$SELECT
  CASE WHEN $4<0
   THEN $3-$1
   ELSE $1+$2
  END AS p$_$;


ALTER FUNCTION chado.project_point_down(bigint, bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: project_point_g2t(bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.project_point_g2t(bigint, bigint, bigint) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$
 DECLARE
    in_p             alias for $1;
    srcf_id          alias for $2;
    t_id             alias for $3;
    e_floc           featureloc%ROWTYPE;
    out_p            BIGINT;
    exon_cvterm_id   BIGINT;
BEGIN
 SELECT INTO exon_cvterm_id get_feature_type_id('exon');
 SELECT INTO out_p
  CASE
   WHEN strand<0 THEN fmax-p
   ELSE p-fmin
   END AS p
  FROM featureloc
   INNER JOIN feature USING (feature_id)
   INNER JOIN feature_relationship ON (feature.feature_id=subject_id)
  WHERE
   object_id = t_id                     AND
   feature.type_id = exon_cvterm_id     AND
   featureloc.srcfeature_id = srcf_id   AND
   in_p >= fmin                         AND
   in_p <= fmax;
  RETURN in_featureloc;
END
$_$;


ALTER FUNCTION chado.project_point_g2t(bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: project_point_up(bigint, bigint, bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.project_point_up(bigint, bigint, bigint, bigint) RETURNS bigint
    LANGUAGE sql
    AS $_$SELECT
  CASE WHEN $4<0
   THEN $3-$1             -- rev strand
   ELSE $1-$2             -- fwd strand
  END AS p$_$;


ALTER FUNCTION chado.project_point_up(bigint, bigint, bigint, bigint) OWNER TO drupaladmin;

--
-- Name: reverse_complement(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.reverse_complement(text) RETURNS text
    LANGUAGE sql
    AS $_$SELECT reverse_string(complement_residues($1))$_$;


ALTER FUNCTION chado.reverse_complement(text) OWNER TO drupaladmin;

--
-- Name: reverse_string(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.reverse_string(text) RETURNS text
    LANGUAGE plpgsql
    AS $_$
 DECLARE
  reversed_string TEXT;
  incoming ALIAS FOR $1;
 BEGIN
   reversed_string = '';
   FOR i IN REVERSE char_length(incoming)..1 loop
     reversed_string = reversed_string || substring(incoming FROM i FOR 1);
   END loop;
 RETURN reversed_string;
END$_$;


ALTER FUNCTION chado.reverse_string(text) OWNER TO drupaladmin;

--
-- Name: share_exons(); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.share_exons() RETURNS void
    LANGUAGE plpgsql
    AS $$
  DECLARE
  BEGIN
    /* Generate a table of shared exons */
    CREATE temporary TABLE shared_exons AS
      SELECT gene.feature_id as gene_feature_id
           , gene.uniquename as gene_uniquename
           , transcript1.uniquename as transcript1
           , exon1.feature_id as exon1_feature_id
           , exon1.uniquename as exon1_uniquename
           , transcript2.uniquename as transcript2
           , exon2.feature_id as exon2_feature_id
           , exon2.uniquename as exon2_uniquename
           , exon1_loc.fmin /* = exon2_loc.fmin */
           , exon1_loc.fmax /* = exon2_loc.fmax */
      FROM feature gene
        JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id
        JOIN cv gene_type_cv USING (cv_id)
        JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id
        JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id
        JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id
        JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id
        JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id
        JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id
        JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id
        JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id
        JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id
        JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id
        JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id
        JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id
        JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id
        JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id
        JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id
        JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id
        JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id
        JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id
      WHERE gene_type_cv.name = 'sequence'
        AND gene_type.name = 'gene'
        AND transcript1_type_cv.name = 'sequence'
        AND transcript1_type.name = 'mRNA'
        AND transcript2_type_cv.name = 'sequence'
        AND transcript2_type.name = 'mRNA'
        AND exon1_type_cv.name = 'sequence'
        AND exon1_type.name = 'exon'
        AND exon2_type_cv.name = 'sequence'
        AND exon2_type.name = 'exon'
        AND exon1.feature_id < exon2.feature_id
        AND exon1_loc.rank = 0
        AND exon2_loc.rank = 0
        AND exon1_loc.fmin = exon2_loc.fmin
        AND exon1_loc.fmax = exon2_loc.fmax
    ;

    /* Choose one of the shared exons to be the canonical representative.
       We pick the one with the smallest feature_id.
     */
    CREATE temporary TABLE canonical_exon_representatives AS
      SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin
      FROM shared_exons
      GROUP BY gene_feature_id,fmin
    ;

    CREATE temporary TABLE exon_replacements AS
      SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id
                    , canonical_exon_representatives.canonical_feature_id
                    , canonical_exon_representatives.fmin
      FROM shared_exons
        JOIN canonical_exon_representatives USING (gene_feature_id)
      WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id
        AND shared_exons.fmin = canonical_exon_representatives.fmin
    ;

    UPDATE feature_relationship
      SET subject_id = (
            SELECT canonical_feature_id
            FROM exon_replacements
            WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id)
      WHERE subject_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );

    UPDATE feature_relationship
      SET object_id = (
            SELECT canonical_feature_id
            FROM exon_replacements
            WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id)
      WHERE object_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );

    UPDATE feature
      SET is_obsolete = true
      WHERE feature_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );
  END;
$$;


ALTER FUNCTION chado.share_exons() OWNER TO drupaladmin;

--
-- Name: store_analysis(character varying, character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_analysis(character varying, character varying, character varying) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$DECLARE
   v_program            ALIAS FOR $1;
   v_programversion     ALIAS FOR $2;
   v_sourcename         ALIAS FOR $3;
   pkval                BIGINT;
 BEGIN
    SELECT INTO pkval analysis_id
      FROM analysis
      WHERE program=v_program AND
            programversion=v_programversion AND
            sourcename=v_sourcename;
    IF NOT FOUND THEN
      INSERT INTO analysis
       (program,programversion,sourcename)
         VALUES
       (v_program,v_programversion,v_sourcename);
      RETURN currval('analysis_analysis_id_seq');
    END IF;
    RETURN pkval;
 END;
$_$;


ALTER FUNCTION chado.store_analysis(character varying, character varying, character varying) OWNER TO drupaladmin;

--
-- Name: store_db(character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_db(character varying) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$DECLARE
   v_name             ALIAS FOR $1;

   v_db_id            BIGINT;
 BEGIN
    SELECT INTO v_db_id db_id
      FROM db
      WHERE name=v_name;
    IF NOT FOUND THEN
      INSERT INTO db
       (name)
         VALUES
       (v_name);
       RETURN currval('db_db_id_seq');
    END IF;
    RETURN v_db_id;
 END;
$_$;


ALTER FUNCTION chado.store_db(character varying) OWNER TO drupaladmin;

--
-- Name: store_dbxref(character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_dbxref(character varying, character varying) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$DECLARE
   v_dbname                ALIAS FOR $1;
   v_accession             ALIAS FOR $2;

   v_db_id                 BIGINT;
   v_dbxref_id             BIGINT;
 BEGIN
    SELECT INTO v_db_id
      store_db(v_dbname);
    SELECT INTO v_dbxref_id dbxref_id
      FROM dbxref
      WHERE db_id=v_db_id       AND
            accession=v_accession;
    IF NOT FOUND THEN
      INSERT INTO dbxref
       (db_id,accession)
         VALUES
       (v_db_id,v_accession);
       RETURN currval('dbxref_dbxref_id_seq');
    END IF;
    RETURN v_dbxref_id;
 END;
$_$;


ALTER FUNCTION chado.store_dbxref(character varying, character varying) OWNER TO drupaladmin;

--
-- Name: store_feature(integer, integer, integer, integer, integer, integer, character varying, character varying, integer, boolean); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_feature(integer, integer, integer, integer, integer, integer, character varying, character varying, integer, boolean) RETURNS integer
    LANGUAGE plpgsql
    AS $_$DECLARE
  v_srcfeature_id       ALIAS FOR $1;
  v_fmin                ALIAS FOR $2;
  v_fmax                ALIAS FOR $3;
  v_strand              ALIAS FOR $4;
  v_dbxref_id           ALIAS FOR $5;
  v_organism_id         ALIAS FOR $6;
  v_name                ALIAS FOR $7;
  v_uniquename          ALIAS FOR $8;
  v_type_id             ALIAS FOR $9;
  v_is_analysis         ALIAS FOR $10;
  v_feature_id          INT;
  v_featureloc_id       INT;
 BEGIN
    IF v_dbxref_id IS NULL THEN
      SELECT INTO v_feature_id feature_id
      FROM feature
      WHERE uniquename=v_uniquename     AND
            organism_id=v_organism_id   AND
            type_id=v_type_id;
    ELSE
      SELECT INTO v_feature_id feature_id
      FROM feature
      WHERE dbxref_id=v_dbxref_id;
    END IF;
    IF NOT FOUND THEN
      INSERT INTO feature
       ( dbxref_id           ,
         organism_id         ,
         name                ,
         uniquename          ,
         type_id             ,
         is_analysis         )
        VALUES
        ( v_dbxref_id           ,
          v_organism_id         ,
          v_name                ,
          v_uniquename          ,
          v_type_id             ,
          v_is_analysis         );
      v_feature_id = currval('feature_feature_id_seq');
    ELSE
      UPDATE feature SET
        dbxref_id   =  v_dbxref_id           ,
        organism_id =  v_organism_id         ,
        name        =  v_name                ,
        uniquename  =  v_uniquename          ,
        type_id     =  v_type_id             ,
        is_analysis =  v_is_analysis
      WHERE
        feature_id=v_feature_id;
    END IF;
  PERFORM store_featureloc(v_feature_id,
                           v_srcfeature_id,
                           v_fmin,
                           v_fmax,
                           v_strand,
                           0,
                           0);
  RETURN v_feature_id;
 END;
$_$;


ALTER FUNCTION chado.store_feature(integer, integer, integer, integer, integer, integer, character varying, character varying, integer, boolean) OWNER TO drupaladmin;

--
-- Name: store_feature_synonym(integer, character varying, integer, boolean, boolean, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_feature_synonym(integer, character varying, integer, boolean, boolean, integer) RETURNS integer
    LANGUAGE plpgsql
    AS $_$DECLARE
  v_feature_id          ALIAS FOR $1;
  v_syn                 ALIAS FOR $2;
  v_type_id             ALIAS FOR $3;
  v_is_current          ALIAS FOR $4;
  v_is_internal         ALIAS FOR $5;
  v_pub_id              ALIAS FOR $6;
  v_synonym_id          INT;
  v_feature_synonym_id  INT;
 BEGIN
    IF v_feature_id IS NULL THEN RAISE EXCEPTION 'feature_id cannot be null';
    END IF;
    SELECT INTO v_synonym_id synonym_id
      FROM synonym
      WHERE name=v_syn                  AND
            type_id=v_type_id;
    IF NOT FOUND THEN
      INSERT INTO synonym
        ( name,
          synonym_sgml,
          type_id)
        VALUES
        ( v_syn,
          v_syn,
          v_type_id);
      v_synonym_id = currval('synonym_synonym_id_seq');
    END IF;
    SELECT INTO v_feature_synonym_id feature_synonym_id
        FROM feature_synonym
        WHERE feature_id=v_feature_id   AND
              synonym_id=v_synonym_id   AND
              pub_id=v_pub_id;
    IF NOT FOUND THEN
      INSERT INTO feature_synonym
        ( feature_id,
          synonym_id,
          pub_id,
          is_current,
          is_internal)
        VALUES
        ( v_feature_id,
          v_synonym_id,
          v_pub_id,
          v_is_current,
          v_is_internal);
      v_feature_synonym_id = currval('feature_synonym_feature_synonym_id_seq');
    ELSE
      UPDATE feature_synonym
        SET is_current=v_is_current, is_internal=v_is_internal
        WHERE feature_synonym_id=v_feature_synonym_id;
    END IF;
  RETURN v_feature_synonym_id;
 END;
$_$;


ALTER FUNCTION chado.store_feature_synonym(integer, character varying, integer, boolean, boolean, integer) OWNER TO drupaladmin;

--
-- Name: store_featureloc(integer, integer, integer, integer, integer, integer, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_featureloc(integer, integer, integer, integer, integer, integer, integer) RETURNS integer
    LANGUAGE plpgsql
    AS $_$DECLARE
  v_feature_id          ALIAS FOR $1;
  v_srcfeature_id       ALIAS FOR $2;
  v_fmin                ALIAS FOR $3;
  v_fmax                ALIAS FOR $4;
  v_strand              ALIAS FOR $5;
  v_rank                ALIAS FOR $6;
  v_locgroup            ALIAS FOR $7;
  v_featureloc_id       INT;
 BEGIN
    IF v_feature_id IS NULL THEN RAISE EXCEPTION 'feature_id cannot be null';
    END IF;
    SELECT INTO v_featureloc_id featureloc_id
      FROM featureloc
      WHERE feature_id=v_feature_id     AND
            rank=v_rank                 AND
            locgroup=v_locgroup;
    IF NOT FOUND THEN
      INSERT INTO featureloc
        ( feature_id,
          srcfeature_id,
          fmin,
          fmax,
          strand,
          rank,
          locgroup)
        VALUES
        (  v_feature_id,
           v_srcfeature_id,
           v_fmin,
           v_fmax,
           v_strand,
           v_rank,
           v_locgroup);
      v_featureloc_id = currval('featureloc_featureloc_id_seq');
    ELSE
      UPDATE featureloc SET
        feature_id    =  v_feature_id,
        srcfeature_id =  v_srcfeature_id,
        fmin          =  v_fmin,
        fmax          =  v_fmax,
        strand        =  v_strand,
        rank          =  v_rank,
        locgroup      =  v_locgroup
      WHERE
        featureloc_id=v_featureloc_id;
    END IF;
  RETURN v_featureloc_id;
 END;
$_$;


ALTER FUNCTION chado.store_featureloc(integer, integer, integer, integer, integer, integer, integer) OWNER TO drupaladmin;

--
-- Name: store_organism(character varying, character varying, character varying); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.store_organism(character varying, character varying, character varying) RETURNS bigint
    LANGUAGE plpgsql
    AS $_$DECLARE
   v_genus            ALIAS FOR $1;
   v_species          ALIAS FOR $2;
   v_common_name      ALIAS FOR $3;

   v_organism_id      BIGINT;
 BEGIN
    SELECT INTO v_organism_id organism_id
      FROM organism
      WHERE genus=v_genus               AND
            species=v_species;
    IF NOT FOUND THEN
      INSERT INTO organism
       (genus,species,common_name)
         VALUES
       (v_genus,v_species,v_common_name);
       RETURN currval('organism_organism_id_seq');
    ELSE
      UPDATE organism
       SET common_name=v_common_name
      WHERE organism_id = v_organism_id;
    END IF;
    RETURN v_organism_id;
 END;
$_$;


ALTER FUNCTION chado.store_organism(character varying, character varying, character varying) OWNER TO drupaladmin;

--
-- Name: subsequence(bigint, bigint, bigint, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence(bigint, bigint, bigint, integer) RETURNS text
    LANGUAGE sql
    AS $_$SELECT
  CASE WHEN $4<0
   THEN reverse_complement(substring(srcf.residues,CAST(($2+1) as int),CAST(($3-$2) as int)))
   ELSE substring(residues,CAST(($2+1) as int),CAST(($3-$2) as int))
  END AS residues
  FROM feature AS srcf
  WHERE
   srcf.feature_id=$1$_$;


ALTER FUNCTION chado.subsequence(bigint, bigint, bigint, integer) OWNER TO drupaladmin;

--
-- Name: subsequence_by_feature(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_feature(bigint) RETURNS text
    LANGUAGE sql
    AS $_$SELECT subsequence_by_feature($1,0,0)$_$;


ALTER FUNCTION chado.subsequence_by_feature(bigint) OWNER TO drupaladmin;

--
-- Name: subsequence_by_feature(bigint, integer, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_feature(bigint, integer, integer) RETURNS text
    LANGUAGE sql
    AS $_$SELECT
  CASE WHEN strand<0
   THEN reverse_complement(substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int)))
   ELSE substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int))
  END AS residues
  FROM feature AS srcf
   INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id)
  WHERE
   featureloc.feature_id=$1 AND
   featureloc.rank=$2 AND
   featureloc.locgroup=$3$_$;


ALTER FUNCTION chado.subsequence_by_feature(bigint, integer, integer) OWNER TO drupaladmin;

--
-- Name: subsequence_by_featureloc(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_featureloc(bigint) RETURNS text
    LANGUAGE sql
    AS $_$SELECT
  CASE WHEN strand<0
   THEN reverse_complement(substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int)))
   ELSE substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int))
  END AS residues
  FROM feature AS srcf
   INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id)
  WHERE
   featureloc_id=$1$_$;


ALTER FUNCTION chado.subsequence_by_featureloc(bigint) OWNER TO drupaladmin;

--
-- Name: subsequence_by_subfeatures(bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_subfeatures(bigint) RETURNS text
    LANGUAGE sql
    AS $_$
SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id('part_of'),0,0)
$_$;


ALTER FUNCTION chado.subsequence_by_subfeatures(bigint) OWNER TO drupaladmin;

--
-- Name: subsequence_by_subfeatures(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_subfeatures(bigint, bigint) RETURNS text
    LANGUAGE sql
    AS $_$SELECT subsequence_by_subfeatures($1,$2,0,0)$_$;


ALTER FUNCTION chado.subsequence_by_subfeatures(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: subsequence_by_subfeatures(bigint, bigint, integer, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_subfeatures(bigint, bigint, integer, integer) RETURNS text
    LANGUAGE plpgsql
    AS $_$
DECLARE v_feature_id ALIAS FOR $1;
DECLARE v_rtype_id   ALIAS FOR $2;
DECLARE v_rank       ALIAS FOR $3;
DECLARE v_locgroup   ALIAS FOR $4;
DECLARE subseq       TEXT;
DECLARE seqrow       RECORD;
BEGIN
  subseq = '';
 FOR seqrow IN
   SELECT
    CASE WHEN strand<0
     THEN reverse_complement(substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int)))
     ELSE substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int))
    END AS residues
    FROM feature AS srcf
     INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id)
     INNER JOIN feature_relationship AS fr
       ON (fr.subject_id=featureloc.feature_id)
    WHERE
     fr.object_id=v_feature_id AND
     fr.type_id=v_rtype_id AND
     featureloc.rank=v_rank AND
     featureloc.locgroup=v_locgroup
    ORDER BY fr.rank
  LOOP
   subseq = subseq  || seqrow.residues;
  END LOOP;
 RETURN subseq;
END
$_$;


ALTER FUNCTION chado.subsequence_by_subfeatures(bigint, bigint, integer, integer) OWNER TO drupaladmin;

--
-- Name: subsequence_by_typed_subfeatures(bigint, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_typed_subfeatures(bigint, bigint) RETURNS text
    LANGUAGE sql
    AS $_$SELECT subsequence_by_typed_subfeatures($1,$2,0,0)$_$;


ALTER FUNCTION chado.subsequence_by_typed_subfeatures(bigint, bigint) OWNER TO drupaladmin;

--
-- Name: subsequence_by_typed_subfeatures(bigint, bigint, integer, integer); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.subsequence_by_typed_subfeatures(bigint, bigint, integer, integer) RETURNS text
    LANGUAGE plpgsql
    AS $_$
DECLARE v_feature_id ALIAS FOR $1;
DECLARE v_ftype_id   ALIAS FOR $2;
DECLARE v_rank       ALIAS FOR $3;
DECLARE v_locgroup   ALIAS FOR $4;
DECLARE subseq       TEXT;
DECLARE seqrow       RECORD;
BEGIN
  subseq = '';
 FOR seqrow IN
   SELECT
    CASE WHEN strand<0
     THEN reverse_complement(substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int)))
     ELSE substring(srcf.residues,CAST(fmin+1 as int),CAST((fmax-fmin) as int))
    END AS residues
  FROM feature AS srcf
   INNER JOIN featureloc ON (srcf.feature_id=featureloc.srcfeature_id)
   INNER JOIN feature AS subf ON (subf.feature_id=featureloc.feature_id)
   INNER JOIN feature_relationship AS fr ON (fr.subject_id=subf.feature_id)
  WHERE
     fr.object_id=v_feature_id AND
     subf.type_id=v_ftype_id AND
     featureloc.rank=v_rank AND
     featureloc.locgroup=v_locgroup
  ORDER BY fr.rank
   LOOP
   subseq = subseq  || seqrow.residues;
  END LOOP;
 RETURN subseq;
END
$_$;


ALTER FUNCTION chado.subsequence_by_typed_subfeatures(bigint, bigint, integer, integer) OWNER TO drupaladmin;

--
-- Name: translate_codon(text, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.translate_codon(text, bigint) RETURNS character
    LANGUAGE sql
    AS $_$SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2$_$;


ALTER FUNCTION chado.translate_codon(text, bigint) OWNER TO drupaladmin;

--
-- Name: translate_dna(text); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.translate_dna(text) RETURNS text
    LANGUAGE sql
    AS $_$SELECT translate_dna($1,1)$_$;


ALTER FUNCTION chado.translate_dna(text) OWNER TO drupaladmin;

--
-- Name: translate_dna(text, bigint); Type: FUNCTION; Schema: chado; Owner: drupaladmin
--

CREATE FUNCTION chado.translate_dna(text, bigint) RETURNS text
    LANGUAGE plpgsql
    AS $_$
 DECLARE
  dnaseq ALIAS FOR $1;
  gcode ALIAS FOR $2;
  translation TEXT;
  dnaseqlen BIGINT;
  codon CHAR(3);
  aa CHAR(1);
  i INT;
 BEGIN
   translation = '';
   dnaseqlen = char_length(dnaseq);
   i=1;
   WHILE i+1 < dnaseqlen loop
     codon = substring(dnaseq,i,3);
     aa = translate_codon(codon,gcode);
     translation = translation || aa;
     i = i+3;
   END loop;
 RETURN translation;
END$_$;


ALTER FUNCTION chado.translate_dna(text, bigint) OWNER TO drupaladmin;

--
-- Name: concat(text); Type: AGGREGATE; Schema: chado; Owner: drupaladmin
--

CREATE AGGREGATE chado.concat(text) (
    SFUNC = chado.concat_pair,
    STYPE = text,
    INITCOND = ''
);


ALTER AGGREGATE chado.concat(text) OWNER TO drupaladmin;

--
-- Name: acquisition; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.acquisition (
    acquisition_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    protocol_id bigint,
    channel_id bigint,
    acquisitiondate timestamp without time zone DEFAULT CURRENT_TIMESTAMP,
    name text,
    uri text
);


ALTER TABLE chado.acquisition OWNER TO drupaladmin;

--
-- Name: TABLE acquisition; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.acquisition IS 'This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.';


--
-- Name: acquisition_acquisition_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.acquisition_acquisition_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.acquisition_acquisition_id_seq OWNER TO drupaladmin;

--
-- Name: acquisition_acquisition_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.acquisition_acquisition_id_seq OWNED BY chado.acquisition.acquisition_id;


--
-- Name: acquisition_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.acquisition_relationship (
    acquisition_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    type_id bigint NOT NULL,
    object_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.acquisition_relationship OWNER TO drupaladmin;

--
-- Name: TABLE acquisition_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.acquisition_relationship IS 'Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.';


--
-- Name: acquisition_relationship_acquisition_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.acquisition_relationship_acquisition_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.acquisition_relationship_acquisition_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: acquisition_relationship_acquisition_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.acquisition_relationship_acquisition_relationship_id_seq OWNED BY chado.acquisition_relationship.acquisition_relationship_id;


--
-- Name: acquisitionprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.acquisitionprop (
    acquisitionprop_id bigint NOT NULL,
    acquisition_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.acquisitionprop OWNER TO drupaladmin;

--
-- Name: TABLE acquisitionprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.acquisitionprop IS 'Parameters associated with image acquisition.';


--
-- Name: acquisitionprop_acquisitionprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.acquisitionprop_acquisitionprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.acquisitionprop_acquisitionprop_id_seq OWNER TO drupaladmin;

--
-- Name: acquisitionprop_acquisitionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.acquisitionprop_acquisitionprop_id_seq OWNED BY chado.acquisitionprop.acquisitionprop_id;


--
-- Name: all_feature_names; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.all_feature_names AS
 SELECT feature.feature_id,
    ("substring"(feature.uniquename, 0, 255))::character varying(255) AS name,
    feature.organism_id
   FROM chado.feature
UNION
 SELECT feature.feature_id,
    feature.name,
    feature.organism_id
   FROM chado.feature
  WHERE (feature.name IS NOT NULL)
UNION
 SELECT fs.feature_id,
    s.name,
    f.organism_id
   FROM chado.feature_synonym fs,
    chado.synonym s,
    chado.feature f
  WHERE ((fs.synonym_id = s.synonym_id) AND (fs.feature_id = f.feature_id))
UNION
 SELECT fp.feature_id,
    ("substring"(fp.value, 0, 255))::character varying(255) AS name,
    f.organism_id
   FROM chado.featureprop fp,
    chado.feature f
  WHERE (f.feature_id = fp.feature_id)
UNION
 SELECT fd.feature_id,
    d.accession AS name,
    f.organism_id
   FROM chado.feature_dbxref fd,
    chado.dbxref d,
    chado.feature f
  WHERE ((fd.dbxref_id = d.dbxref_id) AND (fd.feature_id = f.feature_id));


ALTER TABLE chado.all_feature_names OWNER TO drupaladmin;

--
-- Name: analysis; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis (
    analysis_id bigint NOT NULL,
    name character varying(255),
    description text,
    program character varying(255) NOT NULL,
    programversion character varying(255) NOT NULL,
    algorithm character varying(255),
    sourcename character varying(255),
    sourceversion character varying(255),
    sourceuri text,
    timeexecuted timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL
);


ALTER TABLE chado.analysis OWNER TO drupaladmin;

--
-- Name: TABLE analysis; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysis IS 'An analysis is a particular type of a
    computational analysis; it may be a blast of one sequence against
    another, or an all by all blast, or a different kind of analysis
    altogether. It is a single unit of computation.';


--
-- Name: COLUMN analysis.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.name IS 'A way of grouping analyses. This
    should be a handy short identifier that can help people find an
    analysis they want. For instance "tRNAscan", "cDNA", "FlyPep",
    "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.';


--
-- Name: COLUMN analysis.program; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.program IS 'Program name, e.g. blastx, blastp, sim4, genscan.';


--
-- Name: COLUMN analysis.programversion; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.programversion IS 'Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].';


--
-- Name: COLUMN analysis.algorithm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.algorithm IS 'Algorithm name, e.g. blast.';


--
-- Name: COLUMN analysis.sourcename; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.sourcename IS 'Source name, e.g. cDNA, SwissProt.';


--
-- Name: COLUMN analysis.sourceuri; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis.sourceuri IS 'This is an optional, permanent URL or URI for the source of the  analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).';


--
-- Name: analysis_analysis_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysis_analysis_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysis_analysis_id_seq OWNER TO drupaladmin;

--
-- Name: analysis_analysis_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysis_analysis_id_seq OWNED BY chado.analysis.analysis_id;


--
-- Name: analysis_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis_cvterm (
    analysis_cvterm_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    is_not boolean DEFAULT false NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.analysis_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE analysis_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysis_cvterm IS 'Associate a term from a cv with an analysis.';


--
-- Name: COLUMN analysis_cvterm.is_not; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_cvterm.is_not IS 'If this is set to true, then this
annotation is interpreted as a NEGATIVE annotation - i.e. the analysis does
NOT have the specified term.';


--
-- Name: analysis_cvterm_analysis_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysis_cvterm_analysis_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysis_cvterm_analysis_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: analysis_cvterm_analysis_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysis_cvterm_analysis_cvterm_id_seq OWNED BY chado.analysis_cvterm.analysis_cvterm_id;


--
-- Name: analysis_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis_dbxref (
    analysis_dbxref_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.analysis_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE analysis_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysis_dbxref IS 'Links an analysis to dbxrefs.';


--
-- Name: COLUMN analysis_dbxref.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_dbxref.is_current IS 'True if this dbxref
is the most up to date accession in the corresponding db. Retired
accessions should set this field to false';


--
-- Name: analysis_dbxref_analysis_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysis_dbxref_analysis_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysis_dbxref_analysis_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: analysis_dbxref_analysis_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysis_dbxref_analysis_dbxref_id_seq OWNED BY chado.analysis_dbxref.analysis_dbxref_id;


--
-- Name: analysis_organism; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis_organism (
    analysis_id bigint NOT NULL,
    organism_id bigint NOT NULL
);


ALTER TABLE chado.analysis_organism OWNER TO drupaladmin;

--
-- Name: TABLE analysis_organism; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysis_organism IS 'This view is for associating an organism (via it''s associated features) to an analysis.';


--
-- Name: analysis_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis_pub (
    analysis_pub_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.analysis_pub OWNER TO drupaladmin;

--
-- Name: TABLE analysis_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysis_pub IS 'Provenance. Linking table between analyses and the publications that mention them.';


--
-- Name: analysis_pub_analysis_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysis_pub_analysis_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysis_pub_analysis_pub_id_seq OWNER TO drupaladmin;

--
-- Name: analysis_pub_analysis_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysis_pub_analysis_pub_id_seq OWNED BY chado.analysis_pub.analysis_pub_id;


--
-- Name: analysis_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysis_relationship (
    analysis_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.analysis_relationship OWNER TO drupaladmin;

--
-- Name: COLUMN analysis_relationship.subject_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_relationship.subject_id IS 'analysis_relationship.subject_id i
s the subject of the subj-predicate-obj sentence.';


--
-- Name: COLUMN analysis_relationship.object_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_relationship.object_id IS 'analysis_relationship.object_id
is the object of the subj-predicate-obj sentence.';


--
-- Name: COLUMN analysis_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_relationship.type_id IS 'analysis_relationship.type_id
is relationship type between subject and object. This is a cvterm, typically
from the OBO relationship ontology, although other relationship types are allowed.';


--
-- Name: COLUMN analysis_relationship.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_relationship.value IS 'analysis_relationship.value
is for additional notes or comments.';


--
-- Name: COLUMN analysis_relationship.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysis_relationship.rank IS 'analysis_relationship.rank is
the ordering of subject analysiss with respect to the object analysis may be
important where rank is used to order these; starts from zero.';


--
-- Name: analysis_relationship_analysis_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysis_relationship_analysis_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysis_relationship_analysis_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: analysis_relationship_analysis_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysis_relationship_analysis_relationship_id_seq OWNED BY chado.analysis_relationship.analysis_relationship_id;


--
-- Name: analysisfeature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysisfeature (
    analysisfeature_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    rawscore double precision,
    normscore double precision,
    significance double precision,
    identity double precision
);


ALTER TABLE chado.analysisfeature OWNER TO drupaladmin;

--
-- Name: TABLE analysisfeature; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.analysisfeature IS 'Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries,
 with rank indicating query/subject';


--
-- Name: COLUMN analysisfeature.rawscore; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysisfeature.rawscore IS 'This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.';


--
-- Name: COLUMN analysisfeature.normscore; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysisfeature.normscore IS 'This is the rawscore but
    semi-normalized. Complete normalization to allow comparison of
    features generated by different programs would be nice but too
    difficult. Instead the normalization should strive to enforce the
    following semantics: * normscores are floating point numbers >= 0,
    * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.';


--
-- Name: COLUMN analysisfeature.significance; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysisfeature.significance IS 'This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics:
   * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10
  * low numbers are better than high numbers.';


--
-- Name: COLUMN analysisfeature.identity; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.analysisfeature.identity IS 'Percent identity between the locations compared.  Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.';


--
-- Name: analysisfeature_analysisfeature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysisfeature_analysisfeature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysisfeature_analysisfeature_id_seq OWNER TO drupaladmin;

--
-- Name: analysisfeature_analysisfeature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysisfeature_analysisfeature_id_seq OWNED BY chado.analysisfeature.analysisfeature_id;


--
-- Name: analysisfeatureprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysisfeatureprop (
    analysisfeatureprop_id bigint NOT NULL,
    analysisfeature_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer NOT NULL
);


ALTER TABLE chado.analysisfeatureprop OWNER TO drupaladmin;

--
-- Name: analysisfeatureprop_analysisfeatureprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysisfeatureprop_analysisfeatureprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysisfeatureprop_analysisfeatureprop_id_seq OWNER TO drupaladmin;

--
-- Name: analysisfeatureprop_analysisfeatureprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysisfeatureprop_analysisfeatureprop_id_seq OWNED BY chado.analysisfeatureprop.analysisfeatureprop_id;


--
-- Name: analysisprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.analysisprop (
    analysisprop_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.analysisprop OWNER TO drupaladmin;

--
-- Name: analysisprop_analysisprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.analysisprop_analysisprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.analysisprop_analysisprop_id_seq OWNER TO drupaladmin;

--
-- Name: analysisprop_analysisprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.analysisprop_analysisprop_id_seq OWNED BY chado.analysisprop.analysisprop_id;


--
-- Name: arraydesign; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.arraydesign (
    arraydesign_id bigint NOT NULL,
    manufacturer_id bigint NOT NULL,
    platformtype_id bigint NOT NULL,
    substratetype_id bigint,
    protocol_id bigint,
    dbxref_id bigint,
    name text NOT NULL,
    version text,
    description text,
    array_dimensions text,
    element_dimensions text,
    num_of_elements integer,
    num_array_columns integer,
    num_array_rows integer,
    num_grid_columns integer,
    num_grid_rows integer,
    num_sub_columns integer,
    num_sub_rows integer
);


ALTER TABLE chado.arraydesign OWNER TO drupaladmin;

--
-- Name: TABLE arraydesign; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.arraydesign IS 'General properties about an array.
An array is a template used to generate physical slides, etc.  It
contains layout information, as well as global array properties, such
as material (glass, nylon) and spot dimensions (in rows/columns).';


--
-- Name: arraydesign_arraydesign_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.arraydesign_arraydesign_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.arraydesign_arraydesign_id_seq OWNER TO drupaladmin;

--
-- Name: arraydesign_arraydesign_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.arraydesign_arraydesign_id_seq OWNED BY chado.arraydesign.arraydesign_id;


--
-- Name: arraydesignprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.arraydesignprop (
    arraydesignprop_id bigint NOT NULL,
    arraydesign_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.arraydesignprop OWNER TO drupaladmin;

--
-- Name: TABLE arraydesignprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.arraydesignprop IS 'Extra array design properties that are not accounted for in arraydesign.';


--
-- Name: arraydesignprop_arraydesignprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.arraydesignprop_arraydesignprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.arraydesignprop_arraydesignprop_id_seq OWNER TO drupaladmin;

--
-- Name: arraydesignprop_arraydesignprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.arraydesignprop_arraydesignprop_id_seq OWNED BY chado.arraydesignprop.arraydesignprop_id;


--
-- Name: assay; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.assay (
    assay_id bigint NOT NULL,
    arraydesign_id bigint NOT NULL,
    protocol_id bigint,
    assaydate timestamp without time zone DEFAULT CURRENT_TIMESTAMP,
    arrayidentifier text,
    arraybatchidentifier text,
    operator_id bigint NOT NULL,
    dbxref_id bigint,
    name text,
    description text
);


ALTER TABLE chado.assay OWNER TO drupaladmin;

--
-- Name: TABLE assay; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.assay IS 'An assay consists of a physical instance of
an array, combined with the conditions used to create the array
(protocols, technician information). The assay can be thought of as a hybridization.';


--
-- Name: assay_assay_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.assay_assay_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.assay_assay_id_seq OWNER TO drupaladmin;

--
-- Name: assay_assay_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.assay_assay_id_seq OWNED BY chado.assay.assay_id;


--
-- Name: assay_biomaterial; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.assay_biomaterial (
    assay_biomaterial_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    biomaterial_id bigint NOT NULL,
    channel_id bigint,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.assay_biomaterial OWNER TO drupaladmin;

--
-- Name: TABLE assay_biomaterial; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.assay_biomaterial IS 'A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).';


--
-- Name: assay_biomaterial_assay_biomaterial_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.assay_biomaterial_assay_biomaterial_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.assay_biomaterial_assay_biomaterial_id_seq OWNER TO drupaladmin;

--
-- Name: assay_biomaterial_assay_biomaterial_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.assay_biomaterial_assay_biomaterial_id_seq OWNED BY chado.assay_biomaterial.assay_biomaterial_id;


--
-- Name: assay_project; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.assay_project (
    assay_project_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    project_id bigint NOT NULL
);


ALTER TABLE chado.assay_project OWNER TO drupaladmin;

--
-- Name: TABLE assay_project; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.assay_project IS 'Link assays to projects.';


--
-- Name: assay_project_assay_project_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.assay_project_assay_project_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.assay_project_assay_project_id_seq OWNER TO drupaladmin;

--
-- Name: assay_project_assay_project_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.assay_project_assay_project_id_seq OWNED BY chado.assay_project.assay_project_id;


--
-- Name: assayprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.assayprop (
    assayprop_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.assayprop OWNER TO drupaladmin;

--
-- Name: TABLE assayprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.assayprop IS 'Extra assay properties that are not accounted for in assay.';


--
-- Name: assayprop_assayprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.assayprop_assayprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.assayprop_assayprop_id_seq OWNER TO drupaladmin;

--
-- Name: assayprop_assayprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.assayprop_assayprop_id_seq OWNED BY chado.assayprop.assayprop_id;


--
-- Name: biomaterial; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.biomaterial (
    biomaterial_id bigint NOT NULL,
    taxon_id bigint,
    biosourceprovider_id bigint,
    dbxref_id bigint,
    name text,
    description text
);


ALTER TABLE chado.biomaterial OWNER TO drupaladmin;

--
-- Name: TABLE biomaterial; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.biomaterial IS 'A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.';


--
-- Name: biomaterial_biomaterial_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.biomaterial_biomaterial_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.biomaterial_biomaterial_id_seq OWNER TO drupaladmin;

--
-- Name: biomaterial_biomaterial_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.biomaterial_biomaterial_id_seq OWNED BY chado.biomaterial.biomaterial_id;


--
-- Name: biomaterial_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.biomaterial_dbxref (
    biomaterial_dbxref_id bigint NOT NULL,
    biomaterial_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.biomaterial_dbxref OWNER TO drupaladmin;

--
-- Name: biomaterial_dbxref_biomaterial_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.biomaterial_dbxref_biomaterial_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.biomaterial_dbxref_biomaterial_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: biomaterial_dbxref_biomaterial_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.biomaterial_dbxref_biomaterial_dbxref_id_seq OWNED BY chado.biomaterial_dbxref.biomaterial_dbxref_id;


--
-- Name: biomaterial_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.biomaterial_relationship (
    biomaterial_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    type_id bigint NOT NULL,
    object_id bigint NOT NULL
);


ALTER TABLE chado.biomaterial_relationship OWNER TO drupaladmin;

--
-- Name: TABLE biomaterial_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.biomaterial_relationship IS 'Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.';


--
-- Name: biomaterial_relationship_biomaterial_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.biomaterial_relationship_biomaterial_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.biomaterial_relationship_biomaterial_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: biomaterial_relationship_biomaterial_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.biomaterial_relationship_biomaterial_relationship_id_seq OWNED BY chado.biomaterial_relationship.biomaterial_relationship_id;


--
-- Name: biomaterial_treatment; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.biomaterial_treatment (
    biomaterial_treatment_id bigint NOT NULL,
    biomaterial_id bigint NOT NULL,
    treatment_id bigint NOT NULL,
    unittype_id bigint,
    value real,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.biomaterial_treatment OWNER TO drupaladmin;

--
-- Name: TABLE biomaterial_treatment; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.biomaterial_treatment IS 'Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).';


--
-- Name: biomaterial_treatment_biomaterial_treatment_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.biomaterial_treatment_biomaterial_treatment_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.biomaterial_treatment_biomaterial_treatment_id_seq OWNER TO drupaladmin;

--
-- Name: biomaterial_treatment_biomaterial_treatment_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.biomaterial_treatment_biomaterial_treatment_id_seq OWNED BY chado.biomaterial_treatment.biomaterial_treatment_id;


--
-- Name: biomaterialprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.biomaterialprop (
    biomaterialprop_id bigint NOT NULL,
    biomaterial_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.biomaterialprop OWNER TO drupaladmin;

--
-- Name: TABLE biomaterialprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.biomaterialprop IS 'Extra biomaterial properties that are not accounted for in biomaterial.';


--
-- Name: biomaterialprop_biomaterialprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.biomaterialprop_biomaterialprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.biomaterialprop_biomaterialprop_id_seq OWNER TO drupaladmin;

--
-- Name: biomaterialprop_biomaterialprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.biomaterialprop_biomaterialprop_id_seq OWNED BY chado.biomaterialprop.biomaterialprop_id;


--
-- Name: cell_line; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line (
    cell_line_id bigint NOT NULL,
    name character varying(255),
    uniquename character varying(255) NOT NULL,
    organism_id bigint NOT NULL,
    timeaccessioned timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL,
    timelastmodified timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL
);


ALTER TABLE chado.cell_line OWNER TO drupaladmin;

--
-- Name: cell_line_cell_line_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_cell_line_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_cell_line_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_cell_line_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_cell_line_id_seq OWNED BY chado.cell_line.cell_line_id;


--
-- Name: cell_line_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_cvterm (
    cell_line_cvterm_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cell_line_cvterm OWNER TO drupaladmin;

--
-- Name: cell_line_cvterm_cell_line_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_cvterm_cell_line_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_cvterm_cell_line_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_cvterm_cell_line_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_cvterm_cell_line_cvterm_id_seq OWNED BY chado.cell_line_cvterm.cell_line_cvterm_id;


--
-- Name: cell_line_cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_cvtermprop (
    cell_line_cvtermprop_id bigint NOT NULL,
    cell_line_cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cell_line_cvtermprop OWNER TO drupaladmin;

--
-- Name: cell_line_cvtermprop_cell_line_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_cvtermprop_cell_line_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_cvtermprop_cell_line_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_cvtermprop_cell_line_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_cvtermprop_cell_line_cvtermprop_id_seq OWNED BY chado.cell_line_cvtermprop.cell_line_cvtermprop_id;


--
-- Name: cell_line_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_dbxref (
    cell_line_dbxref_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.cell_line_dbxref OWNER TO drupaladmin;

--
-- Name: cell_line_dbxref_cell_line_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_dbxref_cell_line_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_dbxref_cell_line_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_dbxref_cell_line_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_dbxref_cell_line_dbxref_id_seq OWNED BY chado.cell_line_dbxref.cell_line_dbxref_id;


--
-- Name: cell_line_feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_feature (
    cell_line_feature_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.cell_line_feature OWNER TO drupaladmin;

--
-- Name: cell_line_feature_cell_line_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_feature_cell_line_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_feature_cell_line_feature_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_feature_cell_line_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_feature_cell_line_feature_id_seq OWNED BY chado.cell_line_feature.cell_line_feature_id;


--
-- Name: cell_line_library; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_library (
    cell_line_library_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    library_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.cell_line_library OWNER TO drupaladmin;

--
-- Name: cell_line_library_cell_line_library_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_library_cell_line_library_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_library_cell_line_library_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_library_cell_line_library_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_library_cell_line_library_id_seq OWNED BY chado.cell_line_library.cell_line_library_id;


--
-- Name: cell_line_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_pub (
    cell_line_pub_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.cell_line_pub OWNER TO drupaladmin;

--
-- Name: cell_line_pub_cell_line_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_pub_cell_line_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_pub_cell_line_pub_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_pub_cell_line_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_pub_cell_line_pub_id_seq OWNED BY chado.cell_line_pub.cell_line_pub_id;


--
-- Name: cell_line_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_relationship (
    cell_line_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.cell_line_relationship OWNER TO drupaladmin;

--
-- Name: cell_line_relationship_cell_line_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_relationship_cell_line_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_relationship_cell_line_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_relationship_cell_line_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_relationship_cell_line_relationship_id_seq OWNED BY chado.cell_line_relationship.cell_line_relationship_id;


--
-- Name: cell_line_synonym; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_line_synonym (
    cell_line_synonym_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    synonym_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    is_current boolean DEFAULT false NOT NULL,
    is_internal boolean DEFAULT false NOT NULL
);


ALTER TABLE chado.cell_line_synonym OWNER TO drupaladmin;

--
-- Name: cell_line_synonym_cell_line_synonym_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_line_synonym_cell_line_synonym_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_line_synonym_cell_line_synonym_id_seq OWNER TO drupaladmin;

--
-- Name: cell_line_synonym_cell_line_synonym_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_line_synonym_cell_line_synonym_id_seq OWNED BY chado.cell_line_synonym.cell_line_synonym_id;


--
-- Name: cell_lineprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_lineprop (
    cell_lineprop_id bigint NOT NULL,
    cell_line_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cell_lineprop OWNER TO drupaladmin;

--
-- Name: cell_lineprop_cell_lineprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_lineprop_cell_lineprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_lineprop_cell_lineprop_id_seq OWNER TO drupaladmin;

--
-- Name: cell_lineprop_cell_lineprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_lineprop_cell_lineprop_id_seq OWNED BY chado.cell_lineprop.cell_lineprop_id;


--
-- Name: cell_lineprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cell_lineprop_pub (
    cell_lineprop_pub_id bigint NOT NULL,
    cell_lineprop_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.cell_lineprop_pub OWNER TO drupaladmin;

--
-- Name: cell_lineprop_pub_cell_lineprop_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cell_lineprop_pub_cell_lineprop_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cell_lineprop_pub_cell_lineprop_pub_id_seq OWNER TO drupaladmin;

--
-- Name: cell_lineprop_pub_cell_lineprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cell_lineprop_pub_cell_lineprop_pub_id_seq OWNED BY chado.cell_lineprop_pub.cell_lineprop_pub_id;


--
-- Name: chadoprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.chadoprop (
    chadoprop_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.chadoprop OWNER TO drupaladmin;

--
-- Name: TABLE chadoprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version';


--
-- Name: COLUMN chadoprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.';


--
-- Name: COLUMN chadoprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.';


--
-- Name: COLUMN chadoprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.chadoprop.rank IS 'Property-Value ordering. Any
cv can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used.';


--
-- Name: chadoprop_chadoprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.chadoprop_chadoprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.chadoprop_chadoprop_id_seq OWNER TO drupaladmin;

--
-- Name: chadoprop_chadoprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.chadoprop_chadoprop_id_seq OWNED BY chado.chadoprop.chadoprop_id;


--
-- Name: channel; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.channel (
    channel_id bigint NOT NULL,
    name text NOT NULL,
    definition text NOT NULL
);


ALTER TABLE chado.channel OWNER TO drupaladmin;

--
-- Name: TABLE channel; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.channel IS 'Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).';


--
-- Name: channel_channel_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.channel_channel_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.channel_channel_id_seq OWNER TO drupaladmin;

--
-- Name: channel_channel_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.channel_channel_id_seq OWNED BY chado.channel.channel_id;


--
-- Name: common_ancestor_cvterm; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.common_ancestor_cvterm AS
 SELECT p1.subject_id AS cvterm1_id,
    p2.subject_id AS cvterm2_id,
    p1.object_id AS ancestor_cvterm_id,
    p1.pathdistance AS pathdistance1,
    p2.pathdistance AS pathdistance2,
    (p1.pathdistance + p2.pathdistance) AS total_pathdistance
   FROM chado.cvtermpath p1,
    chado.cvtermpath p2
  WHERE (p1.object_id = p2.object_id);


ALTER TABLE chado.common_ancestor_cvterm OWNER TO drupaladmin;

--
-- Name: VIEW common_ancestor_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.common_ancestor_cvterm IS 'The common ancestor of any
two terms is the intersection of both terms ancestors. Two terms can
have multiple common ancestors. Use total_pathdistance to get the
least common ancestor';


--
-- Name: common_descendant_cvterm; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.common_descendant_cvterm AS
 SELECT p1.object_id AS cvterm1_id,
    p2.object_id AS cvterm2_id,
    p1.subject_id AS ancestor_cvterm_id,
    p1.pathdistance AS pathdistance1,
    p2.pathdistance AS pathdistance2,
    (p1.pathdistance + p2.pathdistance) AS total_pathdistance
   FROM chado.cvtermpath p1,
    chado.cvtermpath p2
  WHERE (p1.subject_id = p2.subject_id);


ALTER TABLE chado.common_descendant_cvterm OWNER TO drupaladmin;

--
-- Name: VIEW common_descendant_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.common_descendant_cvterm IS 'The common descendant of
any two terms is the intersection of both terms descendants. Two terms
can have multiple common descendants. Use total_pathdistance to get
the least common ancestor';


--
-- Name: contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.contact (
    contact_id bigint NOT NULL,
    type_id bigint,
    name character varying(255) NOT NULL,
    description character varying(255)
);


ALTER TABLE chado.contact OWNER TO drupaladmin;

--
-- Name: TABLE contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.contact IS 'Model persons, institutes, groups, organizations, etc.';


--
-- Name: COLUMN contact.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.contact.type_id IS 'What type of contact is this?  E.g. "person", "lab".';


--
-- Name: contact_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.contact_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.contact_contact_id_seq OWNER TO drupaladmin;

--
-- Name: contact_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.contact_contact_id_seq OWNED BY chado.contact.contact_id;


--
-- Name: contact_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.contact_relationship (
    contact_relationship_id bigint NOT NULL,
    type_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL
);


ALTER TABLE chado.contact_relationship OWNER TO drupaladmin;

--
-- Name: TABLE contact_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.contact_relationship IS 'Model relationships between contacts';


--
-- Name: COLUMN contact_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.contact_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.';


--
-- Name: COLUMN contact_relationship.subject_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.contact_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.';


--
-- Name: COLUMN contact_relationship.object_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.contact_relationship.object_id IS 'The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.';


--
-- Name: contact_relationship_contact_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.contact_relationship_contact_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.contact_relationship_contact_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: contact_relationship_contact_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.contact_relationship_contact_relationship_id_seq OWNED BY chado.contact_relationship.contact_relationship_id;


--
-- Name: contactprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.contactprop (
    contactprop_id bigint NOT NULL,
    contact_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.contactprop OWNER TO drupaladmin;

--
-- Name: TABLE contactprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.contactprop IS 'A contact can have any number of slot-value property
tags attached to it. This is an alternative to hardcoding a list of columns in the
relational schema, and is completely extensible.';


--
-- Name: contactprop_contactprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.contactprop_contactprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.contactprop_contactprop_id_seq OWNER TO drupaladmin;

--
-- Name: contactprop_contactprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.contactprop_contactprop_id_seq OWNED BY chado.contactprop.contactprop_id;


--
-- Name: control; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.control (
    control_id bigint NOT NULL,
    type_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    tableinfo_id bigint NOT NULL,
    row_id integer NOT NULL,
    name text,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.control OWNER TO drupaladmin;

--
-- Name: control_control_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.control_control_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.control_control_id_seq OWNER TO drupaladmin;

--
-- Name: control_control_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.control_control_id_seq OWNED BY chado.control.control_id;


--
-- Name: cv; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cv (
    cv_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    definition text
);


ALTER TABLE chado.cv OWNER TO drupaladmin;

--
-- Name: TABLE cv; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cv IS 'A controlled vocabulary or ontology. A cv is
composed of cvterms (AKA terms, classes, types, universals - relations
and properties are also stored in cvterm) and the relationships
between them.';


--
-- Name: COLUMN cv.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cv.name IS 'The name of the ontology. This
corresponds to the obo-format -namespace-. cv names uniquely identify
the cv. In OBO file format, the cv.name is known as the namespace.';


--
-- Name: COLUMN cv.definition; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cv.definition IS 'A text description of the criteria for
membership of this ontology.';


--
-- Name: cv_cv_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cv_cv_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cv_cv_id_seq OWNER TO drupaladmin;

--
-- Name: cv_cv_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cv_cv_id_seq OWNED BY chado.cv.cv_id;


--
-- Name: cv_cvterm_count; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_cvterm_count AS
 SELECT cv.name,
    count(*) AS num_terms_excl_obs
   FROM (chado.cv
     JOIN chado.cvterm USING (cv_id))
  WHERE (cvterm.is_obsolete = 0)
  GROUP BY cv.name;


ALTER TABLE chado.cv_cvterm_count OWNER TO drupaladmin;

--
-- Name: VIEW cv_cvterm_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_cvterm_count IS 'per-cv terms counts (excludes obsoletes)';


--
-- Name: cv_cvterm_count_with_obs; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_cvterm_count_with_obs AS
 SELECT cv.name,
    count(*) AS num_terms_incl_obs
   FROM (chado.cv
     JOIN chado.cvterm USING (cv_id))
  GROUP BY cv.name;


ALTER TABLE chado.cv_cvterm_count_with_obs OWNER TO drupaladmin;

--
-- Name: VIEW cv_cvterm_count_with_obs; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_cvterm_count_with_obs IS 'per-cv terms counts (includes obsoletes)';


--
-- Name: cvterm_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvterm_relationship (
    cvterm_relationship_id bigint NOT NULL,
    type_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL
);


ALTER TABLE chado.cvterm_relationship OWNER TO drupaladmin;

--
-- Name: TABLE cvterm_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvterm_relationship IS 'A relationship linking two
cvterms. Each cvterm_relationship constitutes an edge in the graph
defined by the collection of cvterms and cvterm_relationships. The
meaning of the cvterm_relationship depends on the definition of the
cvterm R refered to by type_id. However, in general the definitions
are such that the statement "all SUBJs REL some OBJ" is true. The
cvterm_relationship statement is about the subject, not the
object. For example "insect wing part_of thorax".';


--
-- Name: COLUMN cvterm_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm_relationship.type_id IS 'The nature of the
relationship between subject and object. Note that relations are also
housed in the cvterm table, typically from the OBO relationship
ontology, although other relationship types are allowed.';


--
-- Name: COLUMN cvterm_relationship.subject_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm_relationship.subject_id IS 'The subject of
the subj-predicate-obj sentence. The cvterm_relationship is about the
subject. In a graph, this typically corresponds to the child node.';


--
-- Name: COLUMN cvterm_relationship.object_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm_relationship.object_id IS 'The object of the
subj-predicate-obj sentence. The cvterm_relationship refers to the
object. In a graph, this typically corresponds to the parent node.';


--
-- Name: cv_leaf; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_leaf AS
 SELECT cvterm.cv_id,
    cvterm.cvterm_id
   FROM chado.cvterm
  WHERE (NOT (cvterm.cvterm_id IN ( SELECT cvterm_relationship.object_id
           FROM chado.cvterm_relationship)));


ALTER TABLE chado.cv_leaf OWNER TO drupaladmin;

--
-- Name: VIEW cv_leaf; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_leaf IS 'the leaves of a cv are the set of terms
which have no children (terms that are not the object of a
relation). All cvs will have at least 1 leaf';


--
-- Name: cv_link_count; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_link_count AS
 SELECT cv.name AS cv_name,
    relation.name AS relation_name,
    relation_cv.name AS relation_cv_name,
    count(*) AS num_links
   FROM ((((chado.cv
     JOIN chado.cvterm ON ((cvterm.cv_id = cv.cv_id)))
     JOIN chado.cvterm_relationship ON ((cvterm.cvterm_id = cvterm_relationship.subject_id)))
     JOIN chado.cvterm relation ON ((cvterm_relationship.type_id = relation.cvterm_id)))
     JOIN chado.cv relation_cv ON ((relation.cv_id = relation_cv.cv_id)))
  GROUP BY cv.name, relation.name, relation_cv.name;


ALTER TABLE chado.cv_link_count OWNER TO drupaladmin;

--
-- Name: VIEW cv_link_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_link_count IS 'per-cv summary of number of
links (cvterm_relationships) broken down by
relationship_type. num_links is the total # of links of the specified
type in which the subject_id of the link is in the named cv';


--
-- Name: cv_path_count; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_path_count AS
 SELECT cv.name AS cv_name,
    relation.name AS relation_name,
    relation_cv.name AS relation_cv_name,
    count(*) AS num_paths
   FROM ((((chado.cv
     JOIN chado.cvterm ON ((cvterm.cv_id = cv.cv_id)))
     JOIN chado.cvtermpath ON ((cvterm.cvterm_id = cvtermpath.subject_id)))
     JOIN chado.cvterm relation ON ((cvtermpath.type_id = relation.cvterm_id)))
     JOIN chado.cv relation_cv ON ((relation.cv_id = relation_cv.cv_id)))
  GROUP BY cv.name, relation.name, relation_cv.name;


ALTER TABLE chado.cv_path_count OWNER TO drupaladmin;

--
-- Name: VIEW cv_path_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_path_count IS 'per-cv summary of number of
paths (cvtermpaths) broken down by relationship_type. num_paths is the
total # of paths of the specified type in which the subject_id of the
path is in the named cv. See also: cv_distinct_relations';


--
-- Name: cv_root; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.cv_root AS
 SELECT cvterm.cv_id,
    cvterm.cvterm_id AS root_cvterm_id
   FROM chado.cvterm
  WHERE ((NOT (cvterm.cvterm_id IN ( SELECT cvterm_relationship.subject_id
           FROM chado.cvterm_relationship))) AND (cvterm.is_obsolete = 0));


ALTER TABLE chado.cv_root OWNER TO drupaladmin;

--
-- Name: VIEW cv_root; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.cv_root IS 'the roots of a cv are the set of terms
which have no parents (terms that are not the subject of a
relation). Most cvs will have a single root, some may have >1. All
will have at least 1';


--
-- Name: cv_root_mview; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cv_root_mview (
    name character varying(255) NOT NULL,
    cvterm_id bigint NOT NULL,
    cv_id bigint NOT NULL,
    cv_name character varying(255) NOT NULL
);


ALTER TABLE chado.cv_root_mview OWNER TO drupaladmin;

--
-- Name: TABLE cv_root_mview; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cv_root_mview IS 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';


--
-- Name: cvprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvprop (
    cvprop_id bigint NOT NULL,
    cv_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cvprop OWNER TO drupaladmin;

--
-- Name: TABLE cvprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvprop IS 'Additional extensible properties can be attached to a cv using this table.  A notable example would be the cv version';


--
-- Name: COLUMN cvprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.';


--
-- Name: COLUMN cvprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.';


--
-- Name: COLUMN cvprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvprop.rank IS 'Property-Value ordering. Any
cv can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used.';


--
-- Name: cvprop_cvprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvprop_cvprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvprop_cvprop_id_seq OWNER TO drupaladmin;

--
-- Name: cvprop_cvprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvprop_cvprop_id_seq OWNED BY chado.cvprop.cvprop_id;


--
-- Name: cvterm_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvterm_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvterm_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: cvterm_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvterm_cvterm_id_seq OWNED BY chado.cvterm.cvterm_id;


--
-- Name: cvterm_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvterm_dbxref (
    cvterm_dbxref_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_for_definition integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cvterm_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE cvterm_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvterm_dbxref IS 'In addition to the primary
identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary
identifiers/dbxrefs, which may refer to records in external
databases. The exact semantics of cvterm_dbxref are not fixed. For
example: the dbxref could be a pubmed ID that is pertinent to the
cvterm, or it could be an equivalent or similar term in another
ontology. For example, GO cvterms are typically linked to InterPro
IDs, even though the nature of the relationship between them is
largely one of statistical association. The dbxref may be have data
records attached in the same database instance, or it could be a
"hanging" dbxref pointing to some external database. NOTE: If the
desired objective is to link two cvterms together, and the nature of
the relation is known and holds for all instances of the subject
cvterm then consider instead using cvterm_relationship together with a
well-defined relation.';


--
-- Name: COLUMN cvterm_dbxref.is_for_definition; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvterm_dbxref.is_for_definition IS 'A
cvterm.definition should be supported by one or more references. If
this column is true, the dbxref is not for a term in an external database -
it is a dbxref for provenance information for the definition.';


--
-- Name: cvterm_dbxref_cvterm_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvterm_dbxref_cvterm_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvterm_dbxref_cvterm_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: cvterm_dbxref_cvterm_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvterm_dbxref_cvterm_dbxref_id_seq OWNED BY chado.cvterm_dbxref.cvterm_dbxref_id;


--
-- Name: cvterm_relationship_cvterm_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvterm_relationship_cvterm_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvterm_relationship_cvterm_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: cvterm_relationship_cvterm_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvterm_relationship_cvterm_relationship_id_seq OWNED BY chado.cvterm_relationship.cvterm_relationship_id;


--
-- Name: cvtermpath_cvtermpath_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvtermpath_cvtermpath_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvtermpath_cvtermpath_id_seq OWNER TO drupaladmin;

--
-- Name: cvtermpath_cvtermpath_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvtermpath_cvtermpath_id_seq OWNED BY chado.cvtermpath.cvtermpath_id;


--
-- Name: cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvtermprop (
    cvtermprop_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text DEFAULT ''::text NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.cvtermprop OWNER TO drupaladmin;

--
-- Name: TABLE cvtermprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvtermprop IS 'Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.';


--
-- Name: COLUMN cvtermprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.';


--
-- Name: COLUMN cvtermprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.';


--
-- Name: COLUMN cvtermprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermprop.rank IS 'Property-Value ordering. Any
cvterm can have multiple values for any particular property type -
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used.';


--
-- Name: cvtermprop_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvtermprop_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvtermprop_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: cvtermprop_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvtermprop_cvtermprop_id_seq OWNED BY chado.cvtermprop.cvtermprop_id;


--
-- Name: cvtermsynonym; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.cvtermsynonym (
    cvtermsynonym_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    synonym character varying(1024) NOT NULL,
    type_id bigint
);


ALTER TABLE chado.cvtermsynonym OWNER TO drupaladmin;

--
-- Name: TABLE cvtermsynonym; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.cvtermsynonym IS 'A cvterm actually represents a
distinct class or concept. A concept can be refered to by different
phrases or names. In addition to the primary name (cvterm.name) there
can be a number of alternative aliases or synonyms. For example, "T
cell" as a synonym for "T lymphocyte".';


--
-- Name: COLUMN cvtermsynonym.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.cvtermsynonym.type_id IS 'A synonym can be exact,
narrower, or broader than.';


--
-- Name: cvtermsynonym_cvtermsynonym_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.cvtermsynonym_cvtermsynonym_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.cvtermsynonym_cvtermsynonym_id_seq OWNER TO drupaladmin;

--
-- Name: cvtermsynonym_cvtermsynonym_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.cvtermsynonym_cvtermsynonym_id_seq OWNED BY chado.cvtermsynonym.cvtermsynonym_id;


--
-- Name: db2cv_mview; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.db2cv_mview (
    cv_id integer NOT NULL,
    cvname character varying(255) NOT NULL,
    db_id integer NOT NULL,
    dbname character varying(255) NOT NULL,
    num_terms integer NOT NULL
);


ALTER TABLE chado.db2cv_mview OWNER TO drupaladmin;

--
-- Name: TABLE db2cv_mview; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.db2cv_mview IS 'A table for quick lookup of the vocabularies and the databases they are associated with.';


--
-- Name: db_db_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.db_db_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.db_db_id_seq OWNER TO drupaladmin;

--
-- Name: db_db_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.db_db_id_seq OWNED BY chado.db.db_id;


--
-- Name: db_dbxref_count; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.db_dbxref_count AS
 SELECT db.name,
    count(*) AS num_dbxrefs
   FROM (chado.db
     JOIN chado.dbxref USING (db_id))
  GROUP BY db.name;


ALTER TABLE chado.db_dbxref_count OWNER TO drupaladmin;

--
-- Name: VIEW db_dbxref_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.db_dbxref_count IS 'per-db dbxref counts';


--
-- Name: dbprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.dbprop (
    dbprop_id bigint NOT NULL,
    db_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.dbprop OWNER TO drupaladmin;

--
-- Name: TABLE dbprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.dbprop IS 'An external database can have any number of
slot-value property tags attached to it. This is an alternative to
hardcoding a list of columns in the relational schema, and is
completely extensible. There is a unique constraint, dbprop_c1, for
the combination of db_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';


--
-- Name: dbprop_dbprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.dbprop_dbprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.dbprop_dbprop_id_seq OWNER TO drupaladmin;

--
-- Name: dbprop_dbprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.dbprop_dbprop_id_seq OWNED BY chado.dbprop.dbprop_id;


--
-- Name: dbxref_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.dbxref_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.dbxref_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: dbxref_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.dbxref_dbxref_id_seq OWNED BY chado.dbxref.dbxref_id;


--
-- Name: dbxrefprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.dbxrefprop (
    dbxrefprop_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text DEFAULT ''::text NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.dbxrefprop OWNER TO drupaladmin;

--
-- Name: TABLE dbxrefprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.dbxrefprop IS 'Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.';


--
-- Name: dbxrefprop_dbxrefprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.dbxrefprop_dbxrefprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.dbxrefprop_dbxrefprop_id_seq OWNER TO drupaladmin;

--
-- Name: dbxrefprop_dbxrefprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.dbxrefprop_dbxrefprop_id_seq OWNED BY chado.dbxrefprop.dbxrefprop_id;


--
-- Name: dfeatureloc; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.dfeatureloc AS
 SELECT featureloc.featureloc_id,
    featureloc.feature_id,
    featureloc.srcfeature_id,
    featureloc.fmin AS nbeg,
    featureloc.is_fmin_partial AS is_nbeg_partial,
    featureloc.fmax AS nend,
    featureloc.is_fmax_partial AS is_nend_partial,
    featureloc.strand,
    featureloc.phase,
    featureloc.residue_info,
    featureloc.locgroup,
    featureloc.rank
   FROM chado.featureloc
  WHERE ((featureloc.strand < 0) OR (featureloc.phase < 0))
UNION
 SELECT featureloc.featureloc_id,
    featureloc.feature_id,
    featureloc.srcfeature_id,
    featureloc.fmax AS nbeg,
    featureloc.is_fmax_partial AS is_nbeg_partial,
    featureloc.fmin AS nend,
    featureloc.is_fmin_partial AS is_nend_partial,
    featureloc.strand,
    featureloc.phase,
    featureloc.residue_info,
    featureloc.locgroup,
    featureloc.rank
   FROM chado.featureloc
  WHERE ((featureloc.strand IS NULL) OR (featureloc.strand >= 0) OR (featureloc.phase >= 0));


ALTER TABLE chado.dfeatureloc OWNER TO drupaladmin;

--
-- Name: eimage; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.eimage (
    eimage_id bigint NOT NULL,
    eimage_data text,
    eimage_type character varying(255) NOT NULL,
    image_uri character varying(255)
);


ALTER TABLE chado.eimage OWNER TO drupaladmin;

--
-- Name: COLUMN eimage.eimage_data; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.eimage.eimage_data IS 'We expect images in eimage_data (e.g. JPEGs) to be uuencoded.';


--
-- Name: COLUMN eimage.eimage_type; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.eimage.eimage_type IS 'Describes the type of data in eimage_data.';


--
-- Name: eimage_eimage_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.eimage_eimage_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.eimage_eimage_id_seq OWNER TO drupaladmin;

--
-- Name: eimage_eimage_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.eimage_eimage_id_seq OWNED BY chado.eimage.eimage_id;


--
-- Name: element; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.element (
    element_id bigint NOT NULL,
    feature_id bigint,
    arraydesign_id bigint NOT NULL,
    type_id bigint,
    dbxref_id bigint
);


ALTER TABLE chado.element OWNER TO drupaladmin;

--
-- Name: TABLE element; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.element IS 'Represents a feature of the array. This is typically a region of the array coated or bound to DNA.';


--
-- Name: element_element_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.element_element_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.element_element_id_seq OWNER TO drupaladmin;

--
-- Name: element_element_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.element_element_id_seq OWNED BY chado.element.element_id;


--
-- Name: element_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.element_relationship (
    element_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    type_id bigint NOT NULL,
    object_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.element_relationship OWNER TO drupaladmin;

--
-- Name: TABLE element_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.element_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.';


--
-- Name: element_relationship_element_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.element_relationship_element_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.element_relationship_element_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: element_relationship_element_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.element_relationship_element_relationship_id_seq OWNED BY chado.element_relationship.element_relationship_id;


--
-- Name: elementresult; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.elementresult (
    elementresult_id bigint NOT NULL,
    element_id bigint NOT NULL,
    quantification_id bigint NOT NULL,
    signal double precision NOT NULL
);


ALTER TABLE chado.elementresult OWNER TO drupaladmin;

--
-- Name: TABLE elementresult; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.elementresult IS 'An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.';


--
-- Name: elementresult_elementresult_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.elementresult_elementresult_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.elementresult_elementresult_id_seq OWNER TO drupaladmin;

--
-- Name: elementresult_elementresult_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.elementresult_elementresult_id_seq OWNED BY chado.elementresult.elementresult_id;


--
-- Name: elementresult_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.elementresult_relationship (
    elementresult_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    type_id bigint NOT NULL,
    object_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.elementresult_relationship OWNER TO drupaladmin;

--
-- Name: TABLE elementresult_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.elementresult_relationship IS 'Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.';


--
-- Name: elementresult_relationship_elementresult_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.elementresult_relationship_elementresult_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.elementresult_relationship_elementresult_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: elementresult_relationship_elementresult_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.elementresult_relationship_elementresult_relationship_id_seq OWNED BY chado.elementresult_relationship.elementresult_relationship_id;


--
-- Name: environment; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.environment (
    environment_id bigint NOT NULL,
    uniquename text NOT NULL,
    description text
);


ALTER TABLE chado.environment OWNER TO drupaladmin;

--
-- Name: TABLE environment; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.environment IS 'The environmental component of a phenotype description.';


--
-- Name: environment_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.environment_cvterm (
    environment_cvterm_id bigint NOT NULL,
    environment_id bigint NOT NULL,
    cvterm_id bigint NOT NULL
);


ALTER TABLE chado.environment_cvterm OWNER TO drupaladmin;

--
-- Name: environment_cvterm_environment_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.environment_cvterm_environment_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.environment_cvterm_environment_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: environment_cvterm_environment_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.environment_cvterm_environment_cvterm_id_seq OWNED BY chado.environment_cvterm.environment_cvterm_id;


--
-- Name: environment_environment_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.environment_environment_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.environment_environment_id_seq OWNER TO drupaladmin;

--
-- Name: environment_environment_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.environment_environment_id_seq OWNED BY chado.environment.environment_id;


--
-- Name: expression; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expression (
    expression_id bigint NOT NULL,
    uniquename text NOT NULL,
    md5checksum character(32),
    description text
);


ALTER TABLE chado.expression OWNER TO drupaladmin;

--
-- Name: TABLE expression; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.expression IS 'The expression table is essentially a bridge table.';


--
-- Name: expression_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expression_cvterm (
    expression_cvterm_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL,
    cvterm_type_id bigint NOT NULL
);


ALTER TABLE chado.expression_cvterm OWNER TO drupaladmin;

--
-- Name: expression_cvterm_expression_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expression_cvterm_expression_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expression_cvterm_expression_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: expression_cvterm_expression_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expression_cvterm_expression_cvterm_id_seq OWNED BY chado.expression_cvterm.expression_cvterm_id;


--
-- Name: expression_cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expression_cvtermprop (
    expression_cvtermprop_id bigint NOT NULL,
    expression_cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.expression_cvtermprop OWNER TO drupaladmin;

--
-- Name: TABLE expression_cvtermprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.expression_cvtermprop IS 'Extensible properties for
expression to cvterm associations. Examples: qualifiers.';


--
-- Name: COLUMN expression_cvtermprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.expression_cvtermprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv.';


--
-- Name: COLUMN expression_cvtermprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.expression_cvtermprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';


--
-- Name: COLUMN expression_cvtermprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.expression_cvtermprop.rank IS 'Property-Value
ordering. Any expression_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used.';


--
-- Name: expression_cvtermprop_expression_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expression_cvtermprop_expression_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expression_cvtermprop_expression_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: expression_cvtermprop_expression_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expression_cvtermprop_expression_cvtermprop_id_seq OWNED BY chado.expression_cvtermprop.expression_cvtermprop_id;


--
-- Name: expression_expression_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expression_expression_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expression_expression_id_seq OWNER TO drupaladmin;

--
-- Name: expression_expression_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expression_expression_id_seq OWNED BY chado.expression.expression_id;


--
-- Name: expression_image; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expression_image (
    expression_image_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    eimage_id bigint NOT NULL
);


ALTER TABLE chado.expression_image OWNER TO drupaladmin;

--
-- Name: expression_image_expression_image_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expression_image_expression_image_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expression_image_expression_image_id_seq OWNER TO drupaladmin;

--
-- Name: expression_image_expression_image_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expression_image_expression_image_id_seq OWNED BY chado.expression_image.expression_image_id;


--
-- Name: expression_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expression_pub (
    expression_pub_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.expression_pub OWNER TO drupaladmin;

--
-- Name: expression_pub_expression_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expression_pub_expression_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expression_pub_expression_pub_id_seq OWNER TO drupaladmin;

--
-- Name: expression_pub_expression_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expression_pub_expression_pub_id_seq OWNED BY chado.expression_pub.expression_pub_id;


--
-- Name: expressionprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.expressionprop (
    expressionprop_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.expressionprop OWNER TO drupaladmin;

--
-- Name: expressionprop_expressionprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.expressionprop_expressionprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.expressionprop_expressionprop_id_seq OWNER TO drupaladmin;

--
-- Name: expressionprop_expressionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.expressionprop_expressionprop_id_seq OWNED BY chado.expressionprop.expressionprop_id;


--
-- Name: f_type; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.f_type AS
 SELECT f.feature_id,
    f.name,
    f.dbxref_id,
    c.name AS type,
    f.residues,
    f.seqlen,
    f.md5checksum,
    f.type_id,
    f.timeaccessioned,
    f.timelastmodified
   FROM chado.feature f,
    chado.cvterm c
  WHERE (f.type_id = c.cvterm_id);


ALTER TABLE chado.f_type OWNER TO drupaladmin;

--
-- Name: f_loc; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.f_loc AS
 SELECT f.feature_id,
    f.name,
    f.dbxref_id,
    fl.nbeg,
    fl.nend,
    fl.strand
   FROM chado.dfeatureloc fl,
    chado.f_type f
  WHERE (f.feature_id = fl.feature_id);


ALTER TABLE chado.f_loc OWNER TO drupaladmin;

--
-- Name: feature_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_contact (
    feature_contact_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    contact_id bigint NOT NULL
);


ALTER TABLE chado.feature_contact OWNER TO drupaladmin;

--
-- Name: TABLE feature_contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_contact IS 'Links contact(s) with a feature.  Used to indicate a particular
person or organization responsible for discovery or that can provide more information on a particular feature.';


--
-- Name: feature_contact_feature_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_contact_feature_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_contact_feature_contact_id_seq OWNER TO drupaladmin;

--
-- Name: feature_contact_feature_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_contact_feature_contact_id_seq OWNED BY chado.feature_contact.feature_contact_id;


--
-- Name: feature_contains; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_contains AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((y.fmin >= x.fmin) AND (y.fmin <= x.fmax)));


ALTER TABLE chado.feature_contains OWNER TO drupaladmin;

--
-- Name: VIEW feature_contains; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_contains IS 'subject intervals contains (or is
same as) object interval. transitive,reflexive';


--
-- Name: feature_cvterm_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_cvterm_dbxref (
    feature_cvterm_dbxref_id bigint NOT NULL,
    feature_cvterm_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.feature_cvterm_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE feature_cvterm_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.';


--
-- Name: feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq OWNED BY chado.feature_cvterm_dbxref.feature_cvterm_dbxref_id;


--
-- Name: feature_cvterm_feature_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_cvterm_feature_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_cvterm_feature_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: feature_cvterm_feature_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_cvterm_feature_cvterm_id_seq OWNED BY chado.feature_cvterm.feature_cvterm_id;


--
-- Name: feature_cvterm_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_cvterm_pub (
    feature_cvterm_pub_id bigint NOT NULL,
    feature_cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.feature_cvterm_pub OWNER TO drupaladmin;

--
-- Name: TABLE feature_cvterm_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_cvterm_pub IS 'Secondary pubs for an
association. Each feature_cvterm association is supported by a single
primary publication. Additional secondary pubs can be added using this
linking table (in a GO gene association file, these corresponding to
any IDs after the pipe symbol in the publications column.';


--
-- Name: feature_cvterm_pub_feature_cvterm_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_cvterm_pub_feature_cvterm_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_cvterm_pub_feature_cvterm_pub_id_seq OWNER TO drupaladmin;

--
-- Name: feature_cvterm_pub_feature_cvterm_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_cvterm_pub_feature_cvterm_pub_id_seq OWNED BY chado.feature_cvterm_pub.feature_cvterm_pub_id;


--
-- Name: feature_cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_cvtermprop (
    feature_cvtermprop_id bigint NOT NULL,
    feature_cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_cvtermprop OWNER TO drupaladmin;

--
-- Name: TABLE feature_cvtermprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_cvtermprop IS 'Extensible properties for
feature to cvterm associations. Examples: GO evidence codes;
qualifiers; metadata such as the date on which the entry was curated
and the source of the association. See the featureprop table for
meanings of type_id, value and rank.';


--
-- Name: COLUMN feature_cvtermprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_cvtermprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. cvterms may come from the OBO evidence code cv.';


--
-- Name: COLUMN feature_cvtermprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_cvtermprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';


--
-- Name: COLUMN feature_cvtermprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_cvtermprop.rank IS 'Property-Value
ordering. Any feature_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used.';


--
-- Name: feature_cvtermprop_feature_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_cvtermprop_feature_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_cvtermprop_feature_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: feature_cvtermprop_feature_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_cvtermprop_feature_cvtermprop_id_seq OWNED BY chado.feature_cvtermprop.feature_cvtermprop_id;


--
-- Name: feature_dbxref_feature_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_dbxref_feature_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_dbxref_feature_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: feature_dbxref_feature_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_dbxref_feature_dbxref_id_seq OWNED BY chado.feature_dbxref.feature_dbxref_id;


--
-- Name: feature_difference; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_difference AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id,
    x.strand AS srcfeature_id,
    x.srcfeature_id AS fmin,
    x.fmin AS fmax,
    y.fmin AS strand
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmin < y.fmin) AND (x.fmax >= y.fmax)))
UNION
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id,
    x.strand AS srcfeature_id,
    x.srcfeature_id AS fmin,
    y.fmax,
    x.fmax AS strand
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax > y.fmax) AND (x.fmin <= y.fmin)));


ALTER TABLE chado.feature_difference OWNER TO drupaladmin;

--
-- Name: VIEW feature_difference; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_difference IS 'size of gap between two features. must be abutting or disjoint';


--
-- Name: feature_disjoint; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_disjoint AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax < y.fmin) AND (x.fmin > y.fmax)));


ALTER TABLE chado.feature_disjoint OWNER TO drupaladmin;

--
-- Name: VIEW feature_disjoint; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_disjoint IS 'featurelocs do not meet. symmetric';


--
-- Name: feature_distance; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_distance AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id,
    x.srcfeature_id,
    x.strand AS subject_strand,
    y.strand AS object_strand,
        CASE
            WHEN (x.fmax <= y.fmin) THEN (x.fmax - y.fmin)
            ELSE (y.fmax - x.fmin)
        END AS distance
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax <= y.fmin) OR (x.fmin >= y.fmax)));


ALTER TABLE chado.feature_distance OWNER TO drupaladmin;

--
-- Name: feature_expression; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_expression (
    feature_expression_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.feature_expression OWNER TO drupaladmin;

--
-- Name: feature_expression_feature_expression_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_expression_feature_expression_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_expression_feature_expression_id_seq OWNER TO drupaladmin;

--
-- Name: feature_expression_feature_expression_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_expression_feature_expression_id_seq OWNED BY chado.feature_expression.feature_expression_id;


--
-- Name: feature_expressionprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_expressionprop (
    feature_expressionprop_id bigint NOT NULL,
    feature_expression_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_expressionprop OWNER TO drupaladmin;

--
-- Name: TABLE feature_expressionprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_expressionprop IS 'Extensible properties for
feature_expression (comments, for example). Modeled on feature_cvtermprop.';


--
-- Name: feature_expressionprop_feature_expressionprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_expressionprop_feature_expressionprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_expressionprop_feature_expressionprop_id_seq OWNER TO drupaladmin;

--
-- Name: feature_expressionprop_feature_expressionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_expressionprop_feature_expressionprop_id_seq OWNED BY chado.feature_expressionprop.feature_expressionprop_id;


--
-- Name: feature_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_feature_id_seq OWNER TO drupaladmin;

--
-- Name: feature_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_feature_id_seq OWNED BY chado.feature.feature_id;


--
-- Name: feature_genotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_genotype (
    feature_genotype_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    genotype_id bigint NOT NULL,
    chromosome_id bigint,
    rank integer NOT NULL,
    cgroup integer NOT NULL,
    cvterm_id bigint NOT NULL
);


ALTER TABLE chado.feature_genotype OWNER TO drupaladmin;

--
-- Name: COLUMN feature_genotype.chromosome_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_genotype.chromosome_id IS 'A feature of SO type "chromosome".';


--
-- Name: COLUMN feature_genotype.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_genotype.rank IS 'rank can be used for
n-ploid organisms or to preserve order.';


--
-- Name: COLUMN feature_genotype.cgroup; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_genotype.cgroup IS 'Spatially distinguishable
group. group can be used for distinguishing the chromosomal groups,
for example (RNAi products and so on can be treated as different
groups, as they do not fall on a particular chromosome).';


--
-- Name: feature_genotype_feature_genotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_genotype_feature_genotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_genotype_feature_genotype_id_seq OWNER TO drupaladmin;

--
-- Name: feature_genotype_feature_genotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_genotype_feature_genotype_id_seq OWNED BY chado.feature_genotype.feature_genotype_id;


--
-- Name: feature_intersection; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_intersection AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id,
    x.srcfeature_id,
    x.strand AS subject_strand,
    y.strand AS object_strand,
        CASE
            WHEN (x.fmin < y.fmin) THEN y.fmin
            ELSE x.fmin
        END AS fmin,
        CASE
            WHEN (x.fmax > y.fmax) THEN y.fmax
            ELSE x.fmax
        END AS fmax
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax >= y.fmin) AND (x.fmin <= y.fmax)));


ALTER TABLE chado.feature_intersection OWNER TO drupaladmin;

--
-- Name: VIEW feature_intersection; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_intersection IS 'set-intersection on interval defined by featureloc. featurelocs must meet';


--
-- Name: feature_meets; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_meets AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax >= y.fmin) AND (x.fmin <= y.fmax)));


ALTER TABLE chado.feature_meets OWNER TO drupaladmin;

--
-- Name: VIEW feature_meets; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_meets IS 'intervals have at least one
interbase point in common (ie overlap OR abut). symmetric,reflexive';


--
-- Name: feature_meets_on_same_strand; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_meets_on_same_strand AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND (x.strand = y.strand) AND ((x.fmax >= y.fmin) AND (x.fmin <= y.fmax)));


ALTER TABLE chado.feature_meets_on_same_strand OWNER TO drupaladmin;

--
-- Name: VIEW feature_meets_on_same_strand; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_meets_on_same_strand IS 'as feature_meets, but
featurelocs must be on the same strand. symmetric,reflexive';


--
-- Name: feature_phenotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_phenotype (
    feature_phenotype_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    phenotype_id bigint NOT NULL
);


ALTER TABLE chado.feature_phenotype OWNER TO drupaladmin;

--
-- Name: TABLE feature_phenotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_phenotype IS 'Linking table between features and phenotypes.';


--
-- Name: feature_phenotype_feature_phenotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_phenotype_feature_phenotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_phenotype_feature_phenotype_id_seq OWNER TO drupaladmin;

--
-- Name: feature_phenotype_feature_phenotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_phenotype_feature_phenotype_id_seq OWNED BY chado.feature_phenotype.feature_phenotype_id;


--
-- Name: feature_pub_feature_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_pub_feature_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_pub_feature_pub_id_seq OWNER TO drupaladmin;

--
-- Name: feature_pub_feature_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_pub_feature_pub_id_seq OWNED BY chado.feature_pub.feature_pub_id;


--
-- Name: feature_pubprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_pubprop (
    feature_pubprop_id bigint NOT NULL,
    feature_pub_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_pubprop OWNER TO drupaladmin;

--
-- Name: TABLE feature_pubprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_pubprop IS 'Property or attribute of a feature_pub link.';


--
-- Name: feature_pubprop_feature_pubprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_pubprop_feature_pubprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_pubprop_feature_pubprop_id_seq OWNER TO drupaladmin;

--
-- Name: feature_pubprop_feature_pubprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_pubprop_feature_pubprop_id_seq OWNED BY chado.feature_pubprop.feature_pubprop_id;


--
-- Name: feature_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_relationship (
    feature_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_relationship OWNER TO drupaladmin;

--
-- Name: TABLE feature_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_relationship IS 'Features can be arranged in
graphs, e.g. "exon part_of transcript part_of gene"; If type is
thought of as a verb, the each arc or edge makes a statement
[Subject Verb Object]. The object can also be thought of as parent
(containing feature), and subject as child (contained feature or
subfeature). We include the relationship rank/order, because even
though most of the time we can order things implicitly by sequence
coordinates, we can not always do this - e.g. transpliced genes. It is also
useful for quickly getting implicit introns.';


--
-- Name: COLUMN feature_relationship.subject_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationship.subject_id IS 'The subject of the subj-predicate-obj sentence. This is typically the subfeature.';


--
-- Name: COLUMN feature_relationship.object_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationship.object_id IS 'The object of the subj-predicate-obj sentence. This is typically the container feature.';


--
-- Name: COLUMN feature_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationship.type_id IS 'Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology.';


--
-- Name: COLUMN feature_relationship.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationship.value IS 'Additional notes or comments.';


--
-- Name: COLUMN feature_relationship.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationship.rank IS 'The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.';


--
-- Name: feature_relationship_feature_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_relationship_feature_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_relationship_feature_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: feature_relationship_feature_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_relationship_feature_relationship_id_seq OWNED BY chado.feature_relationship.feature_relationship_id;


--
-- Name: feature_relationship_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_relationship_pub (
    feature_relationship_pub_id bigint NOT NULL,
    feature_relationship_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.feature_relationship_pub OWNER TO drupaladmin;

--
-- Name: TABLE feature_relationship_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_relationship_pub IS 'Provenance. Attach optional evidence to a feature_relationship in the form of a publication.';


--
-- Name: feature_relationship_pub_feature_relationship_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_relationship_pub_feature_relationship_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_relationship_pub_feature_relationship_pub_id_seq OWNER TO drupaladmin;

--
-- Name: feature_relationship_pub_feature_relationship_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_relationship_pub_feature_relationship_pub_id_seq OWNED BY chado.feature_relationship_pub.feature_relationship_pub_id;


--
-- Name: feature_relationshipprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_relationshipprop (
    feature_relationshipprop_id bigint NOT NULL,
    feature_relationship_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.feature_relationshipprop OWNER TO drupaladmin;

--
-- Name: TABLE feature_relationshipprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_relationshipprop IS 'Extensible properties
for feature_relationships. Analagous structure to featureprop. This
table is largely optional and not used with a high frequency. Typical
scenarios may be if one wishes to attach additional data to a
feature_relationship - for example to say that the
feature_relationship is only true in certain contexts.';


--
-- Name: COLUMN feature_relationshipprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationshipprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. Currently there is no standard ontology for
feature_relationship property types.';


--
-- Name: COLUMN feature_relationshipprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationshipprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';


--
-- Name: COLUMN feature_relationshipprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.feature_relationshipprop.rank IS 'Property-Value
ordering. Any feature_relationship can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used.';


--
-- Name: feature_relationshipprop_feature_relationshipprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_relationshipprop_feature_relationshipprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_relationshipprop_feature_relationshipprop_id_seq OWNER TO drupaladmin;

--
-- Name: feature_relationshipprop_feature_relationshipprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_relationshipprop_feature_relationshipprop_id_seq OWNED BY chado.feature_relationshipprop.feature_relationshipprop_id;


--
-- Name: feature_relationshipprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.feature_relationshipprop_pub (
    feature_relationshipprop_pub_id bigint NOT NULL,
    feature_relationshipprop_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.feature_relationshipprop_pub OWNER TO drupaladmin;

--
-- Name: TABLE feature_relationshipprop_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.feature_relationshipprop_pub IS 'Provenance for feature_relationshipprop.';


--
-- Name: feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq OWNER TO drupaladmin;

--
-- Name: feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq OWNED BY chado.feature_relationshipprop_pub.feature_relationshipprop_pub_id;


--
-- Name: feature_synonym_feature_synonym_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_synonym_feature_synonym_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_synonym_feature_synonym_id_seq OWNER TO drupaladmin;

--
-- Name: feature_synonym_feature_synonym_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.feature_synonym_feature_synonym_id_seq OWNED BY chado.feature_synonym.feature_synonym_id;


--
-- Name: feature_union; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.feature_union AS
 SELECT x.feature_id AS subject_id,
    y.feature_id AS object_id,
    x.srcfeature_id,
    x.strand AS subject_strand,
    y.strand AS object_strand,
        CASE
            WHEN (x.fmin < y.fmin) THEN x.fmin
            ELSE y.fmin
        END AS fmin,
        CASE
            WHEN (x.fmax > y.fmax) THEN x.fmax
            ELSE y.fmax
        END AS fmax
   FROM chado.featureloc x,
    chado.featureloc y
  WHERE ((x.srcfeature_id = y.srcfeature_id) AND ((x.fmax >= y.fmin) AND (x.fmin <= y.fmax)));


ALTER TABLE chado.feature_union OWNER TO drupaladmin;

--
-- Name: VIEW feature_union; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.feature_union IS 'set-union on interval defined by featureloc. featurelocs must meet';


--
-- Name: feature_uniquename_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.feature_uniquename_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.feature_uniquename_seq OWNER TO drupaladmin;

--
-- Name: featureloc_featureloc_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featureloc_featureloc_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featureloc_featureloc_id_seq OWNER TO drupaladmin;

--
-- Name: featureloc_featureloc_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featureloc_featureloc_id_seq OWNED BY chado.featureloc.featureloc_id;


--
-- Name: featureloc_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featureloc_pub (
    featureloc_pub_id bigint NOT NULL,
    featureloc_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.featureloc_pub OWNER TO drupaladmin;

--
-- Name: TABLE featureloc_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featureloc_pub IS 'Provenance of featureloc. Linking table between featurelocs and publications that mention them.';


--
-- Name: featureloc_pub_featureloc_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featureloc_pub_featureloc_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featureloc_pub_featureloc_pub_id_seq OWNER TO drupaladmin;

--
-- Name: featureloc_pub_featureloc_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featureloc_pub_featureloc_pub_id_seq OWNED BY chado.featureloc_pub.featureloc_pub_id;


--
-- Name: featuremap; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremap (
    featuremap_id bigint NOT NULL,
    name character varying(255),
    description text,
    unittype_id bigint
);


ALTER TABLE chado.featuremap OWNER TO drupaladmin;

--
-- Name: featuremap_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremap_contact (
    featuremap_contact_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    contact_id bigint NOT NULL
);


ALTER TABLE chado.featuremap_contact OWNER TO drupaladmin;

--
-- Name: TABLE featuremap_contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featuremap_contact IS 'Links contact(s) with a featuremap.  Used to
indicate a particular person or organization responsible for constrution of or
that can provide more information on a particular featuremap.';


--
-- Name: featuremap_contact_featuremap_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremap_contact_featuremap_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremap_contact_featuremap_contact_id_seq OWNER TO drupaladmin;

--
-- Name: featuremap_contact_featuremap_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremap_contact_featuremap_contact_id_seq OWNED BY chado.featuremap_contact.featuremap_contact_id;


--
-- Name: featuremap_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremap_dbxref (
    featuremap_dbxref_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.featuremap_dbxref OWNER TO drupaladmin;

--
-- Name: featuremap_dbxref_featuremap_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremap_dbxref_featuremap_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremap_dbxref_featuremap_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: featuremap_dbxref_featuremap_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremap_dbxref_featuremap_dbxref_id_seq OWNED BY chado.featuremap_dbxref.featuremap_dbxref_id;


--
-- Name: featuremap_featuremap_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremap_featuremap_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremap_featuremap_id_seq OWNER TO drupaladmin;

--
-- Name: featuremap_featuremap_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremap_featuremap_id_seq OWNED BY chado.featuremap.featuremap_id;


--
-- Name: featuremap_organism; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremap_organism (
    featuremap_organism_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    organism_id bigint NOT NULL
);


ALTER TABLE chado.featuremap_organism OWNER TO drupaladmin;

--
-- Name: TABLE featuremap_organism; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featuremap_organism IS 'Links a featuremap to the organism(s) with which it is associated.';


--
-- Name: featuremap_organism_featuremap_organism_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremap_organism_featuremap_organism_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremap_organism_featuremap_organism_id_seq OWNER TO drupaladmin;

--
-- Name: featuremap_organism_featuremap_organism_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremap_organism_featuremap_organism_id_seq OWNED BY chado.featuremap_organism.featuremap_organism_id;


--
-- Name: featuremap_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremap_pub (
    featuremap_pub_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.featuremap_pub OWNER TO drupaladmin;

--
-- Name: featuremap_pub_featuremap_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremap_pub_featuremap_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremap_pub_featuremap_pub_id_seq OWNER TO drupaladmin;

--
-- Name: featuremap_pub_featuremap_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremap_pub_featuremap_pub_id_seq OWNED BY chado.featuremap_pub.featuremap_pub_id;


--
-- Name: featuremapprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featuremapprop (
    featuremapprop_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.featuremapprop OWNER TO drupaladmin;

--
-- Name: TABLE featuremapprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featuremapprop IS 'A featuremap can have any number of slot-value property
tags attached to it. This is an alternative to hardcoding a list of columns in the
relational schema, and is completely extensible.';


--
-- Name: featuremapprop_featuremapprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featuremapprop_featuremapprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featuremapprop_featuremapprop_id_seq OWNER TO drupaladmin;

--
-- Name: featuremapprop_featuremapprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featuremapprop_featuremapprop_id_seq OWNED BY chado.featuremapprop.featuremapprop_id;


--
-- Name: featurepos; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featurepos (
    featurepos_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    map_feature_id bigint NOT NULL,
    mappos double precision NOT NULL
);


ALTER TABLE chado.featurepos OWNER TO drupaladmin;

--
-- Name: COLUMN featurepos.map_feature_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featurepos.map_feature_id IS 'map_feature_id
links to the feature (map) upon which the feature is being localized.';


--
-- Name: featurepos_featurepos_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featurepos_featurepos_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featurepos_featurepos_id_seq OWNER TO drupaladmin;

--
-- Name: featurepos_featurepos_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featurepos_featurepos_id_seq OWNED BY chado.featurepos.featurepos_id;


--
-- Name: featureposprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featureposprop (
    featureposprop_id bigint NOT NULL,
    featurepos_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.featureposprop OWNER TO drupaladmin;

--
-- Name: TABLE featureposprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featureposprop IS 'Property or attribute of a featurepos record.';


--
-- Name: featureposprop_featureposprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featureposprop_featureposprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featureposprop_featureposprop_id_seq OWNER TO drupaladmin;

--
-- Name: featureposprop_featureposprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featureposprop_featureposprop_id_seq OWNED BY chado.featureposprop.featureposprop_id;


--
-- Name: featureprop_featureprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featureprop_featureprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featureprop_featureprop_id_seq OWNER TO drupaladmin;

--
-- Name: featureprop_featureprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featureprop_featureprop_id_seq OWNED BY chado.featureprop.featureprop_id;


--
-- Name: featureprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featureprop_pub (
    featureprop_pub_id bigint NOT NULL,
    featureprop_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.featureprop_pub OWNER TO drupaladmin;

--
-- Name: TABLE featureprop_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featureprop_pub IS 'Provenance. Any featureprop assignment can optionally be supported by a publication.';


--
-- Name: featureprop_pub_featureprop_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featureprop_pub_featureprop_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featureprop_pub_featureprop_pub_id_seq OWNER TO drupaladmin;

--
-- Name: featureprop_pub_featureprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featureprop_pub_featureprop_pub_id_seq OWNED BY chado.featureprop_pub.featureprop_pub_id;


--
-- Name: featurerange; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.featurerange (
    featurerange_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    leftstartf_id bigint NOT NULL,
    leftendf_id bigint,
    rightstartf_id bigint,
    rightendf_id bigint NOT NULL,
    rangestr character varying(255)
);


ALTER TABLE chado.featurerange OWNER TO drupaladmin;

--
-- Name: TABLE featurerange; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.featurerange IS 'In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.';


--
-- Name: COLUMN featurerange.featuremap_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.featurerange.featuremap_id IS 'featuremap_id is the id of the feature being mapped.';


--
-- Name: featurerange_featurerange_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.featurerange_featurerange_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.featurerange_featurerange_id_seq OWNER TO drupaladmin;

--
-- Name: featurerange_featurerange_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.featurerange_featurerange_id_seq OWNED BY chado.featurerange.featurerange_id;


--
-- Name: featureset_meets; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.featureset_meets AS
 SELECT x.object_id AS subject_id,
    y.object_id
   FROM ((chado.feature_meets r
     JOIN chado.feature_relationship x ON ((r.subject_id = x.subject_id)))
     JOIN chado.feature_relationship y ON ((r.object_id = y.subject_id)));


ALTER TABLE chado.featureset_meets OWNER TO drupaladmin;

--
-- Name: fnr_type; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.fnr_type AS
 SELECT f.feature_id,
    f.name,
    f.dbxref_id,
    c.name AS type,
    f.residues,
    f.seqlen,
    f.md5checksum,
    f.type_id,
    f.timeaccessioned,
    f.timelastmodified
   FROM (chado.feature f
     LEFT JOIN chado.analysisfeature af ON ((f.feature_id = af.feature_id))),
    chado.cvterm c
  WHERE ((f.type_id = c.cvterm_id) AND (af.feature_id IS NULL));


ALTER TABLE chado.fnr_type OWNER TO drupaladmin;

--
-- Name: fp_key; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.fp_key AS
 SELECT fp.feature_id,
    c.name AS pkey,
    fp.value
   FROM chado.featureprop fp,
    chado.cvterm c
  WHERE (fp.featureprop_id = c.cvterm_id);


ALTER TABLE chado.fp_key OWNER TO drupaladmin;

--
-- Name: genotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.genotype (
    genotype_id bigint NOT NULL,
    name text,
    uniquename text NOT NULL,
    description text,
    type_id bigint NOT NULL
);


ALTER TABLE chado.genotype OWNER TO drupaladmin;

--
-- Name: TABLE genotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.genotype IS 'Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.';


--
-- Name: COLUMN genotype.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.genotype.name IS 'Optional alternative name for a genotype,
for display purposes.';


--
-- Name: COLUMN genotype.uniquename; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.genotype.uniquename IS 'The unique name for a genotype;
typically derived from the features making up the genotype.';


--
-- Name: genotype_genotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.genotype_genotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.genotype_genotype_id_seq OWNER TO drupaladmin;

--
-- Name: genotype_genotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.genotype_genotype_id_seq OWNED BY chado.genotype.genotype_id;


--
-- Name: genotypeprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.genotypeprop (
    genotypeprop_id bigint NOT NULL,
    genotype_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.genotypeprop OWNER TO drupaladmin;

--
-- Name: genotypeprop_genotypeprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.genotypeprop_genotypeprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.genotypeprop_genotypeprop_id_seq OWNER TO drupaladmin;

--
-- Name: genotypeprop_genotypeprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.genotypeprop_genotypeprop_id_seq OWNED BY chado.genotypeprop.genotypeprop_id;


--
-- Name: gff3atts; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.gff3atts AS
 SELECT fs.feature_id,
    'Ontology_term'::text AS type,
        CASE
            WHEN ((db.name)::text ~~ '%Gene Ontology%'::text) THEN (('GO:'::text || (dbx.accession)::text))::character varying
            WHEN ((db.name)::text ~~ 'Sequence Ontology%'::text) THEN (('SO:'::text || (dbx.accession)::text))::character varying
            ELSE ((((db.name)::text || ':'::text) || (dbx.accession)::text))::character varying
        END AS attribute
   FROM chado.cvterm s,
    chado.dbxref dbx,
    chado.feature_cvterm fs,
    chado.db
  WHERE ((fs.cvterm_id = s.cvterm_id) AND (s.dbxref_id = dbx.dbxref_id) AND (db.db_id = dbx.db_id))
UNION ALL
 SELECT fs.feature_id,
    'Dbxref'::text AS type,
    (((d.name)::text || ':'::text) || (s.accession)::text) AS attribute
   FROM chado.dbxref s,
    chado.feature_dbxref fs,
    chado.db d
  WHERE ((fs.dbxref_id = s.dbxref_id) AND (s.db_id = d.db_id) AND ((d.name)::text <> 'GFF_source'::text))
UNION ALL
 SELECT f.feature_id,
    'Alias'::text AS type,
    s.name AS attribute
   FROM chado.synonym s,
    chado.feature_synonym fs,
    chado.feature f
  WHERE ((fs.synonym_id = s.synonym_id) AND (f.feature_id = fs.feature_id) AND ((f.name)::text <> (s.name)::text) AND (f.uniquename <> (s.name)::text))
UNION ALL
 SELECT fp.feature_id,
    cv.name AS type,
    fp.value AS attribute
   FROM chado.featureprop fp,
    chado.cvterm cv
  WHERE (fp.type_id = cv.cvterm_id)
UNION ALL
 SELECT fs.feature_id,
    'pub'::text AS type,
    (((s.series_name)::text || ':'::text) || s.title) AS attribute
   FROM chado.pub s,
    chado.feature_pub fs
  WHERE (fs.pub_id = s.pub_id)
UNION ALL
 SELECT fr.subject_id AS feature_id,
    'Parent'::text AS type,
    parent.uniquename AS attribute
   FROM chado.feature_relationship fr,
    chado.feature parent
  WHERE ((fr.object_id = parent.feature_id) AND (fr.type_id = ( SELECT cvterm.cvterm_id
           FROM chado.cvterm
          WHERE (((cvterm.name)::text = 'part_of'::text) AND (cvterm.cv_id IN ( SELECT cv.cv_id
                   FROM chado.cv
                  WHERE ((cv.name)::text = 'relationship'::text)))))))
UNION ALL
 SELECT fr.subject_id AS feature_id,
    'Derives_from'::text AS type,
    parent.uniquename AS attribute
   FROM chado.feature_relationship fr,
    chado.feature parent
  WHERE ((fr.object_id = parent.feature_id) AND (fr.type_id = ( SELECT cvterm.cvterm_id
           FROM chado.cvterm
          WHERE (((cvterm.name)::text = 'derives_from'::text) AND (cvterm.cv_id IN ( SELECT cv.cv_id
                   FROM chado.cv
                  WHERE ((cv.name)::text = 'relationship'::text)))))))
UNION ALL
 SELECT fl.feature_id,
    'Target'::text AS type,
    (((((((target.name)::text || ' '::text) || (fl.fmin + 1)) || ' '::text) || fl.fmax) || ' '::text) || fl.strand) AS attribute
   FROM chado.featureloc fl,
    chado.feature target
  WHERE ((fl.srcfeature_id = target.feature_id) AND (fl.rank <> 0))
UNION ALL
 SELECT feature.feature_id,
    'ID'::text AS type,
    feature.uniquename AS attribute
   FROM chado.feature
  WHERE (NOT (feature.type_id IN ( SELECT cvterm.cvterm_id
           FROM chado.cvterm
          WHERE ((cvterm.name)::text = 'CDS'::text))))
UNION ALL
 SELECT feature.feature_id,
    'chado_feature_id'::text AS type,
    (feature.feature_id)::character varying AS attribute
   FROM chado.feature
UNION ALL
 SELECT feature.feature_id,
    'Name'::text AS type,
    feature.name AS attribute
   FROM chado.feature;


ALTER TABLE chado.gff3atts OWNER TO drupaladmin;

--
-- Name: gff3view; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.gff3view AS
 SELECT f.feature_id,
    sf.name AS ref,
    COALESCE(gffdbx.accession, '.'::character varying(255)) AS source,
    cv.name AS type,
    (fl.fmin + 1) AS fstart,
    fl.fmax AS fend,
    COALESCE((af.significance)::text, '.'::text) AS score,
        CASE
            WHEN (fl.strand = '-1'::integer) THEN '-'::text
            WHEN (fl.strand = 1) THEN '+'::text
            ELSE '.'::text
        END AS strand,
    COALESCE((fl.phase)::text, '.'::text) AS phase,
    f.seqlen,
    f.name,
    f.organism_id
   FROM (((((chado.feature f
     LEFT JOIN chado.featureloc fl ON ((f.feature_id = fl.feature_id)))
     LEFT JOIN chado.feature sf ON ((fl.srcfeature_id = sf.feature_id)))
     LEFT JOIN ( SELECT fd.feature_id,
            d.accession
           FROM ((chado.feature_dbxref fd
             JOIN chado.dbxref d USING (dbxref_id))
             JOIN chado.db USING (db_id))
          WHERE ((db.name)::text = 'GFF_source'::text)) gffdbx ON ((f.feature_id = gffdbx.feature_id)))
     LEFT JOIN chado.cvterm cv ON ((f.type_id = cv.cvterm_id)))
     LEFT JOIN chado.analysisfeature af ON ((f.feature_id = af.feature_id)));


ALTER TABLE chado.gff3view OWNER TO drupaladmin;

--
-- Name: intron_combined_view; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.intron_combined_view AS
 SELECT x1.feature_id AS exon1_id,
    x2.feature_id AS exon2_id,
        CASE
            WHEN (l1.strand = '-1'::integer) THEN l2.fmax
            ELSE l1.fmax
        END AS fmin,
        CASE
            WHEN (l1.strand = '-1'::integer) THEN l1.fmin
            ELSE l2.fmin
        END AS fmax,
    l1.strand,
    l1.srcfeature_id,
    r1.rank AS intron_rank,
    r1.object_id AS transcript_id
   FROM ((((((chado.cvterm
     JOIN chado.feature x1 ON ((x1.type_id = cvterm.cvterm_id)))
     JOIN chado.feature_relationship r1 ON ((x1.feature_id = r1.subject_id)))
     JOIN chado.featureloc l1 ON ((x1.feature_id = l1.feature_id)))
     JOIN chado.feature x2 ON ((x2.type_id = cvterm.cvterm_id)))
     JOIN chado.feature_relationship r2 ON ((x2.feature_id = r2.subject_id)))
     JOIN chado.featureloc l2 ON ((x2.feature_id = l2.feature_id)))
  WHERE (((cvterm.name)::text = 'exon'::text) AND ((r2.rank - r1.rank) = 1) AND (r1.object_id = r2.object_id) AND (l1.strand = l2.strand) AND (l1.srcfeature_id = l2.srcfeature_id) AND (l1.locgroup = 0) AND (l2.locgroup = 0));


ALTER TABLE chado.intron_combined_view OWNER TO drupaladmin;

--
-- Name: intronloc_view; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.intronloc_view AS
 SELECT DISTINCT intron_combined_view.exon1_id,
    intron_combined_view.exon2_id,
    intron_combined_view.fmin,
    intron_combined_view.fmax,
    intron_combined_view.strand,
    intron_combined_view.srcfeature_id
   FROM chado.intron_combined_view;


ALTER TABLE chado.intronloc_view OWNER TO drupaladmin;

--
-- Name: library; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library (
    library_id bigint NOT NULL,
    organism_id bigint NOT NULL,
    name character varying(255),
    uniquename text NOT NULL,
    type_id bigint NOT NULL,
    is_obsolete integer DEFAULT 0 NOT NULL,
    timeaccessioned timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL,
    timelastmodified timestamp without time zone DEFAULT CURRENT_TIMESTAMP NOT NULL
);


ALTER TABLE chado.library OWNER TO drupaladmin;

--
-- Name: COLUMN library.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"';


--
-- Name: library_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_contact (
    library_contact_id bigint NOT NULL,
    library_id bigint NOT NULL,
    contact_id bigint NOT NULL
);


ALTER TABLE chado.library_contact OWNER TO drupaladmin;

--
-- Name: TABLE library_contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_contact IS 'Links contact(s) with a library.  Used to indicate a particular person or organization responsible for creation of or that can provide more information on a particular library.';


--
-- Name: library_contact_library_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_contact_library_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_contact_library_contact_id_seq OWNER TO drupaladmin;

--
-- Name: library_contact_library_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_contact_library_contact_id_seq OWNED BY chado.library_contact.library_contact_id;


--
-- Name: library_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_cvterm (
    library_cvterm_id bigint NOT NULL,
    library_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.library_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE library_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_cvterm IS 'The table library_cvterm links a library to controlled vocabularies which describe the library.  For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.';


--
-- Name: library_cvterm_library_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_cvterm_library_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_cvterm_library_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: library_cvterm_library_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_cvterm_library_cvterm_id_seq OWNED BY chado.library_cvterm.library_cvterm_id;


--
-- Name: library_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_dbxref (
    library_dbxref_id bigint NOT NULL,
    library_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.library_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE library_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_dbxref IS 'Links a library to dbxrefs.';


--
-- Name: library_dbxref_library_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_dbxref_library_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_dbxref_library_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: library_dbxref_library_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_dbxref_library_dbxref_id_seq OWNED BY chado.library_dbxref.library_dbxref_id;


--
-- Name: library_expression; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_expression (
    library_expression_id bigint NOT NULL,
    library_id bigint NOT NULL,
    expression_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.library_expression OWNER TO drupaladmin;

--
-- Name: TABLE library_expression; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_expression IS 'Links a library to expression statements.';


--
-- Name: library_expression_library_expression_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_expression_library_expression_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_expression_library_expression_id_seq OWNER TO drupaladmin;

--
-- Name: library_expression_library_expression_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_expression_library_expression_id_seq OWNED BY chado.library_expression.library_expression_id;


--
-- Name: library_expressionprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_expressionprop (
    library_expressionprop_id bigint NOT NULL,
    library_expression_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.library_expressionprop OWNER TO drupaladmin;

--
-- Name: TABLE library_expressionprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_expressionprop IS 'Attributes of a library_expression relationship.';


--
-- Name: library_expressionprop_library_expressionprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_expressionprop_library_expressionprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_expressionprop_library_expressionprop_id_seq OWNER TO drupaladmin;

--
-- Name: library_expressionprop_library_expressionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_expressionprop_library_expressionprop_id_seq OWNED BY chado.library_expressionprop.library_expressionprop_id;


--
-- Name: library_feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_feature (
    library_feature_id bigint NOT NULL,
    library_id bigint NOT NULL,
    feature_id bigint NOT NULL
);


ALTER TABLE chado.library_feature OWNER TO drupaladmin;

--
-- Name: TABLE library_feature; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_feature IS 'library_feature links a library to the clones which are contained in the library.  Examples of such linked features might be "cDNA_clone" or  "genomic_clone".';


--
-- Name: library_feature_count; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_feature_count (
    library_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    num_features integer NOT NULL,
    feature_type character varying(255) NOT NULL
);


ALTER TABLE chado.library_feature_count OWNER TO drupaladmin;

--
-- Name: TABLE library_feature_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_feature_count IS 'Provides count of feature by type that are associated with all libraries';


--
-- Name: library_feature_library_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_feature_library_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_feature_library_feature_id_seq OWNER TO drupaladmin;

--
-- Name: library_feature_library_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_feature_library_feature_id_seq OWNED BY chado.library_feature.library_feature_id;


--
-- Name: library_featureprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_featureprop (
    library_featureprop_id bigint NOT NULL,
    library_feature_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.library_featureprop OWNER TO drupaladmin;

--
-- Name: TABLE library_featureprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_featureprop IS 'Attributes of a library_feature relationship.';


--
-- Name: library_featureprop_library_featureprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_featureprop_library_featureprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_featureprop_library_featureprop_id_seq OWNER TO drupaladmin;

--
-- Name: library_featureprop_library_featureprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_featureprop_library_featureprop_id_seq OWNED BY chado.library_featureprop.library_featureprop_id;


--
-- Name: library_library_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_library_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_library_id_seq OWNER TO drupaladmin;

--
-- Name: library_library_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_library_id_seq OWNED BY chado.library.library_id;


--
-- Name: library_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_pub (
    library_pub_id bigint NOT NULL,
    library_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.library_pub OWNER TO drupaladmin;

--
-- Name: TABLE library_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_pub IS 'Attribution for a library.';


--
-- Name: library_pub_library_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_pub_library_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_pub_library_pub_id_seq OWNER TO drupaladmin;

--
-- Name: library_pub_library_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_pub_library_pub_id_seq OWNED BY chado.library_pub.library_pub_id;


--
-- Name: library_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_relationship (
    library_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.library_relationship OWNER TO drupaladmin;

--
-- Name: TABLE library_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_relationship IS 'Relationships between libraries.';


--
-- Name: library_relationship_library_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_relationship_library_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_relationship_library_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: library_relationship_library_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_relationship_library_relationship_id_seq OWNED BY chado.library_relationship.library_relationship_id;


--
-- Name: library_relationship_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_relationship_pub (
    library_relationship_pub_id bigint NOT NULL,
    library_relationship_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.library_relationship_pub OWNER TO drupaladmin;

--
-- Name: TABLE library_relationship_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_relationship_pub IS 'Provenance of library_relationship.';


--
-- Name: library_relationship_pub_library_relationship_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_relationship_pub_library_relationship_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_relationship_pub_library_relationship_pub_id_seq OWNER TO drupaladmin;

--
-- Name: library_relationship_pub_library_relationship_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_relationship_pub_library_relationship_pub_id_seq OWNED BY chado.library_relationship_pub.library_relationship_pub_id;


--
-- Name: library_synonym; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.library_synonym (
    library_synonym_id bigint NOT NULL,
    synonym_id bigint NOT NULL,
    library_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL,
    is_internal boolean DEFAULT false NOT NULL
);


ALTER TABLE chado.library_synonym OWNER TO drupaladmin;

--
-- Name: TABLE library_synonym; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.library_synonym IS 'Linking table between library and synonym.';


--
-- Name: COLUMN library_synonym.pub_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.library_synonym.pub_id IS 'The pub_id link is for
relating the usage of a given synonym to the publication in which it was used.';


--
-- Name: COLUMN library_synonym.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.';


--
-- Name: COLUMN library_synonym.is_internal; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.library_synonym.is_internal IS 'Typically a synonym
exists so that somebody querying the database with an obsolete name
can find the object they are looking for under its current name.  If
the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym.   If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.';


--
-- Name: library_synonym_library_synonym_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.library_synonym_library_synonym_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.library_synonym_library_synonym_id_seq OWNER TO drupaladmin;

--
-- Name: library_synonym_library_synonym_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.library_synonym_library_synonym_id_seq OWNED BY chado.library_synonym.library_synonym_id;


--
-- Name: libraryprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.libraryprop (
    libraryprop_id bigint NOT NULL,
    library_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.libraryprop OWNER TO drupaladmin;

--
-- Name: TABLE libraryprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.libraryprop IS 'Tag-value properties - follows standard chado model.';


--
-- Name: libraryprop_libraryprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.libraryprop_libraryprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.libraryprop_libraryprop_id_seq OWNER TO drupaladmin;

--
-- Name: libraryprop_libraryprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.libraryprop_libraryprop_id_seq OWNED BY chado.libraryprop.libraryprop_id;


--
-- Name: libraryprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.libraryprop_pub (
    libraryprop_pub_id bigint NOT NULL,
    libraryprop_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.libraryprop_pub OWNER TO drupaladmin;

--
-- Name: TABLE libraryprop_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.libraryprop_pub IS 'Attribution for libraryprop.';


--
-- Name: libraryprop_pub_libraryprop_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.libraryprop_pub_libraryprop_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.libraryprop_pub_libraryprop_pub_id_seq OWNER TO drupaladmin;

--
-- Name: libraryprop_pub_libraryprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.libraryprop_pub_libraryprop_pub_id_seq OWNED BY chado.libraryprop_pub.libraryprop_pub_id;


--
-- Name: magedocumentation; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.magedocumentation (
    magedocumentation_id bigint NOT NULL,
    mageml_id bigint NOT NULL,
    tableinfo_id bigint NOT NULL,
    row_id integer NOT NULL,
    mageidentifier text NOT NULL
);


ALTER TABLE chado.magedocumentation OWNER TO drupaladmin;

--
-- Name: magedocumentation_magedocumentation_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.magedocumentation_magedocumentation_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.magedocumentation_magedocumentation_id_seq OWNER TO drupaladmin;

--
-- Name: magedocumentation_magedocumentation_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.magedocumentation_magedocumentation_id_seq OWNED BY chado.magedocumentation.magedocumentation_id;


--
-- Name: mageml; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.mageml (
    mageml_id bigint NOT NULL,
    mage_package text NOT NULL,
    mage_ml text NOT NULL
);


ALTER TABLE chado.mageml OWNER TO drupaladmin;

--
-- Name: TABLE mageml; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.mageml IS 'This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.';


--
-- Name: mageml_mageml_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.mageml_mageml_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.mageml_mageml_id_seq OWNER TO drupaladmin;

--
-- Name: mageml_mageml_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.mageml_mageml_id_seq OWNED BY chado.mageml.mageml_id;


--
-- Name: materialized_view; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.materialized_view (
    materialized_view_id integer NOT NULL,
    last_update timestamp without time zone,
    refresh_time integer,
    name character varying(64),
    mv_schema character varying(64),
    mv_table character varying(128),
    mv_specs text,
    indexed text,
    query text,
    special_index text
);


ALTER TABLE chado.materialized_view OWNER TO drupaladmin;

--
-- Name: materialized_view_materialized_view_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.materialized_view_materialized_view_id_seq
    AS integer
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.materialized_view_materialized_view_id_seq OWNER TO drupaladmin;

--
-- Name: materialized_view_materialized_view_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.materialized_view_materialized_view_id_seq OWNED BY chado.materialized_view.materialized_view_id;


--
-- Name: nd_experiment; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment (
    nd_experiment_id bigint NOT NULL,
    nd_geolocation_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment IS 'This is the core table for the natural diversity module,
representing each individual assay that is undertaken (this is usually *not* an
entire experiment). Each nd_experiment should give rise to a single genotype or
phenotype and be described via 1 (or more) protocols. Collections of assays that
relate to each other should be linked to the same record in the project table.';


--
-- Name: nd_experiment_analysis; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_analysis (
    nd_experiment_analysis_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    type_id bigint
);


ALTER TABLE chado.nd_experiment_analysis OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_analysis; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_analysis IS 'An analysis that is used in an experiment';


--
-- Name: nd_experiment_analysis_nd_experiment_analysis_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_analysis_nd_experiment_analysis_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_analysis_nd_experiment_analysis_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_analysis_nd_experiment_analysis_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_analysis_nd_experiment_analysis_id_seq OWNED BY chado.nd_experiment_analysis.nd_experiment_analysis_id;


--
-- Name: nd_experiment_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_contact (
    nd_experiment_contact_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    contact_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_contact OWNER TO drupaladmin;

--
-- Name: nd_experiment_contact_nd_experiment_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_contact_nd_experiment_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_contact_nd_experiment_contact_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_contact_nd_experiment_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_contact_nd_experiment_contact_id_seq OWNED BY chado.nd_experiment_contact.nd_experiment_contact_id;


--
-- Name: nd_experiment_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_dbxref (
    nd_experiment_dbxref_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc';


--
-- Name: nd_experiment_dbxref_nd_experiment_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_dbxref_nd_experiment_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_dbxref_nd_experiment_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_dbxref_nd_experiment_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_dbxref_nd_experiment_dbxref_id_seq OWNED BY chado.nd_experiment_dbxref.nd_experiment_dbxref_id;


--
-- Name: nd_experiment_genotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_genotype (
    nd_experiment_genotype_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    genotype_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_genotype OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_genotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.';


--
-- Name: nd_experiment_genotype_nd_experiment_genotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_genotype_nd_experiment_genotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_genotype_nd_experiment_genotype_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_genotype_nd_experiment_genotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_genotype_nd_experiment_genotype_id_seq OWNED BY chado.nd_experiment_genotype.nd_experiment_genotype_id;


--
-- Name: nd_experiment_nd_experiment_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_nd_experiment_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_nd_experiment_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_nd_experiment_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_nd_experiment_id_seq OWNED BY chado.nd_experiment.nd_experiment_id;


--
-- Name: nd_experiment_phenotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_phenotype (
    nd_experiment_phenotype_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    phenotype_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_phenotype OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_phenotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.';


--
-- Name: nd_experiment_phenotype_nd_experiment_phenotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_phenotype_nd_experiment_phenotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_phenotype_nd_experiment_phenotype_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_phenotype_nd_experiment_phenotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_phenotype_nd_experiment_phenotype_id_seq OWNED BY chado.nd_experiment_phenotype.nd_experiment_phenotype_id;


--
-- Name: nd_experiment_project; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_project (
    nd_experiment_project_id bigint NOT NULL,
    project_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_project OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_project; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_project IS 'Used to group together related nd_experiment records. All nd_experiments
should be linked to at least one project.';


--
-- Name: nd_experiment_project_nd_experiment_project_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_project_nd_experiment_project_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_project_nd_experiment_project_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_project_nd_experiment_project_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_project_nd_experiment_project_id_seq OWNED BY chado.nd_experiment_project.nd_experiment_project_id;


--
-- Name: nd_experiment_protocol; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_protocol (
    nd_experiment_protocol_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    nd_protocol_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_protocol OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_protocol; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.';


--
-- Name: nd_experiment_protocol_nd_experiment_protocol_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_protocol_nd_experiment_protocol_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_protocol_nd_experiment_protocol_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_protocol_nd_experiment_protocol_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_protocol_nd_experiment_protocol_id_seq OWNED BY chado.nd_experiment_protocol.nd_experiment_protocol_id;


--
-- Name: nd_experiment_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_pub (
    nd_experiment_pub_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_pub OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)';


--
-- Name: nd_experiment_pub_nd_experiment_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_pub_nd_experiment_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_pub_nd_experiment_pub_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_pub_nd_experiment_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_pub_nd_experiment_pub_id_seq OWNED BY chado.nd_experiment_pub.nd_experiment_pub_id;


--
-- Name: nd_experiment_stock; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_stock (
    nd_experiment_stock_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_stock OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_stock; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment';


--
-- Name: COLUMN nd_experiment_stock.stock_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';


--
-- Name: nd_experiment_stock_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_stock_dbxref (
    nd_experiment_stock_dbxref_id bigint NOT NULL,
    nd_experiment_stock_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.nd_experiment_stock_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_stock_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc';


--
-- Name: nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq OWNED BY chado.nd_experiment_stock_dbxref.nd_experiment_stock_dbxref_id;


--
-- Name: nd_experiment_stock_nd_experiment_stock_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_stock_nd_experiment_stock_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_stock_nd_experiment_stock_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_stock_nd_experiment_stock_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_stock_nd_experiment_stock_id_seq OWNED BY chado.nd_experiment_stock.nd_experiment_stock_id;


--
-- Name: nd_experiment_stockprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experiment_stockprop (
    nd_experiment_stockprop_id bigint NOT NULL,
    nd_experiment_stock_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.nd_experiment_stockprop OWNER TO drupaladmin;

--
-- Name: TABLE nd_experiment_stockprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment';


--
-- Name: COLUMN nd_experiment_stockprop.nd_experiment_stock_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.';


--
-- Name: COLUMN nd_experiment_stockprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';


--
-- Name: COLUMN nd_experiment_stockprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_experiment_stockprop.value IS 'The value of the property.';


--
-- Name: COLUMN nd_experiment_stockprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.';


--
-- Name: nd_experiment_stockprop_nd_experiment_stockprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experiment_stockprop_nd_experiment_stockprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experiment_stockprop_nd_experiment_stockprop_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experiment_stockprop_nd_experiment_stockprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experiment_stockprop_nd_experiment_stockprop_id_seq OWNED BY chado.nd_experiment_stockprop.nd_experiment_stockprop_id;


--
-- Name: nd_experimentprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_experimentprop (
    nd_experimentprop_id bigint NOT NULL,
    nd_experiment_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.nd_experimentprop OWNER TO drupaladmin;

--
-- Name: TABLE nd_experimentprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_experimentprop IS 'An nd_experiment can have any number of
slot-value property tags attached to it. This is an alternative to
hardcoding a list of columns in the relational schema, and is
completely extensible. There is a unique constraint, stockprop_c1, for
the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';


--
-- Name: nd_experimentprop_nd_experimentprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_experimentprop_nd_experimentprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_experimentprop_nd_experimentprop_id_seq OWNER TO drupaladmin;

--
-- Name: nd_experimentprop_nd_experimentprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_experimentprop_nd_experimentprop_id_seq OWNED BY chado.nd_experimentprop.nd_experimentprop_id;


--
-- Name: nd_geolocation; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_geolocation (
    nd_geolocation_id bigint NOT NULL,
    description text,
    latitude real,
    longitude real,
    geodetic_datum character varying(32),
    altitude real
);


ALTER TABLE chado.nd_geolocation OWNER TO drupaladmin;

--
-- Name: TABLE nd_geolocation; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.';


--
-- Name: COLUMN nd_geolocation.description; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.';


--
-- Name: COLUMN nd_geolocation.latitude; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.';


--
-- Name: COLUMN nd_geolocation.longitude; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.';


--
-- Name: COLUMN nd_geolocation.geodetic_datum; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.';


--
-- Name: COLUMN nd_geolocation.altitude; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.';


--
-- Name: nd_geolocation_nd_geolocation_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_geolocation_nd_geolocation_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_geolocation_nd_geolocation_id_seq OWNER TO drupaladmin;

--
-- Name: nd_geolocation_nd_geolocation_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_geolocation_nd_geolocation_id_seq OWNED BY chado.nd_geolocation.nd_geolocation_id;


--
-- Name: nd_geolocationprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_geolocationprop (
    nd_geolocationprop_id bigint NOT NULL,
    nd_geolocation_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.nd_geolocationprop OWNER TO drupaladmin;

--
-- Name: TABLE nd_geolocationprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment';


--
-- Name: COLUMN nd_geolocationprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';


--
-- Name: COLUMN nd_geolocationprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocationprop.value IS 'The value of the property.';


--
-- Name: COLUMN nd_geolocationprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.';


--
-- Name: nd_geolocationprop_nd_geolocationprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_geolocationprop_nd_geolocationprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_geolocationprop_nd_geolocationprop_id_seq OWNER TO drupaladmin;

--
-- Name: nd_geolocationprop_nd_geolocationprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_geolocationprop_nd_geolocationprop_id_seq OWNED BY chado.nd_geolocationprop.nd_geolocationprop_id;


--
-- Name: nd_protocol; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_protocol (
    nd_protocol_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.nd_protocol OWNER TO drupaladmin;

--
-- Name: TABLE nd_protocol; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_protocol IS 'A protocol can be anything that is done as part of the experiment.';


--
-- Name: COLUMN nd_protocol.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_protocol.name IS 'The protocol name.';


--
-- Name: nd_protocol_nd_protocol_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_protocol_nd_protocol_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_protocol_nd_protocol_id_seq OWNER TO drupaladmin;

--
-- Name: nd_protocol_nd_protocol_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_protocol_nd_protocol_id_seq OWNED BY chado.nd_protocol.nd_protocol_id;


--
-- Name: nd_protocol_reagent; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_protocol_reagent (
    nd_protocol_reagent_id bigint NOT NULL,
    nd_protocol_id bigint NOT NULL,
    reagent_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.nd_protocol_reagent OWNER TO drupaladmin;

--
-- Name: nd_protocol_reagent_nd_protocol_reagent_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_protocol_reagent_nd_protocol_reagent_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_protocol_reagent_nd_protocol_reagent_id_seq OWNER TO drupaladmin;

--
-- Name: nd_protocol_reagent_nd_protocol_reagent_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_protocol_reagent_nd_protocol_reagent_id_seq OWNED BY chado.nd_protocol_reagent.nd_protocol_reagent_id;


--
-- Name: nd_protocolprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_protocolprop (
    nd_protocolprop_id bigint NOT NULL,
    nd_protocol_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.nd_protocolprop OWNER TO drupaladmin;

--
-- Name: TABLE nd_protocolprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_protocolprop IS 'Property/value associations for protocol.';


--
-- Name: COLUMN nd_protocolprop.nd_protocol_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.';


--
-- Name: COLUMN nd_protocolprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';


--
-- Name: COLUMN nd_protocolprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_protocolprop.value IS 'The value of the property.';


--
-- Name: COLUMN nd_protocolprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.';


--
-- Name: nd_protocolprop_nd_protocolprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_protocolprop_nd_protocolprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_protocolprop_nd_protocolprop_id_seq OWNER TO drupaladmin;

--
-- Name: nd_protocolprop_nd_protocolprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_protocolprop_nd_protocolprop_id_seq OWNED BY chado.nd_protocolprop.nd_protocolprop_id;


--
-- Name: nd_reagent; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_reagent (
    nd_reagent_id bigint NOT NULL,
    name character varying(80) NOT NULL,
    type_id bigint NOT NULL,
    feature_id bigint
);


ALTER TABLE chado.nd_reagent OWNER TO drupaladmin;

--
-- Name: TABLE nd_reagent; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.';


--
-- Name: COLUMN nd_reagent.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.';


--
-- Name: COLUMN nd_reagent.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.';


--
-- Name: COLUMN nd_reagent.feature_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.';


--
-- Name: nd_reagent_nd_reagent_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_reagent_nd_reagent_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_reagent_nd_reagent_id_seq OWNER TO drupaladmin;

--
-- Name: nd_reagent_nd_reagent_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_reagent_nd_reagent_id_seq OWNED BY chado.nd_reagent.nd_reagent_id;


--
-- Name: nd_reagent_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_reagent_relationship (
    nd_reagent_relationship_id bigint NOT NULL,
    subject_reagent_id bigint NOT NULL,
    object_reagent_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.nd_reagent_relationship OWNER TO drupaladmin;

--
-- Name: TABLE nd_reagent_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.';


--
-- Name: COLUMN nd_reagent_relationship.subject_reagent_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';


--
-- Name: COLUMN nd_reagent_relationship.object_reagent_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';


--
-- Name: COLUMN nd_reagent_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';


--
-- Name: nd_reagent_relationship_nd_reagent_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_reagent_relationship_nd_reagent_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_reagent_relationship_nd_reagent_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: nd_reagent_relationship_nd_reagent_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_reagent_relationship_nd_reagent_relationship_id_seq OWNED BY chado.nd_reagent_relationship.nd_reagent_relationship_id;


--
-- Name: nd_reagentprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.nd_reagentprop (
    nd_reagentprop_id bigint NOT NULL,
    nd_reagent_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.nd_reagentprop OWNER TO drupaladmin;

--
-- Name: nd_reagentprop_nd_reagentprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.nd_reagentprop_nd_reagentprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.nd_reagentprop_nd_reagentprop_id_seq OWNER TO drupaladmin;

--
-- Name: nd_reagentprop_nd_reagentprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.nd_reagentprop_nd_reagentprop_id_seq OWNED BY chado.nd_reagentprop.nd_reagentprop_id;


--
-- Name: organism; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism (
    organism_id bigint NOT NULL,
    abbreviation character varying(255),
    genus character varying(255) NOT NULL,
    species character varying(255) NOT NULL,
    common_name character varying(255),
    infraspecific_name character varying(1024),
    type_id bigint,
    comment text
);


ALTER TABLE chado.organism OWNER TO drupaladmin;

--
-- Name: TABLE organism; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism IS 'The organismal taxonomic
classification. Note that phylogenies are represented using the
phylogeny module, and taxonomies can be represented using the cvterm
module or the phylogeny module.';


--
-- Name: COLUMN organism.species; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism.species IS 'A type of organism is always
uniquely identified by genus and species. When mapping from the NCBI
taxonomy names.dmp file, this column must be used where it
is present, as the common_name column is not always unique (e.g. environmental
samples). If a particular strain or subspecies is to be represented,
this is appended onto the species name. Follows standard NCBI taxonomy
pattern.';


--
-- Name: COLUMN organism.infraspecific_name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism.infraspecific_name IS 'The scientific name for any taxon
below the rank of species.  The rank should be specified using the type_id field
and the name is provided here.';


--
-- Name: COLUMN organism.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism.type_id IS 'A controlled vocabulary term that
specifies the organism rank below species. It is used when an infraspecific
name is provided.  Ideally, the rank should be a valid ICN name such as
subspecies, varietas, subvarietas, forma and subforma';


--
-- Name: organism_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_cvterm (
    organism_cvterm_id bigint NOT NULL,
    organism_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.organism_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE organism_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_cvterm IS 'organism to cvterm associations. Examples: taxonomic name';


--
-- Name: COLUMN organism_cvterm.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism_cvterm.rank IS 'Property-Value
ordering. Any organism_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used';


--
-- Name: organism_cvterm_organism_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_cvterm_organism_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_cvterm_organism_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: organism_cvterm_organism_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_cvterm_organism_cvterm_id_seq OWNED BY chado.organism_cvterm.organism_cvterm_id;


--
-- Name: organism_cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_cvtermprop (
    organism_cvtermprop_id bigint NOT NULL,
    organism_cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.organism_cvtermprop OWNER TO drupaladmin;

--
-- Name: TABLE organism_cvtermprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_cvtermprop IS 'Extensible properties for
organism to cvterm associations. Examples: qualifiers';


--
-- Name: COLUMN organism_cvtermprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism_cvtermprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. ';


--
-- Name: COLUMN organism_cvtermprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism_cvtermprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';


--
-- Name: COLUMN organism_cvtermprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.organism_cvtermprop.rank IS 'Property-Value
ordering. Any organism_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used';


--
-- Name: organism_cvtermprop_organism_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_cvtermprop_organism_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_cvtermprop_organism_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: organism_cvtermprop_organism_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_cvtermprop_organism_cvtermprop_id_seq OWNED BY chado.organism_cvtermprop.organism_cvtermprop_id;


--
-- Name: organism_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_dbxref (
    organism_dbxref_id bigint NOT NULL,
    organism_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.organism_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE organism_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_dbxref IS 'Links an organism to a dbxref.';


--
-- Name: organism_dbxref_organism_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_dbxref_organism_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_dbxref_organism_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: organism_dbxref_organism_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_dbxref_organism_dbxref_id_seq OWNED BY chado.organism_dbxref.organism_dbxref_id;


--
-- Name: organism_feature_count; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_feature_count (
    organism_id bigint NOT NULL,
    genus character varying(255) NOT NULL,
    species character varying(255) NOT NULL,
    common_name character varying(255),
    num_features integer NOT NULL,
    cvterm_id bigint NOT NULL,
    feature_type character varying(255) NOT NULL
);


ALTER TABLE chado.organism_feature_count OWNER TO drupaladmin;

--
-- Name: TABLE organism_feature_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_feature_count IS 'Stores the type and number of features per organism';


--
-- Name: organism_organism_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_organism_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_organism_id_seq OWNER TO drupaladmin;

--
-- Name: organism_organism_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_organism_id_seq OWNED BY chado.organism.organism_id;


--
-- Name: organism_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_pub (
    organism_pub_id bigint NOT NULL,
    organism_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.organism_pub OWNER TO drupaladmin;

--
-- Name: TABLE organism_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_pub IS 'Attribution for organism.';


--
-- Name: organism_pub_organism_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_pub_organism_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_pub_organism_pub_id_seq OWNER TO drupaladmin;

--
-- Name: organism_pub_organism_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_pub_organism_pub_id_seq OWNED BY chado.organism_pub.organism_pub_id;


--
-- Name: organism_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_relationship (
    organism_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.organism_relationship OWNER TO drupaladmin;

--
-- Name: TABLE organism_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_relationship IS 'Specifies relationships between organisms
that are not taxonomic. For example, in breeding, relationships such as
"sterile_with", "incompatible_with", or "fertile_with" would be appropriate. Taxonomic
relatinoships should be housed in the phylogeny tables.';


--
-- Name: organism_relationship_organism_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organism_relationship_organism_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organism_relationship_organism_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: organism_relationship_organism_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organism_relationship_organism_relationship_id_seq OWNED BY chado.organism_relationship.organism_relationship_id;


--
-- Name: organism_stock_count; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organism_stock_count (
    organism_id bigint NOT NULL,
    genus character varying(255) NOT NULL,
    species character varying(255) NOT NULL,
    common_name character varying(255),
    num_stocks integer NOT NULL,
    cvterm_id bigint NOT NULL,
    stock_type character varying(255) NOT NULL
);


ALTER TABLE chado.organism_stock_count OWNER TO drupaladmin;

--
-- Name: TABLE organism_stock_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organism_stock_count IS 'Stores the type and number of stocks per organism';


--
-- Name: organismprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organismprop (
    organismprop_id bigint NOT NULL,
    organism_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.organismprop OWNER TO drupaladmin;

--
-- Name: TABLE organismprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organismprop IS 'Tag-value properties - follows standard chado model.';


--
-- Name: organismprop_organismprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organismprop_organismprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organismprop_organismprop_id_seq OWNER TO drupaladmin;

--
-- Name: organismprop_organismprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organismprop_organismprop_id_seq OWNED BY chado.organismprop.organismprop_id;


--
-- Name: organismprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.organismprop_pub (
    organismprop_pub_id bigint NOT NULL,
    organismprop_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.organismprop_pub OWNER TO drupaladmin;

--
-- Name: TABLE organismprop_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.organismprop_pub IS 'Attribution for organismprop.';


--
-- Name: organismprop_pub_organismprop_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.organismprop_pub_organismprop_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.organismprop_pub_organismprop_pub_id_seq OWNER TO drupaladmin;

--
-- Name: organismprop_pub_organismprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.organismprop_pub_organismprop_pub_id_seq OWNED BY chado.organismprop_pub.organismprop_pub_id;


--
-- Name: phendesc; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phendesc (
    phendesc_id bigint NOT NULL,
    genotype_id bigint NOT NULL,
    environment_id bigint NOT NULL,
    description text NOT NULL,
    type_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.phendesc OWNER TO drupaladmin;

--
-- Name: TABLE phendesc; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phendesc IS 'A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.';


--
-- Name: phendesc_phendesc_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phendesc_phendesc_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phendesc_phendesc_id_seq OWNER TO drupaladmin;

--
-- Name: phendesc_phendesc_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phendesc_phendesc_id_seq OWNED BY chado.phendesc.phendesc_id;


--
-- Name: phenotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenotype (
    phenotype_id bigint NOT NULL,
    uniquename text NOT NULL,
    name text,
    observable_id bigint,
    attr_id bigint,
    value text,
    cvalue_id bigint,
    assay_id bigint
);


ALTER TABLE chado.phenotype OWNER TO drupaladmin;

--
-- Name: TABLE phenotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phenotype IS 'A phenotypic statement, or a single
atomic phenotypic observation, is a controlled sentence describing
observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.';


--
-- Name: COLUMN phenotype.observable_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phenotype.observable_id IS 'The entity: e.g. anatomy_part, biological_process.';


--
-- Name: COLUMN phenotype.attr_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phenotype.attr_id IS 'Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.';


--
-- Name: COLUMN phenotype.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phenotype.value IS 'Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.';


--
-- Name: COLUMN phenotype.cvalue_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phenotype.cvalue_id IS 'Phenotype attribute value (state).';


--
-- Name: COLUMN phenotype.assay_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phenotype.assay_id IS 'Evidence type.';


--
-- Name: phenotype_comparison; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenotype_comparison (
    phenotype_comparison_id bigint NOT NULL,
    genotype1_id bigint NOT NULL,
    environment1_id bigint NOT NULL,
    genotype2_id bigint NOT NULL,
    environment2_id bigint NOT NULL,
    phenotype1_id bigint NOT NULL,
    phenotype2_id bigint,
    pub_id bigint NOT NULL,
    organism_id bigint NOT NULL
);


ALTER TABLE chado.phenotype_comparison OWNER TO drupaladmin;

--
-- Name: TABLE phenotype_comparison; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phenotype_comparison IS 'Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.';


--
-- Name: phenotype_comparison_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenotype_comparison_cvterm (
    phenotype_comparison_cvterm_id bigint NOT NULL,
    phenotype_comparison_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.phenotype_comparison_cvterm OWNER TO drupaladmin;

--
-- Name: phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq OWNED BY chado.phenotype_comparison_cvterm.phenotype_comparison_cvterm_id;


--
-- Name: phenotype_comparison_phenotype_comparison_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenotype_comparison_phenotype_comparison_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenotype_comparison_phenotype_comparison_id_seq OWNER TO drupaladmin;

--
-- Name: phenotype_comparison_phenotype_comparison_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenotype_comparison_phenotype_comparison_id_seq OWNED BY chado.phenotype_comparison.phenotype_comparison_id;


--
-- Name: phenotype_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenotype_cvterm (
    phenotype_cvterm_id bigint NOT NULL,
    phenotype_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.phenotype_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE phenotype_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phenotype_cvterm IS 'phenotype to cvterm associations.';


--
-- Name: phenotype_cvterm_phenotype_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenotype_cvterm_phenotype_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenotype_cvterm_phenotype_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: phenotype_cvterm_phenotype_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenotype_cvterm_phenotype_cvterm_id_seq OWNED BY chado.phenotype_cvterm.phenotype_cvterm_id;


--
-- Name: phenotype_phenotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenotype_phenotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenotype_phenotype_id_seq OWNER TO drupaladmin;

--
-- Name: phenotype_phenotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenotype_phenotype_id_seq OWNED BY chado.phenotype.phenotype_id;


--
-- Name: phenotypeprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenotypeprop (
    phenotypeprop_id bigint NOT NULL,
    phenotype_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.phenotypeprop OWNER TO drupaladmin;

--
-- Name: TABLE phenotypeprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phenotypeprop IS 'A phenotype can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, phenotypeprop_c1, for the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';


--
-- Name: phenotypeprop_phenotypeprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenotypeprop_phenotypeprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenotypeprop_phenotypeprop_id_seq OWNER TO drupaladmin;

--
-- Name: phenotypeprop_phenotypeprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenotypeprop_phenotypeprop_id_seq OWNED BY chado.phenotypeprop.phenotypeprop_id;


--
-- Name: phenstatement; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phenstatement (
    phenstatement_id bigint NOT NULL,
    genotype_id bigint NOT NULL,
    environment_id bigint NOT NULL,
    phenotype_id bigint NOT NULL,
    type_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.phenstatement OWNER TO drupaladmin;

--
-- Name: TABLE phenstatement; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phenstatement IS 'Phenotypes are things like "larval lethal".  Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.';


--
-- Name: phenstatement_phenstatement_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phenstatement_phenstatement_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phenstatement_phenstatement_id_seq OWNER TO drupaladmin;

--
-- Name: phenstatement_phenstatement_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phenstatement_phenstatement_id_seq OWNED BY chado.phenstatement.phenstatement_id;


--
-- Name: phylonode; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonode (
    phylonode_id bigint NOT NULL,
    phylotree_id bigint NOT NULL,
    parent_phylonode_id bigint,
    left_idx integer NOT NULL,
    right_idx integer NOT NULL,
    type_id bigint,
    feature_id bigint,
    label character varying(255),
    distance double precision
);


ALTER TABLE chado.phylonode OWNER TO drupaladmin;

--
-- Name: TABLE phylonode; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylonode IS 'This is the most pervasive
       element in the phylogeny module, cataloging the "phylonodes" of
       tree graphs. Edges are implied by the parent_phylonode_id
       reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.';


--
-- Name: COLUMN phylonode.parent_phylonode_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylonode.parent_phylonode_id IS 'Root phylonode can have null parent_phylonode_id value.';


--
-- Name: COLUMN phylonode.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylonode.type_id IS 'Type: e.g. root, interior, leaf.';


--
-- Name: COLUMN phylonode.feature_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylonode.feature_id IS 'Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.';


--
-- Name: phylonode_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonode_dbxref (
    phylonode_dbxref_id bigint NOT NULL,
    phylonode_id bigint NOT NULL,
    dbxref_id bigint NOT NULL
);


ALTER TABLE chado.phylonode_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE phylonode_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylonode_dbxref IS 'For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.';


--
-- Name: phylonode_dbxref_phylonode_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonode_dbxref_phylonode_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonode_dbxref_phylonode_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: phylonode_dbxref_phylonode_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonode_dbxref_phylonode_dbxref_id_seq OWNED BY chado.phylonode_dbxref.phylonode_dbxref_id;


--
-- Name: phylonode_organism; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonode_organism (
    phylonode_organism_id bigint NOT NULL,
    phylonode_id bigint NOT NULL,
    organism_id bigint NOT NULL
);


ALTER TABLE chado.phylonode_organism OWNER TO drupaladmin;

--
-- Name: TABLE phylonode_organism; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylonode_organism IS 'This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).';


--
-- Name: COLUMN phylonode_organism.phylonode_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylonode_organism.phylonode_id IS 'One phylonode cannot refer to >1 organism.';


--
-- Name: phylonode_organism_phylonode_organism_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonode_organism_phylonode_organism_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonode_organism_phylonode_organism_id_seq OWNER TO drupaladmin;

--
-- Name: phylonode_organism_phylonode_organism_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonode_organism_phylonode_organism_id_seq OWNED BY chado.phylonode_organism.phylonode_organism_id;


--
-- Name: phylonode_phylonode_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonode_phylonode_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonode_phylonode_id_seq OWNER TO drupaladmin;

--
-- Name: phylonode_phylonode_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonode_phylonode_id_seq OWNED BY chado.phylonode.phylonode_id;


--
-- Name: phylonode_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonode_pub (
    phylonode_pub_id bigint NOT NULL,
    phylonode_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.phylonode_pub OWNER TO drupaladmin;

--
-- Name: phylonode_pub_phylonode_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonode_pub_phylonode_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonode_pub_phylonode_pub_id_seq OWNER TO drupaladmin;

--
-- Name: phylonode_pub_phylonode_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonode_pub_phylonode_pub_id_seq OWNED BY chado.phylonode_pub.phylonode_pub_id;


--
-- Name: phylonode_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonode_relationship (
    phylonode_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL,
    rank integer,
    phylotree_id bigint NOT NULL
);


ALTER TABLE chado.phylonode_relationship OWNER TO drupaladmin;

--
-- Name: TABLE phylonode_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylonode_relationship IS 'This is for
relationships that are not strictly hierarchical; for example,
horizontal gene transfer. Most phylogenetic trees are strictly
hierarchical, nevertheless it is here for completeness.';


--
-- Name: phylonode_relationship_phylonode_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonode_relationship_phylonode_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonode_relationship_phylonode_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: phylonode_relationship_phylonode_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonode_relationship_phylonode_relationship_id_seq OWNED BY chado.phylonode_relationship.phylonode_relationship_id;


--
-- Name: phylonodeprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylonodeprop (
    phylonodeprop_id bigint NOT NULL,
    phylonode_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text DEFAULT ''::text NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.phylonodeprop OWNER TO drupaladmin;

--
-- Name: COLUMN phylonodeprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylonodeprop.type_id IS 'type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.';


--
-- Name: phylonodeprop_phylonodeprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylonodeprop_phylonodeprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylonodeprop_phylonodeprop_id_seq OWNER TO drupaladmin;

--
-- Name: phylonodeprop_phylonodeprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylonodeprop_phylonodeprop_id_seq OWNED BY chado.phylonodeprop.phylonodeprop_id;


--
-- Name: phylotree; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylotree (
    phylotree_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    name character varying(255),
    type_id bigint,
    analysis_id bigint,
    comment text
);


ALTER TABLE chado.phylotree OWNER TO drupaladmin;

--
-- Name: TABLE phylotree; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylotree IS 'Global anchor for phylogenetic tree.';


--
-- Name: COLUMN phylotree.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylotree.type_id IS 'Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".';


--
-- Name: phylotree_phylotree_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylotree_phylotree_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylotree_phylotree_id_seq OWNER TO drupaladmin;

--
-- Name: phylotree_phylotree_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylotree_phylotree_id_seq OWNED BY chado.phylotree.phylotree_id;


--
-- Name: phylotree_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylotree_pub (
    phylotree_pub_id bigint NOT NULL,
    phylotree_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.phylotree_pub OWNER TO drupaladmin;

--
-- Name: TABLE phylotree_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylotree_pub IS 'Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.';


--
-- Name: phylotree_pub_phylotree_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylotree_pub_phylotree_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylotree_pub_phylotree_pub_id_seq OWNER TO drupaladmin;

--
-- Name: phylotree_pub_phylotree_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylotree_pub_phylotree_pub_id_seq OWNED BY chado.phylotree_pub.phylotree_pub_id;


--
-- Name: phylotreeprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.phylotreeprop (
    phylotreeprop_id bigint NOT NULL,
    phylotree_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.phylotreeprop OWNER TO drupaladmin;

--
-- Name: TABLE phylotreeprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.phylotreeprop IS 'A phylotree can have any number of slot-value property
tags attached to it. This is an alternative to hardcoding a list of columns in the
relational schema, and is completely extensible.';


--
-- Name: COLUMN phylotreeprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylotreeprop.type_id IS 'The name of the property/slot is a cvterm.
The meaning of the property is defined in that cvterm.';


--
-- Name: COLUMN phylotreeprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylotreeprop.value IS 'The value of the property, represented as text.
Numeric values are converted to their text representation. This is less efficient than
using native database types, but is easier to query.';


--
-- Name: COLUMN phylotreeprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.phylotreeprop.rank IS 'Property-Value ordering. Any
phylotree can have multiple values for any particular property type
these are ordered in a list using rank, counting from zero. For
properties that are single-valued rather than multi-valued, the
default 0 value should be used';


--
-- Name: phylotreeprop_phylotreeprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.phylotreeprop_phylotreeprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.phylotreeprop_phylotreeprop_id_seq OWNER TO drupaladmin;

--
-- Name: phylotreeprop_phylotreeprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.phylotreeprop_phylotreeprop_id_seq OWNED BY chado.phylotreeprop.phylotreeprop_id;


--
-- Name: project; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project (
    project_id bigint NOT NULL,
    name character varying(255) NOT NULL,
    description text
);


ALTER TABLE chado.project OWNER TO drupaladmin;

--
-- Name: TABLE project; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project IS 'Standard Chado flexible property table for projects.';


--
-- Name: project_analysis; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_analysis (
    project_analysis_id bigint NOT NULL,
    project_id bigint NOT NULL,
    analysis_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.project_analysis OWNER TO drupaladmin;

--
-- Name: TABLE project_analysis; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_analysis IS 'Links an analysis to a project that may contain multiple analyses.
The rank column can be used to specify a simple ordering in which analyses were executed.';


--
-- Name: project_analysis_project_analysis_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_analysis_project_analysis_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_analysis_project_analysis_id_seq OWNER TO drupaladmin;

--
-- Name: project_analysis_project_analysis_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_analysis_project_analysis_id_seq OWNED BY chado.project_analysis.project_analysis_id;


--
-- Name: project_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_contact (
    project_contact_id bigint NOT NULL,
    project_id bigint NOT NULL,
    contact_id bigint NOT NULL
);


ALTER TABLE chado.project_contact OWNER TO drupaladmin;

--
-- Name: TABLE project_contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_contact IS 'Linking table for associating projects and contacts.';


--
-- Name: project_contact_project_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_contact_project_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_contact_project_contact_id_seq OWNER TO drupaladmin;

--
-- Name: project_contact_project_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_contact_project_contact_id_seq OWNED BY chado.project_contact.project_contact_id;


--
-- Name: project_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_dbxref (
    project_dbxref_id bigint NOT NULL,
    project_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.project_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE project_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_dbxref IS 'project_dbxref links a project to dbxrefs.';


--
-- Name: COLUMN project_dbxref.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.project_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked project.';


--
-- Name: project_dbxref_project_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_dbxref_project_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_dbxref_project_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: project_dbxref_project_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_dbxref_project_dbxref_id_seq OWNED BY chado.project_dbxref.project_dbxref_id;


--
-- Name: project_feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_feature (
    project_feature_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    project_id bigint NOT NULL
);


ALTER TABLE chado.project_feature OWNER TO drupaladmin;

--
-- Name: TABLE project_feature; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_feature IS 'This table is intended associate records in the feature table with a project.';


--
-- Name: project_feature_project_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_feature_project_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_feature_project_feature_id_seq OWNER TO drupaladmin;

--
-- Name: project_feature_project_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_feature_project_feature_id_seq OWNED BY chado.project_feature.project_feature_id;


--
-- Name: project_project_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_project_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_project_id_seq OWNER TO drupaladmin;

--
-- Name: project_project_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_project_id_seq OWNED BY chado.project.project_id;


--
-- Name: project_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_pub (
    project_pub_id bigint NOT NULL,
    project_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.project_pub OWNER TO drupaladmin;

--
-- Name: TABLE project_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_pub IS 'Linking table for associating projects and publications.';


--
-- Name: project_pub_project_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_pub_project_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_pub_project_pub_id_seq OWNER TO drupaladmin;

--
-- Name: project_pub_project_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_pub_project_pub_id_seq OWNED BY chado.project_pub.project_pub_id;


--
-- Name: project_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_relationship (
    project_relationship_id bigint NOT NULL,
    subject_project_id bigint NOT NULL,
    object_project_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.project_relationship OWNER TO drupaladmin;

--
-- Name: TABLE project_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_relationship IS 'Linking table for relating projects to each other.  For example, a
given project could be composed of several smaller subprojects';


--
-- Name: COLUMN project_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.project_relationship.type_id IS 'The cvterm type of the relationship being stated, such as "part of".';


--
-- Name: project_relationship_project_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_relationship_project_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_relationship_project_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: project_relationship_project_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_relationship_project_relationship_id_seq OWNED BY chado.project_relationship.project_relationship_id;


--
-- Name: project_stock; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.project_stock (
    project_stock_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    project_id bigint NOT NULL
);


ALTER TABLE chado.project_stock OWNER TO drupaladmin;

--
-- Name: TABLE project_stock; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.project_stock IS 'This table is intended associate records in the stock table with a project.';


--
-- Name: project_stock_project_stock_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.project_stock_project_stock_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.project_stock_project_stock_id_seq OWNER TO drupaladmin;

--
-- Name: project_stock_project_stock_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.project_stock_project_stock_id_seq OWNED BY chado.project_stock.project_stock_id;


--
-- Name: projectprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.projectprop (
    projectprop_id bigint NOT NULL,
    project_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.projectprop OWNER TO drupaladmin;

--
-- Name: projectprop_projectprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.projectprop_projectprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.projectprop_projectprop_id_seq OWNER TO drupaladmin;

--
-- Name: projectprop_projectprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.projectprop_projectprop_id_seq OWNED BY chado.projectprop.projectprop_id;


--
-- Name: protein_coding_gene; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.protein_coding_gene AS
 SELECT DISTINCT gene.feature_id,
    gene.dbxref_id,
    gene.organism_id,
    gene.name,
    gene.uniquename,
    gene.residues,
    gene.seqlen,
    gene.md5checksum,
    gene.type_id,
    gene.is_analysis,
    gene.is_obsolete,
    gene.timeaccessioned,
    gene.timelastmodified
   FROM ((chado.feature gene
     JOIN chado.feature_relationship fr ON ((gene.feature_id = fr.object_id)))
     JOIN so.mrna ON ((mrna.feature_id = fr.subject_id)));


ALTER TABLE chado.protein_coding_gene OWNER TO drupaladmin;

--
-- Name: protocol; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.protocol (
    protocol_id bigint NOT NULL,
    type_id bigint NOT NULL,
    pub_id bigint,
    dbxref_id bigint,
    name text NOT NULL,
    uri text,
    protocoldescription text,
    hardwaredescription text,
    softwaredescription text
);


ALTER TABLE chado.protocol OWNER TO drupaladmin;

--
-- Name: TABLE protocol; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.protocol IS 'Procedural notes on how data was prepared and processed.';


--
-- Name: protocol_protocol_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.protocol_protocol_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.protocol_protocol_id_seq OWNER TO drupaladmin;

--
-- Name: protocol_protocol_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.protocol_protocol_id_seq OWNED BY chado.protocol.protocol_id;


--
-- Name: protocolparam; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.protocolparam (
    protocolparam_id bigint NOT NULL,
    protocol_id bigint NOT NULL,
    name text NOT NULL,
    datatype_id bigint,
    unittype_id bigint,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.protocolparam OWNER TO drupaladmin;

--
-- Name: TABLE protocolparam; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.protocolparam IS 'Parameters related to a
protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.';


--
-- Name: protocolparam_protocolparam_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.protocolparam_protocolparam_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.protocolparam_protocolparam_id_seq OWNER TO drupaladmin;

--
-- Name: protocolparam_protocolparam_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.protocolparam_protocolparam_id_seq OWNED BY chado.protocolparam.protocolparam_id;


--
-- Name: pub_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pub_dbxref (
    pub_dbxref_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.pub_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE pub_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pub_dbxref IS 'Handle links to repositories,
e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...';


--
-- Name: pub_dbxref_pub_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pub_dbxref_pub_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pub_dbxref_pub_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: pub_dbxref_pub_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pub_dbxref_pub_dbxref_id_seq OWNED BY chado.pub_dbxref.pub_dbxref_id;


--
-- Name: pub_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pub_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pub_pub_id_seq OWNER TO drupaladmin;

--
-- Name: pub_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pub_pub_id_seq OWNED BY chado.pub.pub_id;


--
-- Name: pub_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pub_relationship (
    pub_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL
);


ALTER TABLE chado.pub_relationship OWNER TO drupaladmin;

--
-- Name: TABLE pub_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pub_relationship IS 'Handle relationships between
publications, e.g. when one publication makes others obsolete, when one
publication contains errata with respect to other publication(s), or
when one publication also appears in another pub.';


--
-- Name: pub_relationship_pub_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pub_relationship_pub_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pub_relationship_pub_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: pub_relationship_pub_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pub_relationship_pub_relationship_id_seq OWNED BY chado.pub_relationship.pub_relationship_id;


--
-- Name: pubauthor; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pubauthor (
    pubauthor_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    rank integer NOT NULL,
    editor boolean DEFAULT false,
    surname character varying(100) NOT NULL,
    givennames character varying(100),
    suffix character varying(100)
);


ALTER TABLE chado.pubauthor OWNER TO drupaladmin;

--
-- Name: TABLE pubauthor; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pubauthor IS 'An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.';


--
-- Name: COLUMN pubauthor.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pubauthor.rank IS 'Order of author in author list for this pub - order is important.';


--
-- Name: COLUMN pubauthor.editor; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pubauthor.editor IS 'Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.';


--
-- Name: COLUMN pubauthor.givennames; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pubauthor.givennames IS 'First name, initials';


--
-- Name: COLUMN pubauthor.suffix; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.pubauthor.suffix IS 'Jr., Sr., etc';


--
-- Name: pubauthor_contact; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pubauthor_contact (
    pubauthor_contact_id bigint NOT NULL,
    contact_id bigint NOT NULL,
    pubauthor_id bigint NOT NULL
);


ALTER TABLE chado.pubauthor_contact OWNER TO drupaladmin;

--
-- Name: TABLE pubauthor_contact; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pubauthor_contact IS 'An author on a publication may have a corresponding entry in the contact table and this table can link the two.';


--
-- Name: pubauthor_contact_pubauthor_contact_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pubauthor_contact_pubauthor_contact_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pubauthor_contact_pubauthor_contact_id_seq OWNER TO drupaladmin;

--
-- Name: pubauthor_contact_pubauthor_contact_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pubauthor_contact_pubauthor_contact_id_seq OWNED BY chado.pubauthor_contact.pubauthor_contact_id;


--
-- Name: pubauthor_pubauthor_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pubauthor_pubauthor_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pubauthor_pubauthor_id_seq OWNER TO drupaladmin;

--
-- Name: pubauthor_pubauthor_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pubauthor_pubauthor_id_seq OWNED BY chado.pubauthor.pubauthor_id;


--
-- Name: pubprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.pubprop (
    pubprop_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text NOT NULL,
    rank integer
);


ALTER TABLE chado.pubprop OWNER TO drupaladmin;

--
-- Name: TABLE pubprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.pubprop IS 'Property-value pairs for a pub. Follows standard chado pattern.';


--
-- Name: pubprop_pubprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.pubprop_pubprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.pubprop_pubprop_id_seq OWNER TO drupaladmin;

--
-- Name: pubprop_pubprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.pubprop_pubprop_id_seq OWNED BY chado.pubprop.pubprop_id;


--
-- Name: quantification; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.quantification (
    quantification_id bigint NOT NULL,
    acquisition_id bigint NOT NULL,
    operator_id bigint,
    protocol_id bigint,
    analysis_id bigint NOT NULL,
    quantificationdate timestamp without time zone DEFAULT CURRENT_TIMESTAMP,
    name text,
    uri text
);


ALTER TABLE chado.quantification OWNER TO drupaladmin;

--
-- Name: TABLE quantification; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.quantification IS 'Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.';


--
-- Name: quantification_quantification_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.quantification_quantification_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.quantification_quantification_id_seq OWNER TO drupaladmin;

--
-- Name: quantification_quantification_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.quantification_quantification_id_seq OWNED BY chado.quantification.quantification_id;


--
-- Name: quantification_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.quantification_relationship (
    quantification_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    type_id bigint NOT NULL,
    object_id bigint NOT NULL
);


ALTER TABLE chado.quantification_relationship OWNER TO drupaladmin;

--
-- Name: TABLE quantification_relationship; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.quantification_relationship IS 'There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.';


--
-- Name: quantification_relationship_quantification_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.quantification_relationship_quantification_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.quantification_relationship_quantification_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: quantification_relationship_quantification_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.quantification_relationship_quantification_relationship_id_seq OWNED BY chado.quantification_relationship.quantification_relationship_id;


--
-- Name: quantificationprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.quantificationprop (
    quantificationprop_id bigint NOT NULL,
    quantification_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.quantificationprop OWNER TO drupaladmin;

--
-- Name: TABLE quantificationprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.quantificationprop IS 'Extra quantification properties that are not accounted for in quantification.';


--
-- Name: quantificationprop_quantificationprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.quantificationprop_quantificationprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.quantificationprop_quantificationprop_id_seq OWNER TO drupaladmin;

--
-- Name: quantificationprop_quantificationprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.quantificationprop_quantificationprop_id_seq OWNED BY chado.quantificationprop.quantificationprop_id;


--
-- Name: stats_paths_to_root; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.stats_paths_to_root AS
 SELECT cvtermpath.subject_id AS cvterm_id,
    count(DISTINCT cvtermpath.cvtermpath_id) AS total_paths,
    avg(cvtermpath.pathdistance) AS avg_distance,
    min(cvtermpath.pathdistance) AS min_distance,
    max(cvtermpath.pathdistance) AS max_distance
   FROM (chado.cvtermpath
     JOIN chado.cv_root ON ((cvtermpath.object_id = cv_root.root_cvterm_id)))
  GROUP BY cvtermpath.subject_id;


ALTER TABLE chado.stats_paths_to_root OWNER TO drupaladmin;

--
-- Name: VIEW stats_paths_to_root; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.stats_paths_to_root IS 'per-cvterm statistics on its
placement in the DAG relative to the root. There may be multiple paths
from any term to the root. This gives the total number of paths, and
the average minimum and maximum distances. Here distance is defined by
cvtermpath.pathdistance';


--
-- Name: stock; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock (
    stock_id bigint NOT NULL,
    dbxref_id bigint,
    organism_id bigint,
    name character varying(255),
    uniquename text NOT NULL,
    description text,
    type_id bigint NOT NULL,
    is_obsolete boolean DEFAULT false NOT NULL
);


ALTER TABLE chado.stock OWNER TO drupaladmin;

--
-- Name: TABLE stock; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock IS 'Any stock can be globally identified by the
combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.';


--
-- Name: COLUMN stock.dbxref_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock.dbxref_id IS 'The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.';


--
-- Name: COLUMN stock.organism_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.';


--
-- Name: COLUMN stock.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock.name IS 'The name is a human-readable local name for a stock.';


--
-- Name: COLUMN stock.description; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock.description IS 'The description is the genetic description provided in the stock list.';


--
-- Name: COLUMN stock.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock.type_id IS 'The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.';


--
-- Name: stock_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_cvterm (
    stock_cvterm_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint NOT NULL,
    is_not boolean DEFAULT false NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stock_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE stock_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_cvterm IS 'stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.';


--
-- Name: stock_cvterm_stock_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_cvterm_stock_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_cvterm_stock_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: stock_cvterm_stock_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_cvterm_stock_cvterm_id_seq OWNED BY chado.stock_cvterm.stock_cvterm_id;


--
-- Name: stock_cvtermprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_cvtermprop (
    stock_cvtermprop_id bigint NOT NULL,
    stock_cvterm_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stock_cvtermprop OWNER TO drupaladmin;

--
-- Name: TABLE stock_cvtermprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_cvtermprop IS 'Extensible properties for
stock to cvterm associations. Examples: GO evidence codes;
qualifiers; metadata such as the date on which the entry was curated
and the source of the association. See the stockprop table for
meanings of type_id, value and rank.';


--
-- Name: COLUMN stock_cvtermprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_cvtermprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. cvterms may come from the OBO evidence code cv.';


--
-- Name: COLUMN stock_cvtermprop.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_cvtermprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';


--
-- Name: COLUMN stock_cvtermprop.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_cvtermprop.rank IS 'Property-Value
ordering. Any stock_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used.';


--
-- Name: stock_cvtermprop_stock_cvtermprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_cvtermprop_stock_cvtermprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_cvtermprop_stock_cvtermprop_id_seq OWNER TO drupaladmin;

--
-- Name: stock_cvtermprop_stock_cvtermprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_cvtermprop_stock_cvtermprop_id_seq OWNED BY chado.stock_cvtermprop.stock_cvtermprop_id;


--
-- Name: stock_dbxref; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_dbxref (
    stock_dbxref_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    dbxref_id bigint NOT NULL,
    is_current boolean DEFAULT true NOT NULL
);


ALTER TABLE chado.stock_dbxref OWNER TO drupaladmin;

--
-- Name: TABLE stock_dbxref; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_dbxref IS 'stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.';


--
-- Name: COLUMN stock_dbxref.is_current; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_dbxref.is_current IS 'The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.';


--
-- Name: stock_dbxref_stock_dbxref_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_dbxref_stock_dbxref_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_dbxref_stock_dbxref_id_seq OWNER TO drupaladmin;

--
-- Name: stock_dbxref_stock_dbxref_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_dbxref_stock_dbxref_id_seq OWNED BY chado.stock_dbxref.stock_dbxref_id;


--
-- Name: stock_dbxrefprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_dbxrefprop (
    stock_dbxrefprop_id bigint NOT NULL,
    stock_dbxref_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stock_dbxrefprop OWNER TO drupaladmin;

--
-- Name: TABLE stock_dbxrefprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_dbxrefprop IS 'A stock_dbxref can have any number of
slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to
hardcoding a list of columns in the relational schema, and is
completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for
the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';


--
-- Name: stock_dbxrefprop_stock_dbxrefprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_dbxrefprop_stock_dbxrefprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_dbxrefprop_stock_dbxrefprop_id_seq OWNER TO drupaladmin;

--
-- Name: stock_dbxrefprop_stock_dbxrefprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_dbxrefprop_stock_dbxrefprop_id_seq OWNED BY chado.stock_dbxrefprop.stock_dbxrefprop_id;


--
-- Name: stock_feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_feature (
    stock_feature_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    type_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stock_feature OWNER TO drupaladmin;

--
-- Name: TABLE stock_feature; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_feature IS 'Links a stock to a feature.';


--
-- Name: stock_feature_stock_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_feature_stock_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_feature_stock_feature_id_seq OWNER TO drupaladmin;

--
-- Name: stock_feature_stock_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_feature_stock_feature_id_seq OWNED BY chado.stock_feature.stock_feature_id;


--
-- Name: stock_featuremap; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_featuremap (
    stock_featuremap_id bigint NOT NULL,
    featuremap_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    type_id bigint
);


ALTER TABLE chado.stock_featuremap OWNER TO drupaladmin;

--
-- Name: TABLE stock_featuremap; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_featuremap IS 'Links a featuremap to a stock.';


--
-- Name: stock_featuremap_stock_featuremap_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_featuremap_stock_featuremap_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_featuremap_stock_featuremap_id_seq OWNER TO drupaladmin;

--
-- Name: stock_featuremap_stock_featuremap_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_featuremap_stock_featuremap_id_seq OWNED BY chado.stock_featuremap.stock_featuremap_id;


--
-- Name: stock_genotype; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_genotype (
    stock_genotype_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    genotype_id bigint NOT NULL
);


ALTER TABLE chado.stock_genotype OWNER TO drupaladmin;

--
-- Name: TABLE stock_genotype; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_genotype IS 'Simple table linking a stock to
a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.';


--
-- Name: stock_genotype_stock_genotype_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_genotype_stock_genotype_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_genotype_stock_genotype_id_seq OWNER TO drupaladmin;

--
-- Name: stock_genotype_stock_genotype_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_genotype_stock_genotype_id_seq OWNED BY chado.stock_genotype.stock_genotype_id;


--
-- Name: stock_library; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_library (
    stock_library_id bigint NOT NULL,
    library_id bigint NOT NULL,
    stock_id bigint NOT NULL
);


ALTER TABLE chado.stock_library OWNER TO drupaladmin;

--
-- Name: TABLE stock_library; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_library IS 'Links a stock with a library.';


--
-- Name: stock_library_stock_library_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_library_stock_library_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_library_stock_library_id_seq OWNER TO drupaladmin;

--
-- Name: stock_library_stock_library_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_library_stock_library_id_seq OWNED BY chado.stock_library.stock_library_id;


--
-- Name: stock_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_pub (
    stock_pub_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.stock_pub OWNER TO drupaladmin;

--
-- Name: TABLE stock_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_pub IS 'Provenance. Linking table between stocks and, for example, a stocklist computer file.';


--
-- Name: stock_pub_stock_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_pub_stock_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_pub_stock_pub_id_seq OWNER TO drupaladmin;

--
-- Name: stock_pub_stock_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_pub_stock_pub_id_seq OWNED BY chado.stock_pub.stock_pub_id;


--
-- Name: stock_relationship; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_relationship (
    stock_relationship_id bigint NOT NULL,
    subject_id bigint NOT NULL,
    object_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stock_relationship OWNER TO drupaladmin;

--
-- Name: COLUMN stock_relationship.subject_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_relationship.subject_id IS 'stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.';


--
-- Name: COLUMN stock_relationship.object_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_relationship.object_id IS 'stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.';


--
-- Name: COLUMN stock_relationship.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_relationship.type_id IS 'stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.';


--
-- Name: COLUMN stock_relationship.value; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_relationship.value IS 'stock_relationship.value is for additional notes or comments.';


--
-- Name: COLUMN stock_relationship.rank; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stock_relationship.rank IS 'stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.';


--
-- Name: stock_relationship_cvterm; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_relationship_cvterm (
    stock_relationship_cvterm_id bigint NOT NULL,
    stock_relationship_id bigint NOT NULL,
    cvterm_id bigint NOT NULL,
    pub_id bigint
);


ALTER TABLE chado.stock_relationship_cvterm OWNER TO drupaladmin;

--
-- Name: TABLE stock_relationship_cvterm; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_relationship_cvterm IS 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';


--
-- Name: stock_relationship_cvterm_stock_relationship_cvterm_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_relationship_cvterm_stock_relationship_cvterm_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_relationship_cvterm_stock_relationship_cvterm_id_seq OWNER TO drupaladmin;

--
-- Name: stock_relationship_cvterm_stock_relationship_cvterm_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_relationship_cvterm_stock_relationship_cvterm_id_seq OWNED BY chado.stock_relationship_cvterm.stock_relationship_cvterm_id;


--
-- Name: stock_relationship_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stock_relationship_pub (
    stock_relationship_pub_id bigint NOT NULL,
    stock_relationship_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.stock_relationship_pub OWNER TO drupaladmin;

--
-- Name: TABLE stock_relationship_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stock_relationship_pub IS 'Provenance. Attach optional evidence to a stock_relationship in the form of a publication.';


--
-- Name: stock_relationship_pub_stock_relationship_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_relationship_pub_stock_relationship_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_relationship_pub_stock_relationship_pub_id_seq OWNER TO drupaladmin;

--
-- Name: stock_relationship_pub_stock_relationship_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_relationship_pub_stock_relationship_pub_id_seq OWNED BY chado.stock_relationship_pub.stock_relationship_pub_id;


--
-- Name: stock_relationship_stock_relationship_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_relationship_stock_relationship_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_relationship_stock_relationship_id_seq OWNER TO drupaladmin;

--
-- Name: stock_relationship_stock_relationship_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_relationship_stock_relationship_id_seq OWNED BY chado.stock_relationship.stock_relationship_id;


--
-- Name: stock_stock_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stock_stock_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stock_stock_id_seq OWNER TO drupaladmin;

--
-- Name: stock_stock_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stock_stock_id_seq OWNED BY chado.stock.stock_id;


--
-- Name: stockcollection; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockcollection (
    stockcollection_id bigint NOT NULL,
    type_id bigint NOT NULL,
    contact_id bigint,
    name character varying(255),
    uniquename text NOT NULL
);


ALTER TABLE chado.stockcollection OWNER TO drupaladmin;

--
-- Name: TABLE stockcollection; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockcollection IS 'The lab or stock center distributing the stocks in their collection.';


--
-- Name: COLUMN stockcollection.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stockcollection.type_id IS 'type_id is the collection type cv.';


--
-- Name: COLUMN stockcollection.contact_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stockcollection.contact_id IS 'contact_id links to the contact information for the collection.';


--
-- Name: COLUMN stockcollection.name; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stockcollection.name IS 'name is the collection.';


--
-- Name: COLUMN stockcollection.uniquename; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stockcollection.uniquename IS 'uniqename is the value of the collection cv.';


--
-- Name: stockcollection_db; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockcollection_db (
    stockcollection_db_id bigint NOT NULL,
    stockcollection_id bigint NOT NULL,
    db_id bigint NOT NULL
);


ALTER TABLE chado.stockcollection_db OWNER TO drupaladmin;

--
-- Name: TABLE stockcollection_db; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockcollection_db IS 'Stock collections may be respresented
by an external online database. This table associates a stock collection with
a database where its member stocks can be found. Individual stock that are part
of this collction should have entries in the stock_dbxref table with the same
db_id record';


--
-- Name: stockcollection_db_stockcollection_db_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockcollection_db_stockcollection_db_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockcollection_db_stockcollection_db_id_seq OWNER TO drupaladmin;

--
-- Name: stockcollection_db_stockcollection_db_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockcollection_db_stockcollection_db_id_seq OWNED BY chado.stockcollection_db.stockcollection_db_id;


--
-- Name: stockcollection_stock; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockcollection_stock (
    stockcollection_stock_id bigint NOT NULL,
    stockcollection_id bigint NOT NULL,
    stock_id bigint NOT NULL
);


ALTER TABLE chado.stockcollection_stock OWNER TO drupaladmin;

--
-- Name: TABLE stockcollection_stock; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockcollection_stock IS 'stockcollection_stock links
a stock collection to the stocks which are contained in the collection.';


--
-- Name: stockcollection_stock_stockcollection_stock_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockcollection_stock_stockcollection_stock_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockcollection_stock_stockcollection_stock_id_seq OWNER TO drupaladmin;

--
-- Name: stockcollection_stock_stockcollection_stock_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockcollection_stock_stockcollection_stock_id_seq OWNED BY chado.stockcollection_stock.stockcollection_stock_id;


--
-- Name: stockcollection_stockcollection_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockcollection_stockcollection_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockcollection_stockcollection_id_seq OWNER TO drupaladmin;

--
-- Name: stockcollection_stockcollection_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockcollection_stockcollection_id_seq OWNED BY chado.stockcollection.stockcollection_id;


--
-- Name: stockcollectionprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockcollectionprop (
    stockcollectionprop_id bigint NOT NULL,
    stockcollection_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stockcollectionprop OWNER TO drupaladmin;

--
-- Name: TABLE stockcollectionprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockcollectionprop IS 'The table stockcollectionprop
contains the value of the stock collection such as website/email URLs;
the value of the stock collection order URLs.';


--
-- Name: COLUMN stockcollectionprop.type_id; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON COLUMN chado.stockcollectionprop.type_id IS 'The cv for the type_id is "stockcollection property type".';


--
-- Name: stockcollectionprop_stockcollectionprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockcollectionprop_stockcollectionprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockcollectionprop_stockcollectionprop_id_seq OWNER TO drupaladmin;

--
-- Name: stockcollectionprop_stockcollectionprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockcollectionprop_stockcollectionprop_id_seq OWNED BY chado.stockcollectionprop.stockcollectionprop_id;


--
-- Name: stockprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockprop (
    stockprop_id bigint NOT NULL,
    stock_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.stockprop OWNER TO drupaladmin;

--
-- Name: TABLE stockprop; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockprop IS 'A stock can have any number of
slot-value property tags attached to it. This is an alternative to
hardcoding a list of columns in the relational schema, and is
completely extensible. There is a unique constraint, stockprop_c1, for
the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';


--
-- Name: stockprop_pub; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.stockprop_pub (
    stockprop_pub_id bigint NOT NULL,
    stockprop_id bigint NOT NULL,
    pub_id bigint NOT NULL
);


ALTER TABLE chado.stockprop_pub OWNER TO drupaladmin;

--
-- Name: TABLE stockprop_pub; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.stockprop_pub IS 'Provenance. Any stockprop assignment can optionally be supported by a publication.';


--
-- Name: stockprop_pub_stockprop_pub_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockprop_pub_stockprop_pub_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockprop_pub_stockprop_pub_id_seq OWNER TO drupaladmin;

--
-- Name: stockprop_pub_stockprop_pub_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockprop_pub_stockprop_pub_id_seq OWNED BY chado.stockprop_pub.stockprop_pub_id;


--
-- Name: stockprop_stockprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.stockprop_stockprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.stockprop_stockprop_id_seq OWNER TO drupaladmin;

--
-- Name: stockprop_stockprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.stockprop_stockprop_id_seq OWNED BY chado.stockprop.stockprop_id;


--
-- Name: study; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.study (
    study_id bigint NOT NULL,
    contact_id bigint NOT NULL,
    pub_id bigint,
    dbxref_id bigint,
    name text NOT NULL,
    description text
);


ALTER TABLE chado.study OWNER TO drupaladmin;

--
-- Name: study_assay; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.study_assay (
    study_assay_id bigint NOT NULL,
    study_id bigint NOT NULL,
    assay_id bigint NOT NULL
);


ALTER TABLE chado.study_assay OWNER TO drupaladmin;

--
-- Name: study_assay_study_assay_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.study_assay_study_assay_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.study_assay_study_assay_id_seq OWNER TO drupaladmin;

--
-- Name: study_assay_study_assay_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.study_assay_study_assay_id_seq OWNED BY chado.study_assay.study_assay_id;


--
-- Name: study_study_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.study_study_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.study_study_id_seq OWNER TO drupaladmin;

--
-- Name: study_study_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.study_study_id_seq OWNED BY chado.study.study_id;


--
-- Name: studydesign; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studydesign (
    studydesign_id bigint NOT NULL,
    study_id bigint NOT NULL,
    description text
);


ALTER TABLE chado.studydesign OWNER TO drupaladmin;

--
-- Name: studydesign_studydesign_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studydesign_studydesign_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studydesign_studydesign_id_seq OWNER TO drupaladmin;

--
-- Name: studydesign_studydesign_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studydesign_studydesign_id_seq OWNED BY chado.studydesign.studydesign_id;


--
-- Name: studydesignprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studydesignprop (
    studydesignprop_id bigint NOT NULL,
    studydesign_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.studydesignprop OWNER TO drupaladmin;

--
-- Name: studydesignprop_studydesignprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studydesignprop_studydesignprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studydesignprop_studydesignprop_id_seq OWNER TO drupaladmin;

--
-- Name: studydesignprop_studydesignprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studydesignprop_studydesignprop_id_seq OWNED BY chado.studydesignprop.studydesignprop_id;


--
-- Name: studyfactor; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studyfactor (
    studyfactor_id bigint NOT NULL,
    studydesign_id bigint NOT NULL,
    type_id bigint,
    name text NOT NULL,
    description text
);


ALTER TABLE chado.studyfactor OWNER TO drupaladmin;

--
-- Name: studyfactor_studyfactor_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studyfactor_studyfactor_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studyfactor_studyfactor_id_seq OWNER TO drupaladmin;

--
-- Name: studyfactor_studyfactor_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studyfactor_studyfactor_id_seq OWNED BY chado.studyfactor.studyfactor_id;


--
-- Name: studyfactorvalue; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studyfactorvalue (
    studyfactorvalue_id bigint NOT NULL,
    studyfactor_id bigint NOT NULL,
    assay_id bigint NOT NULL,
    factorvalue text,
    name text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.studyfactorvalue OWNER TO drupaladmin;

--
-- Name: studyfactorvalue_studyfactorvalue_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studyfactorvalue_studyfactorvalue_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studyfactorvalue_studyfactorvalue_id_seq OWNER TO drupaladmin;

--
-- Name: studyfactorvalue_studyfactorvalue_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studyfactorvalue_studyfactorvalue_id_seq OWNED BY chado.studyfactorvalue.studyfactorvalue_id;


--
-- Name: studyprop; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studyprop (
    studyprop_id bigint NOT NULL,
    study_id bigint NOT NULL,
    type_id bigint NOT NULL,
    value text,
    rank integer DEFAULT 0 NOT NULL
);


ALTER TABLE chado.studyprop OWNER TO drupaladmin;

--
-- Name: studyprop_feature; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.studyprop_feature (
    studyprop_feature_id bigint NOT NULL,
    studyprop_id bigint NOT NULL,
    feature_id bigint NOT NULL,
    type_id bigint
);


ALTER TABLE chado.studyprop_feature OWNER TO drupaladmin;

--
-- Name: studyprop_feature_studyprop_feature_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studyprop_feature_studyprop_feature_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studyprop_feature_studyprop_feature_id_seq OWNER TO drupaladmin;

--
-- Name: studyprop_feature_studyprop_feature_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studyprop_feature_studyprop_feature_id_seq OWNED BY chado.studyprop_feature.studyprop_feature_id;


--
-- Name: studyprop_studyprop_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.studyprop_studyprop_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.studyprop_studyprop_id_seq OWNER TO drupaladmin;

--
-- Name: studyprop_studyprop_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.studyprop_studyprop_id_seq OWNED BY chado.studyprop.studyprop_id;


--
-- Name: synonym_synonym_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.synonym_synonym_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.synonym_synonym_id_seq OWNER TO drupaladmin;

--
-- Name: synonym_synonym_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.synonym_synonym_id_seq OWNED BY chado.synonym.synonym_id;


--
-- Name: tableinfo; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.tableinfo (
    tableinfo_id bigint NOT NULL,
    name character varying(30) NOT NULL,
    primary_key_column character varying(30),
    is_view integer DEFAULT 0 NOT NULL,
    view_on_table_id bigint,
    superclass_table_id bigint,
    is_updateable integer DEFAULT 1 NOT NULL,
    modification_date date DEFAULT now() NOT NULL
);


ALTER TABLE chado.tableinfo OWNER TO drupaladmin;

--
-- Name: tableinfo_tableinfo_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.tableinfo_tableinfo_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.tableinfo_tableinfo_id_seq OWNER TO drupaladmin;

--
-- Name: tableinfo_tableinfo_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.tableinfo_tableinfo_id_seq OWNED BY chado.tableinfo.tableinfo_id;


--
-- Name: treatment; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.treatment (
    treatment_id bigint NOT NULL,
    rank integer DEFAULT 0 NOT NULL,
    biomaterial_id bigint NOT NULL,
    type_id bigint NOT NULL,
    protocol_id bigint,
    name text
);


ALTER TABLE chado.treatment OWNER TO drupaladmin;

--
-- Name: TABLE treatment; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON TABLE chado.treatment IS 'A biomaterial may undergo multiple
treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.';


--
-- Name: treatment_treatment_id_seq; Type: SEQUENCE; Schema: chado; Owner: drupaladmin
--

CREATE SEQUENCE chado.treatment_treatment_id_seq
    START WITH 1
    INCREMENT BY 1
    NO MINVALUE
    NO MAXVALUE
    CACHE 1;


ALTER TABLE chado.treatment_treatment_id_seq OWNER TO drupaladmin;

--
-- Name: treatment_treatment_id_seq; Type: SEQUENCE OWNED BY; Schema: chado; Owner: drupaladmin
--

ALTER SEQUENCE chado.treatment_treatment_id_seq OWNED BY chado.treatment.treatment_id;


--
-- Name: tripal_gff_temp; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.tripal_gff_temp (
    feature_id integer NOT NULL,
    organism_id integer NOT NULL,
    uniquename text NOT NULL,
    type_name character varying(1024) NOT NULL
);


ALTER TABLE chado.tripal_gff_temp OWNER TO drupaladmin;

--
-- Name: tripal_gffcds_temp; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.tripal_gffcds_temp (
    feature_id integer NOT NULL,
    parent_id integer NOT NULL,
    phase integer,
    strand integer NOT NULL,
    fmin integer NOT NULL,
    fmax integer NOT NULL
);


ALTER TABLE chado.tripal_gffcds_temp OWNER TO drupaladmin;

--
-- Name: tripal_gffprotein_temp; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.tripal_gffprotein_temp (
    feature_id integer NOT NULL,
    parent_id integer NOT NULL,
    fmin integer NOT NULL,
    fmax integer NOT NULL
);


ALTER TABLE chado.tripal_gffprotein_temp OWNER TO drupaladmin;

--
-- Name: tripal_obo_temp; Type: TABLE; Schema: chado; Owner: drupaladmin
--

CREATE TABLE chado.tripal_obo_temp (
    id character varying(255) NOT NULL,
    stanza text NOT NULL,
    type character varying(50) NOT NULL
);


ALTER TABLE chado.tripal_obo_temp OWNER TO drupaladmin;

--
-- Name: type_feature_count; Type: VIEW; Schema: chado; Owner: drupaladmin
--

CREATE VIEW chado.type_feature_count AS
 SELECT t.name AS type,
    count(*) AS num_features
   FROM (chado.cvterm t
     JOIN chado.feature ON ((feature.type_id = t.cvterm_id)))
  GROUP BY t.name;


ALTER TABLE chado.type_feature_count OWNER TO drupaladmin;

--
-- Name: VIEW type_feature_count; Type: COMMENT; Schema: chado; Owner: drupaladmin
--

COMMENT ON VIEW chado.type_feature_count IS 'per-feature-type feature counts';


--
-- Name: acquisition acquisition_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.acquisition ALTER COLUMN acquisition_id SET DEFAULT nextval('chado.acquisition_acquisition_id_seq'::regclass);


--
-- Name: acquisition_relationship acquisition_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.acquisition_relationship ALTER COLUMN acquisition_relationship_id SET DEFAULT nextval('chado.acquisition_relationship_acquisition_relationship_id_seq'::regclass);


--
-- Name: acquisitionprop acquisitionprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.acquisitionprop ALTER COLUMN acquisitionprop_id SET DEFAULT nextval('chado.acquisitionprop_acquisitionprop_id_seq'::regclass);


--
-- Name: analysis analysis_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysis ALTER COLUMN analysis_id SET DEFAULT nextval('chado.analysis_analysis_id_seq'::regclass);


--
-- Name: analysis_cvterm analysis_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysis_cvterm ALTER COLUMN analysis_cvterm_id SET DEFAULT nextval('chado.analysis_cvterm_analysis_cvterm_id_seq'::regclass);


--
-- Name: analysis_dbxref analysis_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysis_dbxref ALTER COLUMN analysis_dbxref_id SET DEFAULT nextval('chado.analysis_dbxref_analysis_dbxref_id_seq'::regclass);


--
-- Name: analysis_pub analysis_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysis_pub ALTER COLUMN analysis_pub_id SET DEFAULT nextval('chado.analysis_pub_analysis_pub_id_seq'::regclass);


--
-- Name: analysis_relationship analysis_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysis_relationship ALTER COLUMN analysis_relationship_id SET DEFAULT nextval('chado.analysis_relationship_analysis_relationship_id_seq'::regclass);


--
-- Name: analysisfeature analysisfeature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysisfeature ALTER COLUMN analysisfeature_id SET DEFAULT nextval('chado.analysisfeature_analysisfeature_id_seq'::regclass);


--
-- Name: analysisfeatureprop analysisfeatureprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysisfeatureprop ALTER COLUMN analysisfeatureprop_id SET DEFAULT nextval('chado.analysisfeatureprop_analysisfeatureprop_id_seq'::regclass);


--
-- Name: analysisprop analysisprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.analysisprop ALTER COLUMN analysisprop_id SET DEFAULT nextval('chado.analysisprop_analysisprop_id_seq'::regclass);


--
-- Name: arraydesign arraydesign_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.arraydesign ALTER COLUMN arraydesign_id SET DEFAULT nextval('chado.arraydesign_arraydesign_id_seq'::regclass);


--
-- Name: arraydesignprop arraydesignprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.arraydesignprop ALTER COLUMN arraydesignprop_id SET DEFAULT nextval('chado.arraydesignprop_arraydesignprop_id_seq'::regclass);


--
-- Name: assay assay_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.assay ALTER COLUMN assay_id SET DEFAULT nextval('chado.assay_assay_id_seq'::regclass);


--
-- Name: assay_biomaterial assay_biomaterial_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.assay_biomaterial ALTER COLUMN assay_biomaterial_id SET DEFAULT nextval('chado.assay_biomaterial_assay_biomaterial_id_seq'::regclass);


--
-- Name: assay_project assay_project_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.assay_project ALTER COLUMN assay_project_id SET DEFAULT nextval('chado.assay_project_assay_project_id_seq'::regclass);


--
-- Name: assayprop assayprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.assayprop ALTER COLUMN assayprop_id SET DEFAULT nextval('chado.assayprop_assayprop_id_seq'::regclass);


--
-- Name: biomaterial biomaterial_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.biomaterial ALTER COLUMN biomaterial_id SET DEFAULT nextval('chado.biomaterial_biomaterial_id_seq'::regclass);


--
-- Name: biomaterial_dbxref biomaterial_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.biomaterial_dbxref ALTER COLUMN biomaterial_dbxref_id SET DEFAULT nextval('chado.biomaterial_dbxref_biomaterial_dbxref_id_seq'::regclass);


--
-- Name: biomaterial_relationship biomaterial_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.biomaterial_relationship ALTER COLUMN biomaterial_relationship_id SET DEFAULT nextval('chado.biomaterial_relationship_biomaterial_relationship_id_seq'::regclass);


--
-- Name: biomaterial_treatment biomaterial_treatment_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.biomaterial_treatment ALTER COLUMN biomaterial_treatment_id SET DEFAULT nextval('chado.biomaterial_treatment_biomaterial_treatment_id_seq'::regclass);


--
-- Name: biomaterialprop biomaterialprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.biomaterialprop ALTER COLUMN biomaterialprop_id SET DEFAULT nextval('chado.biomaterialprop_biomaterialprop_id_seq'::regclass);


--
-- Name: cell_line cell_line_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line ALTER COLUMN cell_line_id SET DEFAULT nextval('chado.cell_line_cell_line_id_seq'::regclass);


--
-- Name: cell_line_cvterm cell_line_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_cvterm ALTER COLUMN cell_line_cvterm_id SET DEFAULT nextval('chado.cell_line_cvterm_cell_line_cvterm_id_seq'::regclass);


--
-- Name: cell_line_cvtermprop cell_line_cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_cvtermprop ALTER COLUMN cell_line_cvtermprop_id SET DEFAULT nextval('chado.cell_line_cvtermprop_cell_line_cvtermprop_id_seq'::regclass);


--
-- Name: cell_line_dbxref cell_line_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_dbxref ALTER COLUMN cell_line_dbxref_id SET DEFAULT nextval('chado.cell_line_dbxref_cell_line_dbxref_id_seq'::regclass);


--
-- Name: cell_line_feature cell_line_feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_feature ALTER COLUMN cell_line_feature_id SET DEFAULT nextval('chado.cell_line_feature_cell_line_feature_id_seq'::regclass);


--
-- Name: cell_line_library cell_line_library_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_library ALTER COLUMN cell_line_library_id SET DEFAULT nextval('chado.cell_line_library_cell_line_library_id_seq'::regclass);


--
-- Name: cell_line_pub cell_line_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_pub ALTER COLUMN cell_line_pub_id SET DEFAULT nextval('chado.cell_line_pub_cell_line_pub_id_seq'::regclass);


--
-- Name: cell_line_relationship cell_line_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_relationship ALTER COLUMN cell_line_relationship_id SET DEFAULT nextval('chado.cell_line_relationship_cell_line_relationship_id_seq'::regclass);


--
-- Name: cell_line_synonym cell_line_synonym_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_line_synonym ALTER COLUMN cell_line_synonym_id SET DEFAULT nextval('chado.cell_line_synonym_cell_line_synonym_id_seq'::regclass);


--
-- Name: cell_lineprop cell_lineprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_lineprop ALTER COLUMN cell_lineprop_id SET DEFAULT nextval('chado.cell_lineprop_cell_lineprop_id_seq'::regclass);


--
-- Name: cell_lineprop_pub cell_lineprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cell_lineprop_pub ALTER COLUMN cell_lineprop_pub_id SET DEFAULT nextval('chado.cell_lineprop_pub_cell_lineprop_pub_id_seq'::regclass);


--
-- Name: chadoprop chadoprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.chadoprop ALTER COLUMN chadoprop_id SET DEFAULT nextval('chado.chadoprop_chadoprop_id_seq'::regclass);


--
-- Name: channel channel_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.channel ALTER COLUMN channel_id SET DEFAULT nextval('chado.channel_channel_id_seq'::regclass);


--
-- Name: contact contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.contact ALTER COLUMN contact_id SET DEFAULT nextval('chado.contact_contact_id_seq'::regclass);


--
-- Name: contact_relationship contact_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.contact_relationship ALTER COLUMN contact_relationship_id SET DEFAULT nextval('chado.contact_relationship_contact_relationship_id_seq'::regclass);


--
-- Name: contactprop contactprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.contactprop ALTER COLUMN contactprop_id SET DEFAULT nextval('chado.contactprop_contactprop_id_seq'::regclass);


--
-- Name: control control_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.control ALTER COLUMN control_id SET DEFAULT nextval('chado.control_control_id_seq'::regclass);


--
-- Name: cv cv_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cv ALTER COLUMN cv_id SET DEFAULT nextval('chado.cv_cv_id_seq'::regclass);


--
-- Name: cvprop cvprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvprop ALTER COLUMN cvprop_id SET DEFAULT nextval('chado.cvprop_cvprop_id_seq'::regclass);


--
-- Name: cvterm cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvterm ALTER COLUMN cvterm_id SET DEFAULT nextval('chado.cvterm_cvterm_id_seq'::regclass);


--
-- Name: cvterm_dbxref cvterm_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvterm_dbxref ALTER COLUMN cvterm_dbxref_id SET DEFAULT nextval('chado.cvterm_dbxref_cvterm_dbxref_id_seq'::regclass);


--
-- Name: cvterm_relationship cvterm_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvterm_relationship ALTER COLUMN cvterm_relationship_id SET DEFAULT nextval('chado.cvterm_relationship_cvterm_relationship_id_seq'::regclass);


--
-- Name: cvtermpath cvtermpath_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvtermpath ALTER COLUMN cvtermpath_id SET DEFAULT nextval('chado.cvtermpath_cvtermpath_id_seq'::regclass);


--
-- Name: cvtermprop cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvtermprop ALTER COLUMN cvtermprop_id SET DEFAULT nextval('chado.cvtermprop_cvtermprop_id_seq'::regclass);


--
-- Name: cvtermsynonym cvtermsynonym_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.cvtermsynonym ALTER COLUMN cvtermsynonym_id SET DEFAULT nextval('chado.cvtermsynonym_cvtermsynonym_id_seq'::regclass);


--
-- Name: db db_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.db ALTER COLUMN db_id SET DEFAULT nextval('chado.db_db_id_seq'::regclass);


--
-- Name: dbprop dbprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.dbprop ALTER COLUMN dbprop_id SET DEFAULT nextval('chado.dbprop_dbprop_id_seq'::regclass);


--
-- Name: dbxref dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.dbxref ALTER COLUMN dbxref_id SET DEFAULT nextval('chado.dbxref_dbxref_id_seq'::regclass);


--
-- Name: dbxrefprop dbxrefprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.dbxrefprop ALTER COLUMN dbxrefprop_id SET DEFAULT nextval('chado.dbxrefprop_dbxrefprop_id_seq'::regclass);


--
-- Name: eimage eimage_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.eimage ALTER COLUMN eimage_id SET DEFAULT nextval('chado.eimage_eimage_id_seq'::regclass);


--
-- Name: element element_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.element ALTER COLUMN element_id SET DEFAULT nextval('chado.element_element_id_seq'::regclass);


--
-- Name: element_relationship element_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.element_relationship ALTER COLUMN element_relationship_id SET DEFAULT nextval('chado.element_relationship_element_relationship_id_seq'::regclass);


--
-- Name: elementresult elementresult_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.elementresult ALTER COLUMN elementresult_id SET DEFAULT nextval('chado.elementresult_elementresult_id_seq'::regclass);


--
-- Name: elementresult_relationship elementresult_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.elementresult_relationship ALTER COLUMN elementresult_relationship_id SET DEFAULT nextval('chado.elementresult_relationship_elementresult_relationship_id_seq'::regclass);


--
-- Name: environment environment_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.environment ALTER COLUMN environment_id SET DEFAULT nextval('chado.environment_environment_id_seq'::regclass);


--
-- Name: environment_cvterm environment_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.environment_cvterm ALTER COLUMN environment_cvterm_id SET DEFAULT nextval('chado.environment_cvterm_environment_cvterm_id_seq'::regclass);


--
-- Name: expression expression_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expression ALTER COLUMN expression_id SET DEFAULT nextval('chado.expression_expression_id_seq'::regclass);


--
-- Name: expression_cvterm expression_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expression_cvterm ALTER COLUMN expression_cvterm_id SET DEFAULT nextval('chado.expression_cvterm_expression_cvterm_id_seq'::regclass);


--
-- Name: expression_cvtermprop expression_cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expression_cvtermprop ALTER COLUMN expression_cvtermprop_id SET DEFAULT nextval('chado.expression_cvtermprop_expression_cvtermprop_id_seq'::regclass);


--
-- Name: expression_image expression_image_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expression_image ALTER COLUMN expression_image_id SET DEFAULT nextval('chado.expression_image_expression_image_id_seq'::regclass);


--
-- Name: expression_pub expression_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expression_pub ALTER COLUMN expression_pub_id SET DEFAULT nextval('chado.expression_pub_expression_pub_id_seq'::regclass);


--
-- Name: expressionprop expressionprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.expressionprop ALTER COLUMN expressionprop_id SET DEFAULT nextval('chado.expressionprop_expressionprop_id_seq'::regclass);


--
-- Name: feature feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature ALTER COLUMN feature_id SET DEFAULT nextval('chado.feature_feature_id_seq'::regclass);


--
-- Name: feature_contact feature_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_contact ALTER COLUMN feature_contact_id SET DEFAULT nextval('chado.feature_contact_feature_contact_id_seq'::regclass);


--
-- Name: feature_cvterm feature_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_cvterm ALTER COLUMN feature_cvterm_id SET DEFAULT nextval('chado.feature_cvterm_feature_cvterm_id_seq'::regclass);


--
-- Name: feature_cvterm_dbxref feature_cvterm_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_cvterm_dbxref ALTER COLUMN feature_cvterm_dbxref_id SET DEFAULT nextval('chado.feature_cvterm_dbxref_feature_cvterm_dbxref_id_seq'::regclass);


--
-- Name: feature_cvterm_pub feature_cvterm_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_cvterm_pub ALTER COLUMN feature_cvterm_pub_id SET DEFAULT nextval('chado.feature_cvterm_pub_feature_cvterm_pub_id_seq'::regclass);


--
-- Name: feature_cvtermprop feature_cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_cvtermprop ALTER COLUMN feature_cvtermprop_id SET DEFAULT nextval('chado.feature_cvtermprop_feature_cvtermprop_id_seq'::regclass);


--
-- Name: feature_dbxref feature_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_dbxref ALTER COLUMN feature_dbxref_id SET DEFAULT nextval('chado.feature_dbxref_feature_dbxref_id_seq'::regclass);


--
-- Name: feature_expression feature_expression_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_expression ALTER COLUMN feature_expression_id SET DEFAULT nextval('chado.feature_expression_feature_expression_id_seq'::regclass);


--
-- Name: feature_expressionprop feature_expressionprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_expressionprop ALTER COLUMN feature_expressionprop_id SET DEFAULT nextval('chado.feature_expressionprop_feature_expressionprop_id_seq'::regclass);


--
-- Name: feature_genotype feature_genotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_genotype ALTER COLUMN feature_genotype_id SET DEFAULT nextval('chado.feature_genotype_feature_genotype_id_seq'::regclass);


--
-- Name: feature_phenotype feature_phenotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_phenotype ALTER COLUMN feature_phenotype_id SET DEFAULT nextval('chado.feature_phenotype_feature_phenotype_id_seq'::regclass);


--
-- Name: feature_pub feature_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_pub ALTER COLUMN feature_pub_id SET DEFAULT nextval('chado.feature_pub_feature_pub_id_seq'::regclass);


--
-- Name: feature_pubprop feature_pubprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_pubprop ALTER COLUMN feature_pubprop_id SET DEFAULT nextval('chado.feature_pubprop_feature_pubprop_id_seq'::regclass);


--
-- Name: feature_relationship feature_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_relationship ALTER COLUMN feature_relationship_id SET DEFAULT nextval('chado.feature_relationship_feature_relationship_id_seq'::regclass);


--
-- Name: feature_relationship_pub feature_relationship_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_relationship_pub ALTER COLUMN feature_relationship_pub_id SET DEFAULT nextval('chado.feature_relationship_pub_feature_relationship_pub_id_seq'::regclass);


--
-- Name: feature_relationshipprop feature_relationshipprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_relationshipprop ALTER COLUMN feature_relationshipprop_id SET DEFAULT nextval('chado.feature_relationshipprop_feature_relationshipprop_id_seq'::regclass);


--
-- Name: feature_relationshipprop_pub feature_relationshipprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_relationshipprop_pub ALTER COLUMN feature_relationshipprop_pub_id SET DEFAULT nextval('chado.feature_relationshipprop_pub_feature_relationshipprop_pub_i_seq'::regclass);


--
-- Name: feature_synonym feature_synonym_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.feature_synonym ALTER COLUMN feature_synonym_id SET DEFAULT nextval('chado.feature_synonym_feature_synonym_id_seq'::regclass);


--
-- Name: featureloc featureloc_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featureloc ALTER COLUMN featureloc_id SET DEFAULT nextval('chado.featureloc_featureloc_id_seq'::regclass);


--
-- Name: featureloc_pub featureloc_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featureloc_pub ALTER COLUMN featureloc_pub_id SET DEFAULT nextval('chado.featureloc_pub_featureloc_pub_id_seq'::regclass);


--
-- Name: featuremap featuremap_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremap ALTER COLUMN featuremap_id SET DEFAULT nextval('chado.featuremap_featuremap_id_seq'::regclass);


--
-- Name: featuremap_contact featuremap_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremap_contact ALTER COLUMN featuremap_contact_id SET DEFAULT nextval('chado.featuremap_contact_featuremap_contact_id_seq'::regclass);


--
-- Name: featuremap_dbxref featuremap_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremap_dbxref ALTER COLUMN featuremap_dbxref_id SET DEFAULT nextval('chado.featuremap_dbxref_featuremap_dbxref_id_seq'::regclass);


--
-- Name: featuremap_organism featuremap_organism_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremap_organism ALTER COLUMN featuremap_organism_id SET DEFAULT nextval('chado.featuremap_organism_featuremap_organism_id_seq'::regclass);


--
-- Name: featuremap_pub featuremap_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremap_pub ALTER COLUMN featuremap_pub_id SET DEFAULT nextval('chado.featuremap_pub_featuremap_pub_id_seq'::regclass);


--
-- Name: featuremapprop featuremapprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featuremapprop ALTER COLUMN featuremapprop_id SET DEFAULT nextval('chado.featuremapprop_featuremapprop_id_seq'::regclass);


--
-- Name: featurepos featurepos_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featurepos ALTER COLUMN featurepos_id SET DEFAULT nextval('chado.featurepos_featurepos_id_seq'::regclass);


--
-- Name: featureposprop featureposprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featureposprop ALTER COLUMN featureposprop_id SET DEFAULT nextval('chado.featureposprop_featureposprop_id_seq'::regclass);


--
-- Name: featureprop featureprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featureprop ALTER COLUMN featureprop_id SET DEFAULT nextval('chado.featureprop_featureprop_id_seq'::regclass);


--
-- Name: featureprop_pub featureprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featureprop_pub ALTER COLUMN featureprop_pub_id SET DEFAULT nextval('chado.featureprop_pub_featureprop_pub_id_seq'::regclass);


--
-- Name: featurerange featurerange_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.featurerange ALTER COLUMN featurerange_id SET DEFAULT nextval('chado.featurerange_featurerange_id_seq'::regclass);


--
-- Name: genotype genotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.genotype ALTER COLUMN genotype_id SET DEFAULT nextval('chado.genotype_genotype_id_seq'::regclass);


--
-- Name: genotypeprop genotypeprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.genotypeprop ALTER COLUMN genotypeprop_id SET DEFAULT nextval('chado.genotypeprop_genotypeprop_id_seq'::regclass);


--
-- Name: library library_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library ALTER COLUMN library_id SET DEFAULT nextval('chado.library_library_id_seq'::regclass);


--
-- Name: library_contact library_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_contact ALTER COLUMN library_contact_id SET DEFAULT nextval('chado.library_contact_library_contact_id_seq'::regclass);


--
-- Name: library_cvterm library_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_cvterm ALTER COLUMN library_cvterm_id SET DEFAULT nextval('chado.library_cvterm_library_cvterm_id_seq'::regclass);


--
-- Name: library_dbxref library_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_dbxref ALTER COLUMN library_dbxref_id SET DEFAULT nextval('chado.library_dbxref_library_dbxref_id_seq'::regclass);


--
-- Name: library_expression library_expression_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_expression ALTER COLUMN library_expression_id SET DEFAULT nextval('chado.library_expression_library_expression_id_seq'::regclass);


--
-- Name: library_expressionprop library_expressionprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_expressionprop ALTER COLUMN library_expressionprop_id SET DEFAULT nextval('chado.library_expressionprop_library_expressionprop_id_seq'::regclass);


--
-- Name: library_feature library_feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_feature ALTER COLUMN library_feature_id SET DEFAULT nextval('chado.library_feature_library_feature_id_seq'::regclass);


--
-- Name: library_featureprop library_featureprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_featureprop ALTER COLUMN library_featureprop_id SET DEFAULT nextval('chado.library_featureprop_library_featureprop_id_seq'::regclass);


--
-- Name: library_pub library_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_pub ALTER COLUMN library_pub_id SET DEFAULT nextval('chado.library_pub_library_pub_id_seq'::regclass);


--
-- Name: library_relationship library_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_relationship ALTER COLUMN library_relationship_id SET DEFAULT nextval('chado.library_relationship_library_relationship_id_seq'::regclass);


--
-- Name: library_relationship_pub library_relationship_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_relationship_pub ALTER COLUMN library_relationship_pub_id SET DEFAULT nextval('chado.library_relationship_pub_library_relationship_pub_id_seq'::regclass);


--
-- Name: library_synonym library_synonym_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.library_synonym ALTER COLUMN library_synonym_id SET DEFAULT nextval('chado.library_synonym_library_synonym_id_seq'::regclass);


--
-- Name: libraryprop libraryprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.libraryprop ALTER COLUMN libraryprop_id SET DEFAULT nextval('chado.libraryprop_libraryprop_id_seq'::regclass);


--
-- Name: libraryprop_pub libraryprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.libraryprop_pub ALTER COLUMN libraryprop_pub_id SET DEFAULT nextval('chado.libraryprop_pub_libraryprop_pub_id_seq'::regclass);


--
-- Name: magedocumentation magedocumentation_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.magedocumentation ALTER COLUMN magedocumentation_id SET DEFAULT nextval('chado.magedocumentation_magedocumentation_id_seq'::regclass);


--
-- Name: mageml mageml_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.mageml ALTER COLUMN mageml_id SET DEFAULT nextval('chado.mageml_mageml_id_seq'::regclass);


--
-- Name: materialized_view materialized_view_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.materialized_view ALTER COLUMN materialized_view_id SET DEFAULT nextval('chado.materialized_view_materialized_view_id_seq'::regclass);


--
-- Name: nd_experiment nd_experiment_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment ALTER COLUMN nd_experiment_id SET DEFAULT nextval('chado.nd_experiment_nd_experiment_id_seq'::regclass);


--
-- Name: nd_experiment_analysis nd_experiment_analysis_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_analysis ALTER COLUMN nd_experiment_analysis_id SET DEFAULT nextval('chado.nd_experiment_analysis_nd_experiment_analysis_id_seq'::regclass);


--
-- Name: nd_experiment_contact nd_experiment_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_contact ALTER COLUMN nd_experiment_contact_id SET DEFAULT nextval('chado.nd_experiment_contact_nd_experiment_contact_id_seq'::regclass);


--
-- Name: nd_experiment_dbxref nd_experiment_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_dbxref ALTER COLUMN nd_experiment_dbxref_id SET DEFAULT nextval('chado.nd_experiment_dbxref_nd_experiment_dbxref_id_seq'::regclass);


--
-- Name: nd_experiment_genotype nd_experiment_genotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_genotype ALTER COLUMN nd_experiment_genotype_id SET DEFAULT nextval('chado.nd_experiment_genotype_nd_experiment_genotype_id_seq'::regclass);


--
-- Name: nd_experiment_phenotype nd_experiment_phenotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_phenotype ALTER COLUMN nd_experiment_phenotype_id SET DEFAULT nextval('chado.nd_experiment_phenotype_nd_experiment_phenotype_id_seq'::regclass);


--
-- Name: nd_experiment_project nd_experiment_project_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_project ALTER COLUMN nd_experiment_project_id SET DEFAULT nextval('chado.nd_experiment_project_nd_experiment_project_id_seq'::regclass);


--
-- Name: nd_experiment_protocol nd_experiment_protocol_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_protocol ALTER COLUMN nd_experiment_protocol_id SET DEFAULT nextval('chado.nd_experiment_protocol_nd_experiment_protocol_id_seq'::regclass);


--
-- Name: nd_experiment_pub nd_experiment_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_pub ALTER COLUMN nd_experiment_pub_id SET DEFAULT nextval('chado.nd_experiment_pub_nd_experiment_pub_id_seq'::regclass);


--
-- Name: nd_experiment_stock nd_experiment_stock_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_stock ALTER COLUMN nd_experiment_stock_id SET DEFAULT nextval('chado.nd_experiment_stock_nd_experiment_stock_id_seq'::regclass);


--
-- Name: nd_experiment_stock_dbxref nd_experiment_stock_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_stock_dbxref ALTER COLUMN nd_experiment_stock_dbxref_id SET DEFAULT nextval('chado.nd_experiment_stock_dbxref_nd_experiment_stock_dbxref_id_seq'::regclass);


--
-- Name: nd_experiment_stockprop nd_experiment_stockprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experiment_stockprop ALTER COLUMN nd_experiment_stockprop_id SET DEFAULT nextval('chado.nd_experiment_stockprop_nd_experiment_stockprop_id_seq'::regclass);


--
-- Name: nd_experimentprop nd_experimentprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_experimentprop ALTER COLUMN nd_experimentprop_id SET DEFAULT nextval('chado.nd_experimentprop_nd_experimentprop_id_seq'::regclass);


--
-- Name: nd_geolocation nd_geolocation_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_geolocation ALTER COLUMN nd_geolocation_id SET DEFAULT nextval('chado.nd_geolocation_nd_geolocation_id_seq'::regclass);


--
-- Name: nd_geolocationprop nd_geolocationprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_geolocationprop ALTER COLUMN nd_geolocationprop_id SET DEFAULT nextval('chado.nd_geolocationprop_nd_geolocationprop_id_seq'::regclass);


--
-- Name: nd_protocol nd_protocol_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_protocol ALTER COLUMN nd_protocol_id SET DEFAULT nextval('chado.nd_protocol_nd_protocol_id_seq'::regclass);


--
-- Name: nd_protocol_reagent nd_protocol_reagent_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_protocol_reagent ALTER COLUMN nd_protocol_reagent_id SET DEFAULT nextval('chado.nd_protocol_reagent_nd_protocol_reagent_id_seq'::regclass);


--
-- Name: nd_protocolprop nd_protocolprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_protocolprop ALTER COLUMN nd_protocolprop_id SET DEFAULT nextval('chado.nd_protocolprop_nd_protocolprop_id_seq'::regclass);


--
-- Name: nd_reagent nd_reagent_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_reagent ALTER COLUMN nd_reagent_id SET DEFAULT nextval('chado.nd_reagent_nd_reagent_id_seq'::regclass);


--
-- Name: nd_reagent_relationship nd_reagent_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_reagent_relationship ALTER COLUMN nd_reagent_relationship_id SET DEFAULT nextval('chado.nd_reagent_relationship_nd_reagent_relationship_id_seq'::regclass);


--
-- Name: nd_reagentprop nd_reagentprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.nd_reagentprop ALTER COLUMN nd_reagentprop_id SET DEFAULT nextval('chado.nd_reagentprop_nd_reagentprop_id_seq'::regclass);


--
-- Name: organism organism_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism ALTER COLUMN organism_id SET DEFAULT nextval('chado.organism_organism_id_seq'::regclass);


--
-- Name: organism_cvterm organism_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism_cvterm ALTER COLUMN organism_cvterm_id SET DEFAULT nextval('chado.organism_cvterm_organism_cvterm_id_seq'::regclass);


--
-- Name: organism_cvtermprop organism_cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism_cvtermprop ALTER COLUMN organism_cvtermprop_id SET DEFAULT nextval('chado.organism_cvtermprop_organism_cvtermprop_id_seq'::regclass);


--
-- Name: organism_dbxref organism_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism_dbxref ALTER COLUMN organism_dbxref_id SET DEFAULT nextval('chado.organism_dbxref_organism_dbxref_id_seq'::regclass);


--
-- Name: organism_pub organism_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism_pub ALTER COLUMN organism_pub_id SET DEFAULT nextval('chado.organism_pub_organism_pub_id_seq'::regclass);


--
-- Name: organism_relationship organism_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organism_relationship ALTER COLUMN organism_relationship_id SET DEFAULT nextval('chado.organism_relationship_organism_relationship_id_seq'::regclass);


--
-- Name: organismprop organismprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organismprop ALTER COLUMN organismprop_id SET DEFAULT nextval('chado.organismprop_organismprop_id_seq'::regclass);


--
-- Name: organismprop_pub organismprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.organismprop_pub ALTER COLUMN organismprop_pub_id SET DEFAULT nextval('chado.organismprop_pub_organismprop_pub_id_seq'::regclass);


--
-- Name: phendesc phendesc_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phendesc ALTER COLUMN phendesc_id SET DEFAULT nextval('chado.phendesc_phendesc_id_seq'::regclass);


--
-- Name: phenotype phenotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenotype ALTER COLUMN phenotype_id SET DEFAULT nextval('chado.phenotype_phenotype_id_seq'::regclass);


--
-- Name: phenotype_comparison phenotype_comparison_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenotype_comparison ALTER COLUMN phenotype_comparison_id SET DEFAULT nextval('chado.phenotype_comparison_phenotype_comparison_id_seq'::regclass);


--
-- Name: phenotype_comparison_cvterm phenotype_comparison_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenotype_comparison_cvterm ALTER COLUMN phenotype_comparison_cvterm_id SET DEFAULT nextval('chado.phenotype_comparison_cvterm_phenotype_comparison_cvterm_id_seq'::regclass);


--
-- Name: phenotype_cvterm phenotype_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenotype_cvterm ALTER COLUMN phenotype_cvterm_id SET DEFAULT nextval('chado.phenotype_cvterm_phenotype_cvterm_id_seq'::regclass);


--
-- Name: phenotypeprop phenotypeprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenotypeprop ALTER COLUMN phenotypeprop_id SET DEFAULT nextval('chado.phenotypeprop_phenotypeprop_id_seq'::regclass);


--
-- Name: phenstatement phenstatement_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phenstatement ALTER COLUMN phenstatement_id SET DEFAULT nextval('chado.phenstatement_phenstatement_id_seq'::regclass);


--
-- Name: phylonode phylonode_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonode ALTER COLUMN phylonode_id SET DEFAULT nextval('chado.phylonode_phylonode_id_seq'::regclass);


--
-- Name: phylonode_dbxref phylonode_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonode_dbxref ALTER COLUMN phylonode_dbxref_id SET DEFAULT nextval('chado.phylonode_dbxref_phylonode_dbxref_id_seq'::regclass);


--
-- Name: phylonode_organism phylonode_organism_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonode_organism ALTER COLUMN phylonode_organism_id SET DEFAULT nextval('chado.phylonode_organism_phylonode_organism_id_seq'::regclass);


--
-- Name: phylonode_pub phylonode_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonode_pub ALTER COLUMN phylonode_pub_id SET DEFAULT nextval('chado.phylonode_pub_phylonode_pub_id_seq'::regclass);


--
-- Name: phylonode_relationship phylonode_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonode_relationship ALTER COLUMN phylonode_relationship_id SET DEFAULT nextval('chado.phylonode_relationship_phylonode_relationship_id_seq'::regclass);


--
-- Name: phylonodeprop phylonodeprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylonodeprop ALTER COLUMN phylonodeprop_id SET DEFAULT nextval('chado.phylonodeprop_phylonodeprop_id_seq'::regclass);


--
-- Name: phylotree phylotree_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylotree ALTER COLUMN phylotree_id SET DEFAULT nextval('chado.phylotree_phylotree_id_seq'::regclass);


--
-- Name: phylotree_pub phylotree_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylotree_pub ALTER COLUMN phylotree_pub_id SET DEFAULT nextval('chado.phylotree_pub_phylotree_pub_id_seq'::regclass);


--
-- Name: phylotreeprop phylotreeprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.phylotreeprop ALTER COLUMN phylotreeprop_id SET DEFAULT nextval('chado.phylotreeprop_phylotreeprop_id_seq'::regclass);


--
-- Name: project project_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project ALTER COLUMN project_id SET DEFAULT nextval('chado.project_project_id_seq'::regclass);


--
-- Name: project_analysis project_analysis_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_analysis ALTER COLUMN project_analysis_id SET DEFAULT nextval('chado.project_analysis_project_analysis_id_seq'::regclass);


--
-- Name: project_contact project_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_contact ALTER COLUMN project_contact_id SET DEFAULT nextval('chado.project_contact_project_contact_id_seq'::regclass);


--
-- Name: project_dbxref project_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_dbxref ALTER COLUMN project_dbxref_id SET DEFAULT nextval('chado.project_dbxref_project_dbxref_id_seq'::regclass);


--
-- Name: project_feature project_feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_feature ALTER COLUMN project_feature_id SET DEFAULT nextval('chado.project_feature_project_feature_id_seq'::regclass);


--
-- Name: project_pub project_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_pub ALTER COLUMN project_pub_id SET DEFAULT nextval('chado.project_pub_project_pub_id_seq'::regclass);


--
-- Name: project_relationship project_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_relationship ALTER COLUMN project_relationship_id SET DEFAULT nextval('chado.project_relationship_project_relationship_id_seq'::regclass);


--
-- Name: project_stock project_stock_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.project_stock ALTER COLUMN project_stock_id SET DEFAULT nextval('chado.project_stock_project_stock_id_seq'::regclass);


--
-- Name: projectprop projectprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.projectprop ALTER COLUMN projectprop_id SET DEFAULT nextval('chado.projectprop_projectprop_id_seq'::regclass);


--
-- Name: protocol protocol_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.protocol ALTER COLUMN protocol_id SET DEFAULT nextval('chado.protocol_protocol_id_seq'::regclass);


--
-- Name: protocolparam protocolparam_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.protocolparam ALTER COLUMN protocolparam_id SET DEFAULT nextval('chado.protocolparam_protocolparam_id_seq'::regclass);


--
-- Name: pub pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pub ALTER COLUMN pub_id SET DEFAULT nextval('chado.pub_pub_id_seq'::regclass);


--
-- Name: pub_dbxref pub_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pub_dbxref ALTER COLUMN pub_dbxref_id SET DEFAULT nextval('chado.pub_dbxref_pub_dbxref_id_seq'::regclass);


--
-- Name: pub_relationship pub_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pub_relationship ALTER COLUMN pub_relationship_id SET DEFAULT nextval('chado.pub_relationship_pub_relationship_id_seq'::regclass);


--
-- Name: pubauthor pubauthor_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pubauthor ALTER COLUMN pubauthor_id SET DEFAULT nextval('chado.pubauthor_pubauthor_id_seq'::regclass);


--
-- Name: pubauthor_contact pubauthor_contact_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pubauthor_contact ALTER COLUMN pubauthor_contact_id SET DEFAULT nextval('chado.pubauthor_contact_pubauthor_contact_id_seq'::regclass);


--
-- Name: pubprop pubprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.pubprop ALTER COLUMN pubprop_id SET DEFAULT nextval('chado.pubprop_pubprop_id_seq'::regclass);


--
-- Name: quantification quantification_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.quantification ALTER COLUMN quantification_id SET DEFAULT nextval('chado.quantification_quantification_id_seq'::regclass);


--
-- Name: quantification_relationship quantification_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.quantification_relationship ALTER COLUMN quantification_relationship_id SET DEFAULT nextval('chado.quantification_relationship_quantification_relationship_id_seq'::regclass);


--
-- Name: quantificationprop quantificationprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.quantificationprop ALTER COLUMN quantificationprop_id SET DEFAULT nextval('chado.quantificationprop_quantificationprop_id_seq'::regclass);


--
-- Name: stock stock_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock ALTER COLUMN stock_id SET DEFAULT nextval('chado.stock_stock_id_seq'::regclass);


--
-- Name: stock_cvterm stock_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_cvterm ALTER COLUMN stock_cvterm_id SET DEFAULT nextval('chado.stock_cvterm_stock_cvterm_id_seq'::regclass);


--
-- Name: stock_cvtermprop stock_cvtermprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_cvtermprop ALTER COLUMN stock_cvtermprop_id SET DEFAULT nextval('chado.stock_cvtermprop_stock_cvtermprop_id_seq'::regclass);


--
-- Name: stock_dbxref stock_dbxref_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_dbxref ALTER COLUMN stock_dbxref_id SET DEFAULT nextval('chado.stock_dbxref_stock_dbxref_id_seq'::regclass);


--
-- Name: stock_dbxrefprop stock_dbxrefprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_dbxrefprop ALTER COLUMN stock_dbxrefprop_id SET DEFAULT nextval('chado.stock_dbxrefprop_stock_dbxrefprop_id_seq'::regclass);


--
-- Name: stock_feature stock_feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_feature ALTER COLUMN stock_feature_id SET DEFAULT nextval('chado.stock_feature_stock_feature_id_seq'::regclass);


--
-- Name: stock_featuremap stock_featuremap_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_featuremap ALTER COLUMN stock_featuremap_id SET DEFAULT nextval('chado.stock_featuremap_stock_featuremap_id_seq'::regclass);


--
-- Name: stock_genotype stock_genotype_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_genotype ALTER COLUMN stock_genotype_id SET DEFAULT nextval('chado.stock_genotype_stock_genotype_id_seq'::regclass);


--
-- Name: stock_library stock_library_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_library ALTER COLUMN stock_library_id SET DEFAULT nextval('chado.stock_library_stock_library_id_seq'::regclass);


--
-- Name: stock_pub stock_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_pub ALTER COLUMN stock_pub_id SET DEFAULT nextval('chado.stock_pub_stock_pub_id_seq'::regclass);


--
-- Name: stock_relationship stock_relationship_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_relationship ALTER COLUMN stock_relationship_id SET DEFAULT nextval('chado.stock_relationship_stock_relationship_id_seq'::regclass);


--
-- Name: stock_relationship_cvterm stock_relationship_cvterm_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_relationship_cvterm ALTER COLUMN stock_relationship_cvterm_id SET DEFAULT nextval('chado.stock_relationship_cvterm_stock_relationship_cvterm_id_seq'::regclass);


--
-- Name: stock_relationship_pub stock_relationship_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stock_relationship_pub ALTER COLUMN stock_relationship_pub_id SET DEFAULT nextval('chado.stock_relationship_pub_stock_relationship_pub_id_seq'::regclass);


--
-- Name: stockcollection stockcollection_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockcollection ALTER COLUMN stockcollection_id SET DEFAULT nextval('chado.stockcollection_stockcollection_id_seq'::regclass);


--
-- Name: stockcollection_db stockcollection_db_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockcollection_db ALTER COLUMN stockcollection_db_id SET DEFAULT nextval('chado.stockcollection_db_stockcollection_db_id_seq'::regclass);


--
-- Name: stockcollection_stock stockcollection_stock_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockcollection_stock ALTER COLUMN stockcollection_stock_id SET DEFAULT nextval('chado.stockcollection_stock_stockcollection_stock_id_seq'::regclass);


--
-- Name: stockcollectionprop stockcollectionprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockcollectionprop ALTER COLUMN stockcollectionprop_id SET DEFAULT nextval('chado.stockcollectionprop_stockcollectionprop_id_seq'::regclass);


--
-- Name: stockprop stockprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockprop ALTER COLUMN stockprop_id SET DEFAULT nextval('chado.stockprop_stockprop_id_seq'::regclass);


--
-- Name: stockprop_pub stockprop_pub_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.stockprop_pub ALTER COLUMN stockprop_pub_id SET DEFAULT nextval('chado.stockprop_pub_stockprop_pub_id_seq'::regclass);


--
-- Name: study study_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.study ALTER COLUMN study_id SET DEFAULT nextval('chado.study_study_id_seq'::regclass);


--
-- Name: study_assay study_assay_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.study_assay ALTER COLUMN study_assay_id SET DEFAULT nextval('chado.study_assay_study_assay_id_seq'::regclass);


--
-- Name: studydesign studydesign_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studydesign ALTER COLUMN studydesign_id SET DEFAULT nextval('chado.studydesign_studydesign_id_seq'::regclass);


--
-- Name: studydesignprop studydesignprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studydesignprop ALTER COLUMN studydesignprop_id SET DEFAULT nextval('chado.studydesignprop_studydesignprop_id_seq'::regclass);


--
-- Name: studyfactor studyfactor_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studyfactor ALTER COLUMN studyfactor_id SET DEFAULT nextval('chado.studyfactor_studyfactor_id_seq'::regclass);


--
-- Name: studyfactorvalue studyfactorvalue_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studyfactorvalue ALTER COLUMN studyfactorvalue_id SET DEFAULT nextval('chado.studyfactorvalue_studyfactorvalue_id_seq'::regclass);


--
-- Name: studyprop studyprop_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studyprop ALTER COLUMN studyprop_id SET DEFAULT nextval('chado.studyprop_studyprop_id_seq'::regclass);


--
-- Name: studyprop_feature studyprop_feature_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.studyprop_feature ALTER COLUMN studyprop_feature_id SET DEFAULT nextval('chado.studyprop_feature_studyprop_feature_id_seq'::regclass);


--
-- Name: synonym synonym_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.synonym ALTER COLUMN synonym_id SET DEFAULT nextval('chado.synonym_synonym_id_seq'::regclass);


--
-- Name: tableinfo tableinfo_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.tableinfo ALTER COLUMN tableinfo_id SET DEFAULT nextval('chado.tableinfo_tableinfo_id_seq'::regclass);


--
-- Name: treatment treatment_id; Type: DEFAULT; Schema: chado; Owner: drupaladmin
--

ALTER TABLE ONLY chado.treatment ALTER COLUMN treatment_id SET DEFAULT nextval('chado.treatment_treatment_id_seq'::regclass);


--
-- Data for Name: acquisition; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.acquisition (acquisition_id, assay_id, protocol_id, channel_id, acquisitiondate, name, uri) FROM stdin;
\.


--
-- Data for Name: acquisition_relationship; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.acquisition_relationship (acquisition_relationship_id, subject_id, type_id, object_id, value, rank) FROM stdin;
\.


--
-- Data for Name: acquisitionprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.acquisitionprop (acquisitionprop_id, acquisition_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: analysis; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis (analysis_id, name, description, program, programversion, algorithm, sourcename, sourceversion, sourceuri, timeexecuted) FROM stdin;
1	Annotation of Tripalus databasica subspecies chadoii	Forgive me, hero. Please, help me out.\r\n\r\nI know your efforts were a big driving force in pushing back the enemy, but I'm afraid I must ask even more of you now. It's true, the enemy is on the run, but we'd be fools to let them run and regroup. Hero, I need you to do the dirty work. Seek them out and get rid of those cruel low lives. I'll join you, if you'll have me. It'll be my pleasure. \r\n\r\nBe wary hero, they're stronger than they look those low lives. You can take out as many of them as you like, the less of those low lives there are in this world, the better. I will be able to reward you greatly, should you return successfully. Make haste hero, but tread carefully.	figmentOfImagination	-200	\N	The Ether	infinity		2023-12-15 22:11:11.136186
2	Sequence Assembly of Tripalus databasica subspecies chadoii	Pardon me, traveler. I'm glad you're here.\r\n\r\nThere's a magnificent old creature which roams our lands. It's an elephant, older than almost all of us, but unfortunately its age is taking its toll. The predators are no longer afraid to attack it, more and more scars show up on its skin each day. Normally we'd let nature run its course, but this elephant is special, it means a lot to us. Hero, could you please try to lead the elephant towards our town, we have a build a sanctuary for it, so it can live out its final days in peace.\r\n\r\nI'm afraid there's not much I can reward you with, but I think I can still make it worth your troubles.	figmentOfImagination	-200	\N	The depths of imagination	infinity		2023-12-15 22:12:44.695562
3	Prank of the Spiders	Excuse me, adventurer. Your help would be much appreciated.\r\n\r\nI want to pull a prank on my sister and I have the best idea to do so. You see, she's scared of spiders, so I want to put some spiders in her bed. Hahaha, I can't wait to see her face when she discovers them. Anyway, I need you to collect some spiders for me. Put them in this jar, I don't want to have to touch them, they're cree.. I mean, they might get away if they're not in a jar.\r\n\r\nI don't have something amazing to reward you with, but I'll still be able to reward you with somethind decent.	quest	1	generator	sister who is scared of spiders	younger		2023-12-15 22:27:38.850761
4	Collection of the Relics	Excuse me, champion. Would you lend me your aid.\r\n\r\nA storm has destroyed part of our museum, a terrible tragedy. All of those relics, covered in rubble once again or worse, they might be destroyed. We're still working on clearing the rubble, but it's taking too long, those relics have to be recovered before they destroyed forever. Please, hero, find as many relics as you can, but be careful! There's a lot of loose rubble, don't get caught by surprise.\r\n\r\nI will be able to reward you greatly, if you decide to help me of course.	quest	1	generator	destroyed museum tragedy	recent		2023-12-15 22:28:50.521141
5	Saviour of the Forest Creatures	Please excuse me, champion. Your help would be much apprecited.\r\n\r\nA disease is plaguing the critters of our forest, it's horrible. Fortunately I think I can find a cure, but I will need some of those critters to study them and try out the cure. Hero, take these traps, set them out in the forest and wait for them to trap a creature. Bring me back about 6 critters, it doesn't matter what kind. Just be careful of other creatures which might get stuck in the traps as well, they might not be as friendly.\r\n\r\nIt pains me to say I won't be able to reward you with a lot, but I'll do my best to make it worth your while.	quest	1	generator	sick forest creatures	healing		2023-12-15 22:30:46.437246
6	Sequence Assembly of Gramen griseo subphylum populus	Forgive me, hero. I hope you could help me out.\r\n\r\nI love the feeling of moss beneath my feet, it's probably the greatest feeling ever. Now, I've come up with a plan which will cover the floors of my house in moss, so I can always experience the greatest feeling ever. The best moss grows in darkwood forest to the South, but I'm too scared to go in there and get the moss myself. It's so dark and creepy in there. Could you gather the moss for me?\r\n\r\nI don't have something amazing to reward you with, but I'll still be able to reward you with something decent.	mosswood	infinity	\N	Gramen griseo subphylum populus	unknown		2023-12-16 00:19:15.155019
7	Annotation of Gramen griseo subphylum populus	Forgive me, champion. Please, help me out.\r\n\r\nThis old treasure map has been handed down from generation to generation and now it is mine. I decided to figure out where it leads to, but I'm a little lost now. The treasure should be around here, but I can't figure out the last part of this map. Mind helping me out with this?\r\n\r\nIf you decide to help me I will repay you handsomely, it'll be worth your troubles.	treasure map	1	\N	treasure map	1		2023-12-16 00:31:52.113037
\.


--
-- Data for Name: analysis_cvterm; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis_cvterm (analysis_cvterm_id, analysis_id, cvterm_id, is_not, rank) FROM stdin;
\.


--
-- Data for Name: analysis_dbxref; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis_dbxref (analysis_dbxref_id, analysis_id, dbxref_id, is_current) FROM stdin;
\.


--
-- Data for Name: analysis_organism; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis_organism (analysis_id, organism_id) FROM stdin;
\.


--
-- Data for Name: analysis_pub; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis_pub (analysis_pub_id, analysis_id, pub_id) FROM stdin;
\.


--
-- Data for Name: analysis_relationship; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysis_relationship (analysis_relationship_id, subject_id, object_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: analysisfeature; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysisfeature (analysisfeature_id, feature_id, analysis_id, rawscore, normscore, significance, identity) FROM stdin;
1	2	1	\N	\N	\N	\N
2	3	1	\N	\N	\N	\N
3	4	1	\N	\N	\N	\N
4	5	1	\N	\N	\N	\N
5	6	1	\N	\N	\N	\N
6	7	1	\N	\N	\N	\N
7	8	1	\N	\N	\N	\N
8	9	1	\N	\N	\N	\N
9	10	1	\N	\N	\N	\N
10	11	1	\N	\N	\N	\N
11	12	1	\N	\N	\N	\N
12	13	1	\N	\N	\N	\N
13	14	1	\N	\N	\N	\N
14	15	1	\N	\N	\N	\N
15	16	1	\N	\N	\N	\N
16	17	1	\N	\N	\N	\N
17	18	1	\N	\N	\N	\N
18	19	1	\N	\N	\N	\N
19	20	1	\N	\N	\N	\N
20	21	1	\N	\N	\N	\N
21	22	1	\N	\N	\N	\N
22	23	1	\N	\N	\N	\N
23	24	1	\N	\N	\N	\N
24	25	1	\N	\N	\N	\N
25	26	1	\N	\N	\N	\N
26	27	1	\N	\N	\N	\N
27	28	1	\N	\N	\N	\N
28	29	1	\N	\N	\N	\N
29	30	1	\N	\N	\N	\N
30	31	1	\N	\N	\N	\N
31	32	1	\N	\N	\N	\N
32	33	1	\N	\N	\N	\N
33	34	1	\N	\N	\N	\N
34	35	1	\N	\N	\N	\N
35	36	1	\N	\N	\N	\N
36	37	1	\N	\N	\N	\N
37	38	1	\N	\N	\N	\N
38	39	1	\N	\N	\N	\N
39	40	1	\N	\N	\N	\N
40	41	1	\N	\N	\N	\N
41	42	1	\N	\N	\N	\N
42	43	1	\N	\N	\N	\N
43	44	1	\N	\N	\N	\N
44	45	1	\N	\N	\N	\N
45	46	1	\N	\N	\N	\N
46	47	1	\N	\N	\N	\N
47	48	1	\N	\N	\N	\N
48	49	1	\N	\N	\N	\N
49	50	1	\N	\N	\N	\N
50	51	1	\N	\N	\N	\N
51	52	1	\N	\N	\N	\N
52	53	1	\N	\N	\N	\N
53	54	1	\N	\N	\N	\N
54	55	1	\N	\N	\N	\N
55	56	1	\N	\N	\N	\N
56	57	1	\N	\N	\N	\N
57	58	1	\N	\N	\N	\N
58	59	1	\N	\N	\N	\N
59	60	1	\N	\N	\N	\N
60	61	1	\N	\N	\N	\N
61	62	1	\N	\N	\N	\N
62	63	1	\N	\N	\N	\N
63	64	1	\N	\N	\N	\N
64	65	1	\N	\N	\N	\N
65	66	1	\N	\N	\N	\N
66	67	1	\N	\N	\N	\N
67	68	1	\N	\N	\N	\N
68	69	1	\N	\N	\N	\N
69	70	1	\N	\N	\N	\N
70	71	1	\N	\N	\N	\N
71	72	1	\N	\N	\N	\N
72	73	1	\N	\N	\N	\N
73	74	1	\N	\N	\N	\N
74	75	1	\N	\N	\N	\N
75	76	1	\N	\N	\N	\N
76	77	1	\N	\N	\N	\N
77	78	1	\N	\N	\N	\N
78	79	1	\N	\N	\N	\N
79	80	1	\N	\N	\N	\N
80	81	1	\N	\N	\N	\N
81	82	1	\N	\N	\N	\N
82	83	1	\N	\N	\N	\N
83	84	1	\N	\N	\N	\N
84	85	1	\N	\N	\N	\N
85	86	1	\N	\N	\N	\N
86	87	1	\N	\N	\N	\N
87	88	1	\N	\N	\N	\N
88	89	1	\N	\N	\N	\N
89	90	1	\N	\N	\N	\N
90	91	1	\N	\N	\N	\N
91	92	1	\N	\N	\N	\N
92	93	1	\N	\N	\N	\N
93	94	1	\N	\N	\N	\N
94	95	1	\N	\N	\N	\N
95	96	1	\N	\N	\N	\N
96	97	1	\N	\N	\N	\N
97	98	1	\N	\N	\N	\N
98	99	1	\N	\N	\N	\N
99	100	1	\N	\N	\N	\N
100	101	1	\N	\N	\N	\N
101	102	1	\N	\N	\N	\N
102	103	1	\N	\N	\N	\N
103	104	1	\N	\N	\N	\N
104	105	1	\N	\N	\N	\N
105	106	1	\N	\N	\N	\N
106	107	1	\N	\N	\N	\N
107	108	1	\N	\N	\N	\N
108	109	1	\N	\N	\N	\N
109	110	1	\N	\N	\N	\N
110	111	1	\N	\N	\N	\N
111	112	1	\N	\N	\N	\N
112	113	1	\N	\N	\N	\N
113	114	1	\N	\N	\N	\N
114	115	1	\N	\N	\N	\N
115	116	1	\N	\N	\N	\N
116	117	1	\N	\N	\N	\N
117	118	1	\N	\N	\N	\N
118	119	1	\N	\N	\N	\N
119	120	1	\N	\N	\N	\N
120	121	1	\N	\N	\N	\N
121	122	1	\N	\N	\N	\N
122	123	1	\N	\N	\N	\N
123	124	1	\N	\N	\N	\N
124	125	1	\N	\N	\N	\N
125	126	1	\N	\N	\N	\N
126	127	1	\N	\N	\N	\N
127	128	1	\N	\N	\N	\N
128	129	1	\N	\N	\N	\N
129	130	1	\N	\N	\N	\N
130	131	1	\N	\N	\N	\N
131	132	1	\N	\N	\N	\N
132	133	1	\N	\N	\N	\N
133	134	1	\N	\N	\N	\N
134	135	1	\N	\N	\N	\N
135	136	1	\N	\N	\N	\N
136	137	1	\N	\N	\N	\N
137	138	1	\N	\N	\N	\N
138	139	1	\N	\N	\N	\N
139	140	1	\N	\N	\N	\N
140	141	1	\N	\N	\N	\N
141	142	1	\N	\N	\N	\N
142	143	1	\N	\N	\N	\N
143	144	1	\N	\N	\N	\N
144	145	1	\N	\N	\N	\N
145	146	1	\N	\N	\N	\N
146	147	1	\N	\N	\N	\N
147	148	1	\N	\N	\N	\N
148	149	1	\N	\N	\N	\N
149	150	1	\N	\N	\N	\N
150	151	1	\N	\N	\N	\N
151	152	1	\N	\N	\N	\N
152	153	1	\N	\N	\N	\N
153	154	1	\N	\N	\N	\N
154	155	1	\N	\N	\N	\N
155	156	1	\N	\N	\N	\N
156	157	1	\N	\N	\N	\N
157	158	1	\N	\N	\N	\N
158	159	1	\N	\N	\N	\N
159	160	1	\N	\N	\N	\N
160	161	1	\N	\N	\N	\N
161	162	1	\N	\N	\N	\N
162	163	1	\N	\N	\N	\N
163	164	1	\N	\N	\N	\N
164	165	1	\N	\N	\N	\N
165	166	1	\N	\N	\N	\N
166	167	1	\N	\N	\N	\N
167	168	1	\N	\N	\N	\N
168	169	1	\N	\N	\N	\N
169	170	1	\N	\N	\N	\N
170	171	1	\N	\N	\N	\N
171	172	1	\N	\N	\N	\N
172	173	1	\N	\N	\N	\N
173	174	1	\N	\N	\N	\N
174	175	1	\N	\N	\N	\N
175	176	1	\N	\N	\N	\N
176	177	1	\N	\N	\N	\N
177	178	1	\N	\N	\N	\N
178	179	1	\N	\N	\N	\N
179	180	1	\N	\N	\N	\N
180	181	1	\N	\N	\N	\N
181	182	1	\N	\N	\N	\N
182	183	1	\N	\N	\N	\N
183	184	1	\N	\N	\N	\N
184	185	1	\N	\N	\N	\N
185	186	1	\N	\N	\N	\N
186	187	1	\N	\N	\N	\N
187	188	1	\N	\N	\N	\N
188	189	1	\N	\N	\N	\N
189	190	1	\N	\N	\N	\N
190	191	1	\N	\N	\N	\N
191	192	1	\N	\N	\N	\N
192	193	1	\N	\N	\N	\N
193	194	1	\N	\N	\N	\N
194	195	1	\N	\N	\N	\N
195	196	1	\N	\N	\N	\N
196	197	1	\N	\N	\N	\N
197	198	1	\N	\N	\N	\N
198	199	1	\N	\N	\N	\N
199	200	1	\N	\N	\N	\N
200	201	1	\N	\N	\N	\N
201	202	1	\N	\N	\N	\N
202	203	1	\N	\N	\N	\N
203	204	1	\N	\N	\N	\N
204	205	1	\N	\N	\N	\N
205	206	1	\N	\N	\N	\N
206	207	1	\N	\N	\N	\N
207	208	1	\N	\N	\N	\N
208	209	1	\N	\N	\N	\N
209	210	1	\N	\N	\N	\N
210	211	1	\N	\N	\N	\N
211	212	1	\N	\N	\N	\N
212	213	1	\N	\N	\N	\N
213	214	1	\N	\N	\N	\N
214	215	1	\N	\N	\N	\N
215	216	1	\N	\N	\N	\N
216	217	1	\N	\N	\N	\N
217	218	1	\N	\N	\N	\N
218	219	1	\N	\N	\N	\N
219	220	1	\N	\N	\N	\N
220	221	1	\N	\N	\N	\N
221	222	1	\N	\N	\N	\N
222	223	1	\N	\N	\N	\N
223	224	1	\N	\N	\N	\N
224	225	1	\N	\N	\N	\N
225	226	1	\N	\N	\N	\N
226	227	1	\N	\N	\N	\N
227	228	1	\N	\N	\N	\N
228	229	1	\N	\N	\N	\N
229	230	1	\N	\N	\N	\N
230	231	1	\N	\N	\N	\N
231	232	1	\N	\N	\N	\N
232	233	1	\N	\N	\N	\N
233	234	1	\N	\N	\N	\N
234	235	1	\N	\N	\N	\N
235	236	1	\N	\N	\N	\N
236	237	1	\N	\N	\N	\N
237	238	1	\N	\N	\N	\N
238	239	1	\N	\N	\N	\N
239	240	1	\N	\N	\N	\N
240	241	1	\N	\N	\N	\N
241	242	1	\N	\N	\N	\N
242	243	1	\N	\N	\N	\N
243	244	1	\N	\N	\N	\N
244	245	1	\N	\N	\N	\N
245	246	1	\N	\N	\N	\N
246	247	1	\N	\N	\N	\N
247	248	1	\N	\N	\N	\N
248	249	1	\N	\N	\N	\N
249	250	1	\N	\N	\N	\N
250	251	1	\N	\N	\N	\N
251	252	1	\N	\N	\N	\N
252	253	1	\N	\N	\N	\N
253	254	1	\N	\N	\N	\N
254	255	1	\N	\N	\N	\N
255	256	1	\N	\N	\N	\N
256	257	1	\N	\N	\N	\N
257	258	1	\N	\N	\N	\N
258	259	1	\N	\N	\N	\N
259	260	1	\N	\N	\N	\N
260	261	1	\N	\N	\N	\N
261	262	1	\N	\N	\N	\N
262	263	1	\N	\N	\N	\N
263	264	1	\N	\N	\N	\N
264	265	1	\N	\N	\N	\N
265	266	1	\N	\N	\N	\N
266	267	1	\N	\N	\N	\N
267	268	1	\N	\N	\N	\N
268	269	1	\N	\N	\N	\N
269	270	1	\N	\N	\N	\N
270	271	1	\N	\N	\N	\N
271	272	1	\N	\N	\N	\N
272	273	1	\N	\N	\N	\N
273	274	1	\N	\N	\N	\N
274	275	1	\N	\N	\N	\N
275	276	1	\N	\N	\N	\N
276	277	1	\N	\N	\N	\N
277	278	1	\N	\N	\N	\N
278	279	1	\N	\N	\N	\N
279	280	1	\N	\N	\N	\N
280	281	1	\N	\N	\N	\N
281	282	1	\N	\N	\N	\N
282	283	1	\N	\N	\N	\N
283	284	1	\N	\N	\N	\N
284	285	1	\N	\N	\N	\N
285	286	1	\N	\N	\N	\N
286	287	1	\N	\N	\N	\N
287	288	1	\N	\N	\N	\N
288	289	1	\N	\N	\N	\N
289	290	1	\N	\N	\N	\N
290	291	1	\N	\N	\N	\N
291	292	1	\N	\N	\N	\N
292	293	1	\N	\N	\N	\N
293	294	1	\N	\N	\N	\N
294	295	1	\N	\N	\N	\N
295	296	1	\N	\N	\N	\N
296	297	1	\N	\N	\N	\N
297	298	1	\N	\N	\N	\N
298	299	1	\N	\N	\N	\N
299	300	1	\N	\N	\N	\N
300	301	1	\N	\N	\N	\N
301	302	1	\N	\N	\N	\N
302	303	1	\N	\N	\N	\N
303	304	1	\N	\N	\N	\N
304	305	1	\N	\N	\N	\N
305	306	1	\N	\N	\N	\N
306	307	1	\N	\N	\N	\N
307	308	1	\N	\N	\N	\N
308	309	1	\N	\N	\N	\N
309	310	1	\N	\N	\N	\N
310	311	1	\N	\N	\N	\N
311	312	1	\N	\N	\N	\N
312	313	1	\N	\N	\N	\N
313	314	1	\N	\N	\N	\N
314	315	1	\N	\N	\N	\N
315	316	1	\N	\N	\N	\N
316	317	1	\N	\N	\N	\N
317	318	1	\N	\N	\N	\N
318	319	1	\N	\N	\N	\N
319	320	1	\N	\N	\N	\N
320	321	1	\N	\N	\N	\N
321	322	1	\N	\N	\N	\N
322	323	1	\N	\N	\N	\N
323	324	1	\N	\N	\N	\N
324	325	1	\N	\N	\N	\N
325	326	1	\N	\N	\N	\N
326	327	1	\N	\N	\N	\N
327	328	1	\N	\N	\N	\N
328	329	1	\N	\N	\N	\N
329	330	1	\N	\N	\N	\N
330	331	1	\N	\N	\N	\N
331	332	1	\N	\N	\N	\N
332	333	1	\N	\N	\N	\N
333	334	1	\N	\N	\N	\N
334	335	1	\N	\N	\N	\N
335	336	1	\N	\N	\N	\N
336	337	1	\N	\N	\N	\N
337	338	1	\N	\N	\N	\N
338	339	1	\N	\N	\N	\N
339	340	1	\N	\N	\N	\N
340	341	1	\N	\N	\N	\N
341	342	1	\N	\N	\N	\N
342	343	1	\N	\N	\N	\N
343	344	1	\N	\N	\N	\N
344	345	1	\N	\N	\N	\N
345	346	1	\N	\N	\N	\N
346	347	1	\N	\N	\N	\N
347	348	1	\N	\N	\N	\N
348	349	1	\N	\N	\N	\N
349	350	1	\N	\N	\N	\N
350	351	1	\N	\N	\N	\N
351	352	1	\N	\N	\N	\N
352	353	1	\N	\N	\N	\N
353	354	1	\N	\N	\N	\N
354	355	1	\N	\N	\N	\N
355	356	1	\N	\N	\N	\N
356	357	1	\N	\N	\N	\N
357	358	1	\N	\N	\N	\N
358	359	1	\N	\N	\N	\N
359	360	1	\N	\N	\N	\N
360	361	1	\N	\N	\N	\N
361	362	1	\N	\N	\N	\N
362	363	1	\N	\N	\N	\N
363	364	1	\N	\N	\N	\N
364	365	1	\N	\N	\N	\N
365	366	1	\N	\N	\N	\N
366	367	1	\N	\N	\N	\N
367	368	1	\N	\N	\N	\N
368	369	1	\N	\N	\N	\N
369	370	1	\N	\N	\N	\N
370	371	1	\N	\N	\N	\N
371	372	1	\N	\N	\N	\N
372	373	1	\N	\N	\N	\N
373	374	1	\N	\N	\N	\N
374	375	1	\N	\N	\N	\N
375	376	1	\N	\N	\N	\N
376	377	1	\N	\N	\N	\N
377	378	1	\N	\N	\N	\N
378	379	1	\N	\N	\N	\N
379	380	1	\N	\N	\N	\N
380	381	1	\N	\N	\N	\N
381	382	1	\N	\N	\N	\N
382	383	1	\N	\N	\N	\N
383	384	1	\N	\N	\N	\N
384	385	1	\N	\N	\N	\N
385	386	1	\N	\N	\N	\N
386	387	1	\N	\N	\N	\N
387	388	1	\N	\N	\N	\N
388	389	1	\N	\N	\N	\N
389	390	1	\N	\N	\N	\N
390	391	1	\N	\N	\N	\N
391	392	1	\N	\N	\N	\N
392	393	1	\N	\N	\N	\N
393	394	1	\N	\N	\N	\N
394	395	1	\N	\N	\N	\N
395	396	1	\N	\N	\N	\N
396	397	1	\N	\N	\N	\N
397	398	1	\N	\N	\N	\N
398	399	1	\N	\N	\N	\N
399	400	1	\N	\N	\N	\N
400	401	1	\N	\N	\N	\N
401	402	1	\N	\N	\N	\N
402	403	1	\N	\N	\N	\N
403	404	1	\N	\N	\N	\N
404	405	1	\N	\N	\N	\N
405	406	1	\N	\N	\N	\N
406	407	1	\N	\N	\N	\N
407	408	1	\N	\N	\N	\N
408	409	1	\N	\N	\N	\N
409	410	1	\N	\N	\N	\N
410	411	1	\N	\N	\N	\N
411	412	1	\N	\N	\N	\N
412	413	1	\N	\N	\N	\N
413	414	1	\N	\N	\N	\N
414	415	1	\N	\N	\N	\N
415	416	1	\N	\N	\N	\N
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417	418	1	\N	\N	\N	\N
418	419	1	\N	\N	\N	\N
419	420	1	\N	\N	\N	\N
420	421	1	\N	\N	\N	\N
421	422	1	\N	\N	\N	\N
422	423	1	\N	\N	\N	\N
423	424	1	\N	\N	\N	\N
424	425	1	\N	\N	\N	\N
425	426	1	\N	\N	\N	\N
426	427	1	\N	\N	\N	\N
427	428	1	\N	\N	\N	\N
428	429	1	\N	\N	\N	\N
429	430	1	\N	\N	\N	\N
430	431	1	\N	\N	\N	\N
431	432	1	\N	\N	\N	\N
432	433	1	\N	\N	\N	\N
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434	435	1	\N	\N	\N	\N
435	436	1	\N	\N	\N	\N
436	437	1	\N	\N	\N	\N
437	438	1	\N	\N	\N	\N
438	439	1	\N	\N	\N	\N
439	440	1	\N	\N	\N	\N
440	441	1	\N	\N	\N	\N
441	442	1	\N	\N	\N	\N
442	443	1	\N	\N	\N	\N
443	444	1	\N	\N	\N	\N
444	445	1	\N	\N	\N	\N
445	446	1	\N	\N	\N	\N
446	447	1	\N	\N	\N	\N
447	448	1	\N	\N	\N	\N
448	449	1	\N	\N	\N	\N
449	450	1	\N	\N	\N	\N
450	451	1	\N	\N	\N	\N
451	452	1	\N	\N	\N	\N
452	453	1	\N	\N	\N	\N
453	454	1	\N	\N	\N	\N
454	455	1	\N	\N	\N	\N
455	456	1	\N	\N	\N	\N
456	457	1	\N	\N	\N	\N
457	458	1	\N	\N	\N	\N
458	459	1	\N	\N	\N	\N
459	460	1	\N	\N	\N	\N
460	461	1	\N	\N	\N	\N
461	462	1	\N	\N	\N	\N
462	463	1	\N	\N	\N	\N
463	464	1	\N	\N	\N	\N
464	465	1	\N	\N	\N	\N
465	466	1	\N	\N	\N	\N
466	467	1	\N	\N	\N	\N
467	468	1	\N	\N	\N	\N
468	469	1	\N	\N	\N	\N
469	470	1	\N	\N	\N	\N
470	471	1	\N	\N	\N	\N
471	472	1	\N	\N	\N	\N
472	473	1	\N	\N	\N	\N
473	474	1	\N	\N	\N	\N
474	475	1	\N	\N	\N	\N
475	476	1	\N	\N	\N	\N
476	477	1	\N	\N	\N	\N
477	478	1	\N	\N	\N	\N
478	479	1	\N	\N	\N	\N
479	480	1	\N	\N	\N	\N
480	481	1	\N	\N	\N	\N
481	482	1	\N	\N	\N	\N
482	483	1	\N	\N	\N	\N
483	484	1	\N	\N	\N	\N
484	485	1	\N	\N	\N	\N
485	486	1	\N	\N	\N	\N
486	487	1	\N	\N	\N	\N
487	488	1	\N	\N	\N	\N
488	489	1	\N	\N	\N	\N
489	490	1	\N	\N	\N	\N
490	491	1	\N	\N	\N	\N
491	492	1	\N	\N	\N	\N
492	493	1	\N	\N	\N	\N
493	494	1	\N	\N	\N	\N
494	495	1	\N	\N	\N	\N
495	496	1	\N	\N	\N	\N
496	497	1	\N	\N	\N	\N
497	498	1	\N	\N	\N	\N
498	499	1	\N	\N	\N	\N
499	500	1	\N	\N	\N	\N
500	501	1	\N	\N	\N	\N
501	502	1	\N	\N	\N	\N
502	503	1	\N	\N	\N	\N
503	504	1	\N	\N	\N	\N
504	505	1	\N	\N	\N	\N
505	506	1	\N	\N	\N	\N
506	507	1	\N	\N	\N	\N
507	508	1	\N	\N	\N	\N
508	509	1	\N	\N	\N	\N
509	510	1	\N	\N	\N	\N
510	511	1	\N	\N	\N	\N
511	512	1	\N	\N	\N	\N
512	513	1	\N	\N	\N	\N
513	514	1	\N	\N	\N	\N
514	515	1	\N	\N	\N	\N
515	516	1	\N	\N	\N	\N
516	517	1	\N	\N	\N	\N
517	518	1	\N	\N	\N	\N
518	519	1	\N	\N	\N	\N
519	520	1	\N	\N	\N	\N
520	521	1	\N	\N	\N	\N
521	522	1	\N	\N	\N	\N
522	523	1	\N	\N	\N	\N
523	524	1	\N	\N	\N	\N
524	525	1	\N	\N	\N	\N
525	526	1	\N	\N	\N	\N
526	527	1	\N	\N	\N	\N
527	528	1	\N	\N	\N	\N
528	529	1	\N	\N	\N	\N
529	530	1	\N	\N	\N	\N
530	531	1	\N	\N	\N	\N
531	532	1	\N	\N	\N	\N
532	533	1	\N	\N	\N	\N
533	534	1	\N	\N	\N	\N
534	535	1	\N	\N	\N	\N
535	536	1	\N	\N	\N	\N
536	537	1	\N	\N	\N	\N
537	538	1	\N	\N	\N	\N
538	539	1	\N	\N	\N	\N
539	540	1	\N	\N	\N	\N
540	541	1	\N	\N	\N	\N
541	542	1	\N	\N	\N	\N
542	543	1	\N	\N	\N	\N
543	544	1	\N	\N	\N	\N
544	545	1	\N	\N	\N	\N
545	546	1	\N	\N	\N	\N
546	547	1	\N	\N	\N	\N
547	548	1	\N	\N	\N	\N
548	549	1	\N	\N	\N	\N
549	550	1	\N	\N	\N	\N
550	551	1	\N	\N	\N	\N
551	552	1	\N	\N	\N	\N
552	553	1	\N	\N	\N	\N
553	554	1	\N	\N	\N	\N
554	555	1	\N	\N	\N	\N
555	556	1	\N	\N	\N	\N
556	557	1	\N	\N	\N	\N
557	558	1	\N	\N	\N	\N
558	559	1	\N	\N	\N	\N
559	560	1	\N	\N	\N	\N
560	561	1	\N	\N	\N	\N
561	562	1	\N	\N	\N	\N
562	563	1	\N	\N	\N	\N
563	564	1	\N	\N	\N	\N
564	565	1	\N	\N	\N	\N
565	566	1	\N	\N	\N	\N
566	567	1	\N	\N	\N	\N
567	568	1	\N	\N	\N	\N
568	569	1	\N	\N	\N	\N
569	570	1	\N	\N	\N	\N
570	571	1	\N	\N	\N	\N
571	572	1	\N	\N	\N	\N
572	573	1	\N	\N	\N	\N
573	574	1	\N	\N	\N	\N
574	575	1	\N	\N	\N	\N
575	576	1	\N	\N	\N	\N
576	577	1	\N	\N	\N	\N
577	578	1	\N	\N	\N	\N
578	579	1	\N	\N	\N	\N
579	580	1	\N	\N	\N	\N
580	581	1	\N	\N	\N	\N
581	582	1	\N	\N	\N	\N
582	583	1	\N	\N	\N	\N
583	584	1	\N	\N	\N	\N
584	585	1	\N	\N	\N	\N
585	586	1	\N	\N	\N	\N
586	587	1	\N	\N	\N	\N
587	588	1	\N	\N	\N	\N
588	589	1	\N	\N	\N	\N
589	590	1	\N	\N	\N	\N
590	591	1	\N	\N	\N	\N
591	592	1	\N	\N	\N	\N
592	593	1	\N	\N	\N	\N
593	594	1	\N	\N	\N	\N
594	595	1	\N	\N	\N	\N
595	596	1	\N	\N	\N	\N
596	597	1	\N	\N	\N	\N
597	598	1	\N	\N	\N	\N
598	599	1	\N	\N	\N	\N
599	600	1	\N	\N	\N	\N
600	601	1	\N	\N	\N	\N
601	602	1	\N	\N	\N	\N
602	603	1	\N	\N	\N	\N
603	604	1	\N	\N	\N	\N
604	605	1	\N	\N	\N	\N
605	606	1	\N	\N	\N	\N
606	607	1	\N	\N	\N	\N
607	608	1	\N	\N	\N	\N
608	609	1	\N	\N	\N	\N
609	610	1	\N	\N	\N	\N
610	611	1	\N	\N	\N	\N
611	612	1	\N	\N	\N	\N
612	613	1	\N	\N	\N	\N
613	614	1	\N	\N	\N	\N
614	615	1	\N	\N	\N	\N
615	616	1	\N	\N	\N	\N
616	617	1	\N	\N	\N	\N
617	618	1	\N	\N	\N	\N
618	619	1	\N	\N	\N	\N
619	620	1	\N	\N	\N	\N
620	621	1	\N	\N	\N	\N
621	622	1	\N	\N	\N	\N
622	623	1	\N	\N	\N	\N
623	624	1	\N	\N	\N	\N
624	625	1	\N	\N	\N	\N
625	626	1	\N	\N	\N	\N
626	627	1	\N	\N	\N	\N
627	628	1	\N	\N	\N	\N
628	629	1	\N	\N	\N	\N
629	630	1	\N	\N	\N	\N
630	631	1	\N	\N	\N	\N
631	632	1	\N	\N	\N	\N
632	633	1	\N	\N	\N	\N
633	634	1	\N	\N	\N	\N
634	635	1	\N	\N	\N	\N
635	636	1	\N	\N	\N	\N
636	637	1	\N	\N	\N	\N
637	638	1	\N	\N	\N	\N
638	639	1	\N	\N	\N	\N
639	640	1	\N	\N	\N	\N
640	641	1	\N	\N	\N	\N
641	642	1	\N	\N	\N	\N
642	643	1	\N	\N	\N	\N
643	644	1	\N	\N	\N	\N
644	645	1	\N	\N	\N	\N
645	646	1	\N	\N	\N	\N
646	647	1	\N	\N	\N	\N
647	648	1	\N	\N	\N	\N
648	649	1	\N	\N	\N	\N
649	650	1	\N	\N	\N	\N
650	651	1	\N	\N	\N	\N
651	652	1	\N	\N	\N	\N
652	653	1	\N	\N	\N	\N
653	654	1	\N	\N	\N	\N
654	655	1	\N	\N	\N	\N
655	656	1	\N	\N	\N	\N
656	657	1	\N	\N	\N	\N
657	658	1	\N	\N	\N	\N
658	659	1	\N	\N	\N	\N
659	660	1	\N	\N	\N	\N
660	661	1	\N	\N	\N	\N
661	662	1	\N	\N	\N	\N
662	663	1	\N	\N	\N	\N
663	664	1	\N	\N	\N	\N
664	665	1	\N	\N	\N	\N
665	666	1	\N	\N	\N	\N
666	667	1	\N	\N	\N	\N
667	668	1	\N	\N	\N	\N
668	669	1	\N	\N	\N	\N
669	670	1	\N	\N	\N	\N
670	671	1	\N	\N	\N	\N
671	672	1	\N	\N	\N	\N
672	673	1	\N	\N	\N	\N
673	674	1	\N	\N	\N	\N
674	675	1	\N	\N	\N	\N
675	676	1	\N	\N	\N	\N
676	677	1	\N	\N	\N	\N
677	678	1	\N	\N	\N	\N
678	679	1	\N	\N	\N	\N
679	680	1	\N	\N	\N	\N
680	681	1	\N	\N	\N	\N
681	682	1	\N	\N	\N	\N
682	683	1	\N	\N	\N	\N
683	684	1	\N	\N	\N	\N
684	685	1	\N	\N	\N	\N
685	686	1	\N	\N	\N	\N
686	687	1	\N	\N	\N	\N
687	688	1	\N	\N	\N	\N
688	689	1	\N	\N	\N	\N
689	690	1	\N	\N	\N	\N
690	691	1	\N	\N	\N	\N
691	692	1	\N	\N	\N	\N
692	693	1	\N	\N	\N	\N
693	694	1	\N	\N	\N	\N
694	695	1	\N	\N	\N	\N
695	696	1	\N	\N	\N	\N
696	697	1	\N	\N	\N	\N
697	698	1	\N	\N	\N	\N
698	699	1	\N	\N	\N	\N
699	700	1	\N	\N	\N	\N
700	701	1	\N	\N	\N	\N
701	702	1	\N	\N	\N	\N
702	703	1	\N	\N	\N	\N
703	704	1	\N	\N	\N	\N
704	705	1	\N	\N	\N	\N
705	706	1	\N	\N	\N	\N
706	707	1	\N	\N	\N	\N
707	708	1	\N	\N	\N	\N
708	709	1	\N	\N	\N	\N
709	710	1	\N	\N	\N	\N
710	711	1	\N	\N	\N	\N
711	712	1	\N	\N	\N	\N
712	713	1	\N	\N	\N	\N
713	714	1	\N	\N	\N	\N
714	715	1	\N	\N	\N	\N
715	716	1	\N	\N	\N	\N
716	717	1	\N	\N	\N	\N
717	718	1	\N	\N	\N	\N
718	719	1	\N	\N	\N	\N
719	720	1	\N	\N	\N	\N
720	721	1	\N	\N	\N	\N
721	722	1	\N	\N	\N	\N
722	723	1	\N	\N	\N	\N
723	724	1	\N	\N	\N	\N
724	725	1	\N	\N	\N	\N
725	726	1	\N	\N	\N	\N
726	727	1	\N	\N	\N	\N
727	728	1	\N	\N	\N	\N
728	729	1	\N	\N	\N	\N
729	730	1	\N	\N	\N	\N
730	731	1	\N	\N	\N	\N
731	732	1	\N	\N	\N	\N
732	733	1	\N	\N	\N	\N
733	734	1	\N	\N	\N	\N
734	735	1	\N	\N	\N	\N
735	736	1	\N	\N	\N	\N
736	737	1	\N	\N	\N	\N
737	738	1	\N	\N	\N	\N
738	739	1	\N	\N	\N	\N
739	740	1	\N	\N	\N	\N
740	741	6	\N	\N	\N	\N
741	742	6	\N	\N	\N	\N
\.


--
-- Data for Name: analysisfeatureprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysisfeatureprop (analysisfeatureprop_id, analysisfeature_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: analysisprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.analysisprop (analysisprop_id, analysis_id, type_id, value, rank) FROM stdin;
1	1	32	Genome annotation	0
2	2	32	Genome annotation	0
3	6	31	genome assembly	0
4	7	32	Genome annotation	0
\.


--
-- Data for Name: arraydesign; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.arraydesign (arraydesign_id, manufacturer_id, platformtype_id, substratetype_id, protocol_id, dbxref_id, name, version, description, array_dimensions, element_dimensions, num_of_elements, num_array_columns, num_array_rows, num_grid_columns, num_grid_rows, num_sub_columns, num_sub_rows) FROM stdin;
\.


--
-- Data for Name: arraydesignprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.arraydesignprop (arraydesignprop_id, arraydesign_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: assay; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.assay (assay_id, arraydesign_id, protocol_id, assaydate, arrayidentifier, arraybatchidentifier, operator_id, dbxref_id, name, description) FROM stdin;
\.


--
-- Data for Name: assay_biomaterial; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.assay_biomaterial (assay_biomaterial_id, assay_id, biomaterial_id, channel_id, rank) FROM stdin;
\.


--
-- Data for Name: assay_project; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.assay_project (assay_project_id, assay_id, project_id) FROM stdin;
\.


--
-- Data for Name: assayprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.assayprop (assayprop_id, assay_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: biomaterial; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.biomaterial (biomaterial_id, taxon_id, biosourceprovider_id, dbxref_id, name, description) FROM stdin;
\.


--
-- Data for Name: biomaterial_dbxref; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.biomaterial_dbxref (biomaterial_dbxref_id, biomaterial_id, dbxref_id) FROM stdin;
\.


--
-- Data for Name: biomaterial_relationship; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.biomaterial_relationship (biomaterial_relationship_id, subject_id, type_id, object_id) FROM stdin;
\.


--
-- Data for Name: biomaterial_treatment; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.biomaterial_treatment (biomaterial_treatment_id, biomaterial_id, treatment_id, unittype_id, value, rank) FROM stdin;
\.


--
-- Data for Name: biomaterialprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.biomaterialprop (biomaterialprop_id, biomaterial_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: cell_line; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line (cell_line_id, name, uniquename, organism_id, timeaccessioned, timelastmodified) FROM stdin;
\.


--
-- Data for Name: cell_line_cvterm; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_cvterm (cell_line_cvterm_id, cell_line_id, cvterm_id, pub_id, rank) FROM stdin;
\.


--
-- Data for Name: cell_line_cvtermprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_cvtermprop (cell_line_cvtermprop_id, cell_line_cvterm_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: cell_line_dbxref; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_dbxref (cell_line_dbxref_id, cell_line_id, dbxref_id, is_current) FROM stdin;
\.


--
-- Data for Name: cell_line_feature; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_feature (cell_line_feature_id, cell_line_id, feature_id, pub_id) FROM stdin;
\.


--
-- Data for Name: cell_line_library; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_library (cell_line_library_id, cell_line_id, library_id, pub_id) FROM stdin;
\.


--
-- Data for Name: cell_line_pub; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_pub (cell_line_pub_id, cell_line_id, pub_id) FROM stdin;
\.


--
-- Data for Name: cell_line_relationship; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_relationship (cell_line_relationship_id, subject_id, object_id, type_id) FROM stdin;
\.


--
-- Data for Name: cell_line_synonym; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_line_synonym (cell_line_synonym_id, cell_line_id, synonym_id, pub_id, is_current, is_internal) FROM stdin;
\.


--
-- Data for Name: cell_lineprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_lineprop (cell_lineprop_id, cell_line_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: cell_lineprop_pub; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cell_lineprop_pub (cell_lineprop_pub_id, cell_lineprop_id, pub_id) FROM stdin;
\.


--
-- Data for Name: chadoprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.chadoprop (chadoprop_id, type_id, value, rank) FROM stdin;
1	2	1.3	0
\.


--
-- Data for Name: channel; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.channel (channel_id, name, definition) FROM stdin;
\.


--
-- Data for Name: contact; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.contact (contact_id, type_id, name, description) FROM stdin;
1	\N	null	null
2	2909	Lowell Knight	She's whimsical, capable, eager and perhaps a little too uncontrolled. Which isn't out of the ordinary for someone with her position.
3	2909	Robin Irwin	He was born and grew up in a successful family in a large port, he lived in peace until he was about 12 years old, but at that point everything changed.
4	2909	Gwendolyn Hunt	But only time will tell; she is currently exploring everything. She feels like there's more than meets the eye in this world. Luckily she has a close group of friends to support her.
5	149	State of Embron	Built upon the sacrifices, leadership and honor of its past, this company is now among the most successful in its corner of the world. Their export, clean water and fuel production are among its current greatest strengths.
6	149	Creed of Devotion	Built upon the darker times, dignity and strong minds of its past, the employees ive gloomy lives, but while education is really lacking, their trade helps relief some of their issues. Religion holds a fair deal of importance in their lives.
7	2959	Mastermind Illustrated	Provides a multitude of articles which illustrate how you too can be a mastermind.
\.


--
-- Data for Name: contact_relationship; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.contact_relationship (contact_relationship_id, type_id, subject_id, object_id) FROM stdin;
\.


--
-- Data for Name: contactprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.contactprop (contactprop_id, contact_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: control; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.control (control_id, type_id, assay_id, tableinfo_id, row_id, name, value, rank) FROM stdin;
\.


--
-- Data for Name: cv; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cv (cv_id, name, definition) FROM stdin;
3	Statistical Terms	Locally created terms for statistics
4	chado_properties	Terms that are used in the chadoprop table to describe the state of the database
5	germplasm_ontology	GCP germplasm ontology
6	dc	DCMI Metadata Terms
7	EDAM	Bioscientific data analysis ontology
8	efo	The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org
9	ero	The Eagle-I Research Resource Ontology models research resources such instruments. protocols, reagents, animal models and biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/).
10	OBCS	Ontology of Biological and Clinical Statistics
11	obi	Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific
12	ogi	Ontology for Biomedical Investigation. The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific
13	IAO	Information Artifact Ontology
1	null	No vocabulary
2	local	Locally created terms
14	organism_property	A local vocabulary that contains locally defined properties for organisms
15	analysis_property	A local vocabulary that contains locally defined properties for analyses
16	tripal_phylogeny	Terms used by the Tripal phylotree module for phylogenetic and taxonomic trees
17	feature_relationship	A local vocabulary that contains types of relationships between features
18	feature_property	A local vocabulary that contains properties for genomic features
19	contact_property	A local vocabulary that contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.
20	contact_type	A local vocabulary that contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.
31	tripal_pub	Tripal Publication Ontology
22	contact_relationship	A local vocabulary that contains types of relationships between contacts.
23	featuremap_units	A local vocabulary that contains map unit types for the unittype_id column of the featuremap table.
24	featurepos_property	A local vocabulary that contains terms map properties.
25	featuremap_property	A local vocabulary that contains positional types for the feature positions.
26	library_property	A local vocabulary that contains properties for libraries.
27	library_type	A local vocabulary that contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).
28	project_property	A local vocabulary that contains properties for projects.
29	study_property	A local vocabulary that contains properties for studies.
30	project_relationship	A local vocabulary that contains Types of relationships between projects
32	pub_type	A local vocabulary that contains types of publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.
33	pub_property	A local vocabulary that contains properties for publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.
34	pub_relationship	A local vocabulary that contains types of relationships between publications.
35	stock_relationship	A local vocabulary that contains types of relationships between stocks.
36	stock_property	A local vocabulary that contains properties for stocks.
37	stock_type	A local vocabulary that contains a list of types for stocks.
38	tripal_analysis	A local vocabulary that contains terms used for analyses.
39	nd_experiment_types	A local vocabulary that contains terms used for the Natural Diverisity module's experiment types.
40	nd_geolocation_property	A local vocabulary that contains terms used for the Natural Diverisity module's geolocation property.
41	sbo	Systems Biology.  Terms commonly used in Systems Biology, and in particular in computational modeling.
42	swo	Bioinformatics operations, data types, formats, identifiers and topics
43	PMID	PubMed.
44	uo	Units of Measurement Ontology
45	ncit	NCI Thesaurus OBO Edition
46	ncbitaxon	NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy
47	rdfs	Resource Description Framework Schema
48	ro	Relationship Ontology (legacy)
49	cellular_component	Gene Ontology Cellular Component Vocabulary
50	biological_process	Gene Ontology Biological Process Vocabulary
21	tripal_contact	Tripal Contact Ontology
51	molecular_function	Gene Ontology Molecular Function Vocabulary
52	sequence	The Sequence Ontology
53	taxonomic_rank	Taxonomic Rank
54	foaf	Friend of a Friend. A dictionary of people-related terms that can be used in structured data).
55	hydra	A Vocabulary for Hypermedia-Driven Web APIs.
56	rdf	Resource Description Framework
57	schema	Schema.org. Schema.org is sponsored by Google, Microsoft, Yahoo and Yandex. The vocabularies are developed by an open community process.
58	sep	A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.
59	SIO	The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.
60	synonym_type	\N
\.


--
-- Data for Name: cv_root_mview; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cv_root_mview (name, cvterm_id, cv_id, cv_name) FROM stdin;
sequence_feature	161	52	sequence
sequence_attribute	780	52	sequence
sequence_collection	1363	52	sequence
Contact Type	2907	21	tripal_contact
sequence_variant	165	52	sequence
Publication	171	31	tripal_pub
Address	2925	21	tripal_contact
taxonomic_rank	2847	53	taxonomic_rank
Affiliation	2921	21	tripal_contact
\.


--
-- Data for Name: cvprop; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cvprop (cvprop_id, cv_id, type_id, value, rank) FROM stdin;
\.


--
-- Data for Name: cvterm; Type: TABLE DATA; Schema: chado; Owner: drupaladmin
--

COPY chado.cvterm (cvterm_id, cv_id, name, definition, dbxref_id, is_obsolete, is_relationshiptype) FROM stdin;
1	1	null	\N	1	0	0
2	4	version	Chado schema version	2	0	0
3	5	accession		3	0	0
4	5	generated germplasm		4	0	0
5	5	cultivar		5	0	0
6	5	414 inbred line		6	0	0
7	6	Service	A system that provides one or more functions.	7	0	0
8	7	Sequence length	The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.	8	0	0
9	7	Sequence checksum	A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.	9	0	0
10	7	Accession	A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.	10	0	0
11	7	Sequence	One or more molecular sequences, possibly with associated annotation.	11	0	0
12	7	Sequence record	A molecular sequence and associated metadata.	12	0	0
13	7	Identifier	A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).	13	0	0
14	7	Protein sequence	One or more protein sequences, possibly with associated annotation.	14	0	0
15	7	Image	Biological or biomedical data has been rendered into an image, typically for display on screen.	15	0	0
16	7	Map	A map of (typically one) DNA sequence annotated with positional or non-positional features.	16	0	0
17	7	Genetic map	A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.	17	0	0
18	7	Physical map	A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.	18	0	0
19	7	Sequence coordinates	A position in a map (for example a genetic map), either a single position (point) or a region / interval.	19	0	0
20	7	Database name	The name of a biological or bioinformatics database.	20	0	0
21	7	Database ID	An identifier of a biological or bioinformatics database.	21	0	0
22	7	URI	The name of a biological or bioinformatics database.	22	0	0
23	7	Translation phase specification	Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.	23	0	0
24	7	DNA sense specification	The strand of a DNA sequence (forward or reverse).	24	0	0
25	7	Annotation track	Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. Synonym: Sequence annotation track.	25	0	0
26	7	Phylogenetic tree	The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.	26	0	0
27	7	Species tree	A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.	27	0	0
28	7	Gene tree	A phylogenetic tree that is an estimate of the character's phylogeny.	28	0	0
29	7	Phylogenetic tree visualisation	A phylogenetic tree that is an estimate of the character's phylogeny.	29	0	0
30	7	Sequence visualisation	Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown.	30	0	0
31	7	genome assembly		31	0	0
32	7	Genome annotation 		32	0	0
33	7	Analysis	Apply analytical methods to existing data of a specific type.	33	0	0
34	8	instrument	An instrument is a device which provides a mechanical or electronic function.	34	0	0
36	8	substrate type	Controlled terms for descriptors of types of array substrates.	36	0	0
37	8	array manufacturer		37	0	0
35	8	array design	An instrument design which describes the design of the array.	35	0	0
38	9	database	A database is an organized collection of data, today typically in digital form.	38	0	0
39	9	data acquisition	A technique that samples real world physical conditions and conversion of the resulting samples into digital numeric values that can be manipulated by a computer.	39	0	0
40	10	rank order	A data item that represents an arrangement according to a rank, i.e., the position of a particular case relative to other cases on a defined scale.	40	0	0
41	11	organism	A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.	41	0	0
42	11	assay	A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.	42	0	0
43	12	location on map		43	0	0
44	13	definition	The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.	44	0	0
45	13	version number	A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.	45	0	0
46	13	algorithm	An algorithm is a set of instructions for performing a particular calculation.	46	0	0
47	2	property	A generic term indicating that represents an attribute, quality or characteristic of something.	47	0	0
48	2	time_last_modified	The time at which the record was last modified.	48	0	0
49	2	time_accessioned	The time at which the record was first added.	49	0	0
50	2	time_executed	The time when the task was executed.	50	0	0
51	2	infraspecific_type	The connector type (e.g. subspecies, varietas, forma, etc.) for the infraspecific name	51	0	0
52	2	abbreviation	A shortened name (or abbreviation) for the item.	52	0	0
53	2	expression	Curated expression data	53	0	0
54	2	is_analysis	Indicates if this feature was predicted computationally using another feature.	54	0	0
55	2	is_obsolete	Indicates if this record is obsolete.	55	0	0
56	2	is_current	Indicates if this record is current.	56	0	0
57	2	is_internal	Indicates if this record is internal and not normally available outside of a local setting.	57	0	0
58	2	Mini-ref	A small in-house unique identifier for a publication.	58	0	0
59	2	Array Batch Identifier	A unique identifier for an array batch.	59	0	0
60	2	clause subject	The subject of a relationship clause.	60	0	0
61	2	clause predicate	The object of a relationship clause.	61	0	0
62	2	relationship type	The relationship type.	62	0	0
63	2	fasta_definition	The definition line for a FASTA formatted sequence	63	0	0
64	2	Reference Feature	A genomic or genetic feature on which other features are mapped.	64	0	0
65	2	minimal boundary	The leftmost, minimal boundary in the linear range represented by the feature location. Sometimes this is called start although this is confusing because it does not necessarily represent the 5-prime coordinate.	65	0	0
66	2	maximal boundary	The rightmost, maximal boundary in the linear range represented by the featureloc. Sometimes this is called end although this is confusing because it does not necessarily represent the 3-prime coordinate	66	0	0
67	2	analysis	A process as a method of studying the nature of something or of determining its essential features and their relations. (Random House Kernerman Webster's College Dictionary, © 2010 K Dictionaries Ltd).	67	0	0
68	2	source_data	The location where data that is being used come from.	68	0	0
69	2	contact	An entity (e.g. individual or organization) through whom a person can gain access to information, favors, influential people, and the like.	69	0	0
70	2	relationship	The way in which two things are connected.	70	0	0
71	2	biomaterial	A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.	71	0	0
72	2	array_dimensions	The dimensions of an array.	72	0	0
73	2	element_dimensions	The dimensions of an element.	73	0	0
74	2	num_of_elements	The number of elements.	74	0	0
75	2	num_array_columns	The number of columns in an array.	75	0	0
76	2	num_array_rows	The number of rows in an array.	76	0	0
77	2	num_grid_columns	The number of columns in a grid.	77	0	0
78	2	num_grid_rows	The number of rows in a grid.	78	0	0
79	2	num_sub_columns	The number of sub columns.	79	0	0
80	2	num_sub_rows	The number of sub rows.	80	0	0
81	2	Genome Project	A project for whole genome analysis that can include assembly and annotation.	81	0	0
82	14	rank	A taxonmic rank	82	0	0
83	14	lineage		83	0	0
84	14	genetic_code_name		84	0	0
85	14	mitochondrial_genetic_code		85	0	0
86	14	mitochondrial_genetic_code_name		86	0	0
87	14	division		87	0	0
88	14	genbank_common_name		88	0	0
89	14	synonym		89	0	0
90	14	other_name		90	0	0
91	14	equivalent_name		91	0	0
92	14	anamorph		92	0	0
93	15	Analysis Type	The type of analysis that was performed.	93	0	0
94	16	phylo_leaf	A leaf node in a phylogenetic tree.	94	0	0
95	16	phylo_root	The root node of a phylogenetic tree.	95	0	0
96	16	phylo_interior	An interior node in a phylogenetic tree.	96	0	0
97	16	taxonomy	Deprecated: A term used to indicate if a phylotree is a taxonomic tree	97	0	0
98	23	cM	Centimorgan units	98	0	0
99	23	bp	Base pairs units	99	0	0
100	23	bin_unit	The bin unit	100	0	0
101	23	marker_order	Units simply to define marker order.	101	0	0
102	23	undefined	A catch-all for an undefined unit type	102	0	0
103	24	start	The start coordinate for a map feature.	103	0	0
104	24	stop	The end coordinate for a map feature	104	0	0
105	25	Map Dbxref	A unique identifer for the map in a remote database.  The format is a database abbreviation and a unique accession separated by a colon.  (e.g. Gramene:tsh1996a)	105	0	0
106	25	Map Type	The type of Map (e.g. QTL, Physical, etc.)	106	0	0
107	25	Genome Group		107	0	0
108	25	URL	A univeral resource locator (URL) reference where the publication can be found.  For maps found online, this would be the web address for the map.	108	0	0
109	25	Population Type	A brief description of the population type used to generate the map (e.g. RIL, F2, BC1, etc).	109	0	0
1257	52	edit_operation		1282	1	0
110	25	Population Size	The size of the population used to construct the map.	110	0	0
111	25	Methods	A brief description of the methods used to construct the map.	111	0	0
112	25	Software	The software used to construct the map.	112	0	0
113	26	Library	A group of physical entities organized into a collection	113	0	0
114	26	Library Description	Description of a library	114	0	0
115	27	cdna_library	cDNA library	115	0	0
116	27	bac_library	Bacterial Artifical Chromsome (BAC) library	116	0	0
117	27	fosmid_library	Fosmid library	117	0	0
118	27	cosmid_library	Cosmid library	118	0	0
119	27	yac_library	Yeast Artificial Chromosome (YAC) library	119	0	0
120	27	genomic_library	Genomic Library	120	0	0
121	28	Project Description	Description of a project	121	0	0
122	28	Project Type	A type of project	122	0	0
123	29	Study Type	A type of study	123	0	0
124	38	analysis_date	The date that an analysis was performed.	124	0	0
125	38	analysis_short_name	A computer legible (no spaces or special characters) abbreviation for the analysis.	125	0	0
126	39	Genotyping	An experiment where genotypes of individuals are identified.	126	0	0
127	39	Phenotyping	An experiment where phenotypes of individuals are identified.	127	0	0
128	40	Location	The name of the location.	128	0	0
129	41	phenotype	A biochemical network can generate phenotypes or affects biological processes. Such processes can take place at different levels and are independent of the biochemical network itself.	129	0	0
130	41	database cross reference	An annotation which directs one to information contained within a database.	130	0	0
131	41	relationship	Connectedness between entities and/or interactions representing their relatedness or influence.	131	0	0
132	42	software	Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.	132	0	0
133	44	unit	A unit of measurement is a standardized quantity of a physical quality.	133	0	0
134	45	Date	The particular day, month and year an event has happened or will happen.	134	0	0
135	45	Operator	A person that operates some apparatus or machine	135	0	0
136	45	Technology Platform	The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment.	136	0	0
137	45	Value	A numerical quantity measured or assigned or computed.	137	0	0
138	45	Channel	An independent acquisition scheme, i.e., a route or conduit through which flows data consisting of one particular measurement using one particular parameter.	138	0	0
139	45	Controlled Vocabulary	A set of terms that are selected and defined based on the requirements set out by the user group, usually a set of vocabulary is chosen to promote consistency across data collection projects. [ NCI ]	139	0	0
140	45	Term	A word or expression used for some particular thing. [ NCI ]	140	0	0
141	45	Expression	A combination of symbols that represents a value. [ NCI ]	141	0	0
142	45	Phenotype	The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. [ NCI ]	142	0	0
143	45	Genotype	The genetic constitution of an organism or cell, as distinct from its expressed features or phenotype. [ NCI ]	143	0	0
144	45	Location	A position, site, or point in space where something can be found. [ NCI ]	144	0	0
145	45	Reagent	Any natural or synthetic substance used in a chemical or biological reaction in order to produce, identify, or measure another substance. [ NCI ]	145	0	0
146	45	Environment	The totality of surrounding conditions. [ NCI ]	146	0	0
147	45	Tree Node	A term that refers to any individual item or entity in a hierarchy or pedigree. [ NCI ]	147	0	0
148	45	Study Design	A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc. [ NCI ]	148	0	0
149	45	Company	Any formal business entity for profit, which may be a corporation, a partnership, association or individual proprietorship.	149	0	0
150	45	Project	Any specifically defined piece of work that is undertaken or attempted to meet a single requirement.	150	0	0
151	45	DNA Library	A collection of DNA molecules that have been cloned in vectors.	151	0	0
152	45	Trait	Any genetically determined characteristic.	152	0	0
153	45	Subgroup	A subdivision of a larger group with members often exhibiting similar characteristics. [ NCI ]	153	0	0
154	45	Namespace	In general, a namespace is an abstract container, which is or could be filled by names, or technical terms, or words, and these represent or stand for real-world things. A description logic terminology namespace is a collection of Kind, Role, Property and Concept definitions. As in computer programming, context namespaces are intended to allow multiple knowledge bases to reside in the same physical database. (from Apelon) [ NCI ]	154	0	0
155	45	Biospecimen	Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions.	155	0	0
156	45	Communication Contact	A channel for communication between groups.	156	0	0
157	46	common name		157	0	0
158	47	comment	A human-readable description of a resource.	158	0	0
159	47	type	The type of resource.	159	0	0
160	47	label	A human-readable version of a resource's name.	160	0	0
2401	52	polymorphic_pseudogene_processed_transcript	A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2665	0	0
2763	52	sequence_variant_causing_partial_loss_of_function_of_polypeptide		3044	1	0
171	31	Publication		171	0	0
172	55	Collection	A collection holding references to a number of related resources.	172	0	0
173	55	member	A member of the collection	173	0	0
174	55	description	A description.	174	0	0
175	55	totalItems	The total number of items referenced by a collection.	175	0	0
176	55	title	A title, often used along with a description.	176	0	0
177	55	PartialCollectionView	A PartialCollectionView describes a partial view of a Collection. Multiple PartialCollectionViews can be connected with the the next/previous properties to allow a client to retrieve all members of the collection.	177	0	0
178	57	name	The name of the item.	178	0	0
179	57	alternateName	An alias for the item.	179	0	0
180	57	comment	Comments, typically from users.	180	0	0
181	57	description	A description of the item.	181	0	0
182	57	publication	A publication event associated with the item.	182	0	0
183	57	url	URL of the item.	183	0	0
184	57	additionalType	An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in.	184	0	0
185	57	ItemPage	A page devoted to a single item, such as a particular product or hotel.	185	0	0
186	58	biological sample	A biological sample analysed by a particular technology.	186	0	0
187	58	protocol	A protocol is a process which is a parameterizable description of a process.	187	0	0
188	59	namespace	A namespace is an informational entity that defines a logical container for a set of symbols or identifiers.	188	0	0
189	59	clause	A clause consists of a subject and a predicate.	189	0	0
190	59	references	references is a relation between one entity and the entity that it makes reference to by name, but is not described by it.	190	0	0
191	59	position	A measurement of a spatial location relative to a frame of reference or other objects.	191	0	0
192	59	annotation	An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information.	192	0	0
193	59	negation	NOT is a logical operator in that has the value true if its operand is false.	193	0	0
194	59	record identifier	A record identifier is an identifier for a database entry.	194	0	0
195	59	vocabulary	A vocabulary is a collection of terms.	195	0	0
196	59	email address	an email address is an identifier to send mail to particular electronic mailbox.	196	0	0
197	59	assay	An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.	197	0	0
198	59	cell line	A cell line is a collection of genetically identifical cells.	198	0	0
199	59	study	A study is a process that realizes the steps of a study design.	199	0	0
204	52	adjacent_to	A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. [PMID:20226267, SO:ke]	204	0	1
205	52	associated_with		205	0	1
206	52	complete_evidence_for_feature	B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A. [SO:ke]	206	0	1
207	52	is_a		207	0	1
208	52	evidence_for_feature	B is evidence_for_feature A, if an instance of B supports the existence of A. [SO:ke]	208	0	1
209	52	connects_on	X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z. [PMID:20226267]	209	0	1
264	52	PCR_product	A region amplified by a PCR reaction. [SO:ke]	264	0	0
265	52	reagent	A sequence used in experiment. [SO:ke]	265	0	0
164	52	QTL	A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. [http://rgd.mcw.edu/tu/qtls/]	164	0	0
165	52	sequence_variant	A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. [SO:ke]	165	0	0
167	52	heritable_phenotypic_marker	A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. [JAX:hdene]	167	0	0
166	52	genetic_marker	A measurable sequence feature that varies within a population. [SO:db]	166	0	0
201	60	broad		201	0	0
168	53	genus		168	0	0
169	53	species		169	0	0
170	53	infraspecies		170	0	0
202	60	narrow		202	0	0
210	52	contained_by	X contained_by Y iff X starts after start of Y and X ends before end of Y. [PMID:20226267]	210	0	1
211	52	contains	The inverse of contained_by. [PMID:20226267]	211	0	1
212	52	derives_from		212	0	1
213	52	disconnected_from	X is disconnected_from Y iff it is not the case that X overlaps Y. [PMID:20226267]	213	0	1
214	52	edited_from		214	0	1
215	52	edited_to		215	0	1
216	52	exemplar_of	X is exemplar of Y if X is the best evidence for Y. [SO:ke]	216	0	1
217	52	finished_by	Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary. [PMID:20226267]	217	0	1
218	52	finishes	X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary. [PMID:20226267]	218	0	1
219	52	gained	X gained Y if X is a variant_of X' and Y part of X but not X'. [SO:ke]	219	0	1
220	52	genome_of		220	0	1
221	52	guided_by		221	0	1
222	52	guides		222	0	1
223	52	has_integral_part	X has_integral_part Y if and only if: X has_part Y and Y part_of X. [http://precedings.nature.com/documents/3495/version/1]	223	0	1
224	52	has_part	Inverse of part_of. [http://precedings.nature.com/documents/3495/version/1]	224	0	1
225	52	has_origin		225	0	1
226	52	has_quality		226	0	1
227	52	homologous_to		227	0	1
228	52	similar_to		228	0	1
229	52	integral_part_of	X integral_part_of Y if and only if: X part_of Y and Y has_part X. [http://precedings.nature.com/documents/3495/version/1]	229	0	1
230	52	part_of	X part_of Y if X is a subregion of Y. [http://precedings.nature.com/documents/3495/version/1]	230	0	1
231	52	is_consecutive_sequence_of	R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical). [PMID:20226267]	231	0	1
232	52	lost	X lost Y if X is a variant_of X' and Y part of X' but not X. [SO:ke]	232	0	1
233	52	maximally_overlaps	A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. [PMID:20226267]	233	0	1
234	52	member_of		234	0	1
235	52	non_functional_homolog_of	A relationship between a pseudogenic feature and its functional ancestor. [SO:ke]	235	0	1
236	52	orthologous_to		236	0	1
237	52	overlaps	X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. [PMID:20226267]	237	0	1
238	52	paralogous_to		238	0	1
239	52	partial_evidence_for_feature	B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. [SO:ke]	239	0	1
240	52	position_of		240	0	1
241	52	processed_from	Inverse of processed_into. [http://precedings.nature.com/documents/3495/version/1]	241	0	1
242	52	processed_into	X is processed_into Y if a region X is modified to create Y. [http://precedings.nature.com/documents/3495/version/1]	242	0	1
243	52	recombined_from		243	0	1
244	52	recombined_to		244	0	1
245	52	sequence_of		245	0	1
246	52	started_by	X is strted_by Y if Y is part_of X and X and Y share a 5' boundary. [PMID:20226267]	246	0	1
247	52	starts	X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary. [PMID:20226267]	247	0	1
248	52	trans_spliced_from		248	0	1
249	52	trans_spliced_to		249	0	1
250	52	transcribed_from	X is transcribed_from Y if X is synthesized from template Y. [http://precedings.nature.com/documents/3495/version/1]	250	0	1
251	52	transcribed_to	Inverse of transcribed_from. [http://precedings.nature.com/documents/3495/version/1]	251	0	1
252	52	translates_to	Inverse of translation _of. [http://precedings.nature.com/documents/3495/version/1]	252	0	1
253	52	translation_of	X is translation of Y if Y is translated by ribosome to create X. [http://precedings.nature.com/documents/3495/version/1]	253	0	1
254	52	variant_of	A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A. [SO:immuno_workshop]	254	0	1
255	52	Sequence_Ontology		255	1	0
256	52	region	A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. [SO:ke]	256	0	0
161	52	sequence_feature	Any extent of continuous biological sequence. [LAMHDI:mb, SO:ke]	161	0	0
257	52	sequence_secondary_structure	A folded sequence. [SO:ke]	257	0	0
258	52	biological_region	A region defined by its disposition to be involved in a biological process. [SO:cb]	258	0	0
259	52	G_quartet	G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]	259	0	0
260	52	interior_coding_exon	A coding exon that is not the most 3-prime or the most 5-prime in a given transcript. []	260	0	0
261	52	coding_exon	An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). [SO:ke]	261	0	0
262	52	satellite_DNA	The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. [http://www.insdc.org/files/feature_table.html]	262	0	0
263	52	tandem_repeat	Two or more adjacent copies of a region (of length greater than 1). [SO:ke]	263	0	0
266	52	read_pair	One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. [SO:ls]	266	0	0
267	52	read	A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. [SO:rd]	267	0	0
268	52	contig	A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. [SO:ls]	268	0	0
269	52	paired_end_fragment	An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). [SO:ke]	269	0	0
270	52	gene_sensu_your_favorite_organism		270	1	0
271	52	gene_class		271	1	0
272	52	protein_coding	A gene which, when transcribed, can be translated into a protein. []	272	0	0
273	52	gene_attribute	An attribute describing a gene. []	273	0	0
274	52	non_protein_coding	A gene which can be transcribed, but will not be translated into a protein. []	274	0	0
275	52	scRNA_primary_transcript	The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote. [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]	275	0	0
276	52	nc_primary_transcript	A primary transcript that is never translated into a protein. [SO:ke]	276	0	0
277	52	scRNA	A small non coding RNA sequence, present in the cytoplasm. [SO:ke]	277	0	0
278	52	ncRNA	An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. [SO:ke]	278	0	0
279	52	INR_motif	A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. [PMID:12651739, PMID:16858867]	279	0	0
280	52	core_eukaryotic_promoter_element	An element that only exists within the promoter region of a eukaryotic gene. [GREEKC:cl]	280	0	0
281	52	RNApol_II_core_promoter	The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. [PMID:16858867]	281	0	0
282	52	DPE_motif	A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). [PMID:12515390, PMID:12537576, PMID:12651739, PMID:16858867]	282	0	0
283	52	BREu_motif	A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. [PMID:12651739, PMID:16858867]	283	0	0
284	52	PSE_motif	A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes. [PMID:11390411, PMID:12621023, PMID:12651739, PMID:23166507, PMID:8339931]	284	0	0
285	52	DNA_motif	A motif that is active in the DNA form of the sequence. [SO:ke]	285	0	0
286	52	promoter	A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription. [SO:regcreative]	286	0	0
287	52	linkage_group	A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. [ISBN:038752046]	287	0	0
288	52	RNA_internal_loop	A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. [SO:ke]	288	0	0
289	52	RNA_motif	A motif that is active in RNA sequence. [SO:ke]	289	0	0
290	52	asymmetric_RNA_internal_loop	An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. [SO:ke]	290	0	0
291	52	A_minor_RNA_motif	A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. [SO:ke]	291	0	0
292	52	K_turn_RNA_motif	The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. [SO:ke]	292	0	0
293	52	sarcin_like_RNA_motif	A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. [http://www.ncbi.nlm.nih.gov/pubmed/7897662]	293	0	0
294	52	symmetric_RNA_internal_loop	An internal RNA loop where the extent of the loop on both stands is the same size. [SO:ke]	294	0	0
295	52	RNA_junction_loop		295	0	0
296	52	RNA_hook_turn		296	0	0
297	52	base_pair	Two bases paired opposite each other by hydrogen bonds creating a secondary structure. []	297	0	0
298	52	WC_base_pair	The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. [PMID:12177293]	298	0	0
299	52	sugar_edge_base_pair	A type of non-canonical base-pairing. [PMID:12177293]	299	0	0
300	52	aptamer	DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. [http://aptamer.icmb.utexas.edu]	300	0	0
301	52	oligo	A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. [SO:ma]	301	0	0
302	52	DNA_aptamer	DNA molecules that have been selected from random pools based on their ability to bind other molecules. [http:aptamer.icmb.utexas.edu]	302	0	0
1258	52	insert_U	An edit to insert a U. [SO:ke]	1283	1	0
303	52	RNA_aptamer	RNA molecules that have been selected from random pools based on their ability to bind other molecules. [http://aptamer.icmb.utexas.edu]	303	0	0
304	52	morpholino_oligo	Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. [http://www.gene-tools.com/]	304	0	0
305	52	synthetic_oligo	An oligo composed of synthetic nucleotides. [SO:ke]	305	0	0
306	52	morpholino_backbone	An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. [RSC:cb]	306	0	0
307	52	riboswitch	A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. [PMID:2820954]	307	0	0
308	52	mRNA_region	A region of an mRNA. [SO:cb]	308	0	0
163	52	mRNA	Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. [SO:ma]	163	0	0
309	52	matrix_attachment_site	A DNA region that is required for the binding of chromatin to the nuclear matrix. [SO:ma]	309	0	0
310	52	chromosomal_regulatory_element	Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix. []	310	0	0
311	52	locus_control_region	A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. [SO:ma]	311	0	0
312	52	cis_regulatory_module	A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs. [PMID:19660565, SO:SG]	312	0	0
313	52	match_set	A collection of match parts. [SO:ke]	313	1	0
314	52	match_part	A part of a match, for example an hsp from blast is a match_part. [SO:ke]	314	0	0
315	52	experimental_feature	A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. [SO:cb]	315	0	0
316	52	match	A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. [SO:ke]	316	0	0
317	52	genomic_clone	A clone of a DNA region of a genome. [SO:ma]	317	0	0
318	52	clone	A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. [SO:ke]	318	0	0
319	52	genomic_DNA	DNA located in the genome and able to be transmitted to the offspring. [BCS:etrwz]	319	0	0
320	52	sequence_operation	An operation that can be applied to a sequence, that results in a change. [SO:ke]	320	1	0
321	52	pseudogene_attribute	An attribute of a pseudogene (SO:0000336). [SO:ma]	321	1	0
322	52	processed_pseudogene	A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	322	0	0
323	52	pseudogene	A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog). [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	323	0	0
324	52	pseudogene_by_unequal_crossing_over	A pseudogene caused by unequal crossing over at recombination. [SO:ke]	324	0	0
325	52	non_processed_pseudogene	A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, SO:ke]	325	0	0
326	52	delete	To remove a subsection of sequence. [SO:ke]	326	1	0
327	52	insert	To insert a subsection of sequence. [SO:ke]	327	1	0
328	52	invert	To invert a subsection of sequence. [SO:ke]	328	1	0
329	52	substitute	To substitute a subsection of sequence for another. [SO:ke]	329	1	0
330	52	translocate	To translocate a subsection of sequence. [SO:ke]	330	1	0
331	52	gene_part	A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. [SO:ke]	331	1	0
332	52	probe	A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. [SO:ma]	332	0	0
333	52	assortment_derived_deficiency		333	1	0
334	52	sequence_variant_affecting_regulatory_region	A sequence_variant_effect which changes the regulatory region of a gene. [SO:ke]	334	1	0
335	52	aneuploid	A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. [SO:ke]	335	0	0
336	52	chromosome_number_variation	A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. [SO:ke]	336	0	0
385	52	kinetoplast_gene	A gene located in kinetoplast sequence. [SO:xp]	385	0	0
337	52	hyperploid	A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. [SO:ke]	337	0	0
338	52	hypoploid	A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. [SO:ke]	338	0	0
339	52	operator	A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. [SO:ma]	339	0	0
340	52	transcriptional_cis_regulatory_region	A regulatory_region that modulates the transcription of a gene or genes. [PMID:9679020, SO:regcreative]	340	0	0
341	52	assortment_derived_aneuploid		341	1	0
342	52	nuclease_binding_site	A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. [SO:cb]	342	0	0
343	52	nucleotide_to_protein_binding_site	A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. [SO:ke]	343	0	0
344	52	compound_chromosome_arm	One arm of a compound chromosome. []	344	0	0
345	52	compound_chromosome	A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms. [SO:ke]	345	0	0
346	52	restriction_enzyme_binding_site	A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. [SO:cb]	346	0	0
347	52	deficient_intrachromosomal_transposition	An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. [FB:reference_manual]	347	0	0
348	52	chromosomal_deletion	An incomplete chromosome. [SO:ke]	348	0	0
349	52	intrachromosomal_transposition	A chromosome structure variation whereby a transposition occurred within a chromosome. [SO:ke]	349	0	0
350	52	deletion	The point at which one or more contiguous nucleotides were excised. [SO:ke]	350	0	0
351	52	deficient_interchromosomal_transposition	An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. [SO:ke]	351	0	0
352	52	interchromosomal_transposition	A chromosome structure variation whereby a transposition occurred between chromosomes. [SO:ke]	352	0	0
353	52	gene_by_transcript_attribute		353	1	0
354	52	free_chromosome_arm	A chromosome structure variation whereby an arm exists as an individual chromosome element. [SO:ke]	354	0	0
355	52	chromosome_structure_variation	An alteration of the genome that leads to a change in the structure or number of one or more chromosomes. []	355	0	0
356	52	gene_by_polyadenylation_attribute		356	1	0
357	52	gene_to_gene_feature		357	0	0
358	52	overlapping	An attribute describing a gene that has a sequence that overlaps the sequence of another gene. [SO:ke]	358	0	0
359	52	inside_intron	An attribute to describe a gene when it is located within the intron of another gene. [SO:ke]	359	0	0
360	52	inside_intron_antiparallel	An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. [SO:ke]	360	0	0
361	52	inside_intron_parallel	An attribute to describe a gene when it is located within the intron of another gene and on the same strand. [SO:ke]	361	0	0
362	52	end_overlapping_gene		362	1	0
363	52	five_prime_three_prime_overlap	An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. [SO:ke]	363	0	0
364	52	five_prime_five_prime_overlap	An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. [SO:ke]	364	0	0
365	52	three_prime_three_prime_overlap	An attribute to describe a gene when the 3' region overlaps with another gene's 3' region. [SO:ke]	365	0	0
366	52	three_prime_five_prime_overlap	An attribute to describe a gene when the 3' region overlaps with another gene's 5' region. [SO:ke]	366	0	0
367	52	antisense	A region sequence that is complementary to a sequence of messenger RNA. [SO:ke]	367	0	0
368	52	polycistronic_transcript	A transcript that is polycistronic. [SO:xp]	368	0	0
369	52	transcript	An RNA synthesized on a DNA or RNA template by an RNA polymerase. [SO:ma]	369	0	0
370	52	polycistronic	An attribute describing a sequence that contains the code for more than one gene product. [SO:ke]	370	0	0
371	52	dicistronic_transcript	A transcript that is dicistronic. [SO:ke]	371	0	0
372	52	dicistronic	An attribute describing a sequence that contains the code for two gene products. [SO:ke]	372	0	0
373	52	operon_member	A gene that is a member of an operon, which is a set of genes transcribed together as a unit. []	373	0	0
374	52	gene_array_member		374	0	0
375	52	processed_transcript_attribute		375	1	0
376	52	macronuclear_sequence	DNA belonging to the macronuclei of ciliates. []	376	0	0
377	52	organelle_sequence	A sequence of DNA that originates from a an organelle. []	377	0	0
378	52	micronuclear_sequence	DNA belonging to the micronuclei of a cell. []	378	0	0
379	52	gene_by_genome_location		379	1	0
380	52	gene_by_organelle_of_genome		380	1	0
381	52	nuclear_gene	A gene from nuclear sequence. [SO:xp]	381	0	0
162	52	gene	A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. [SO:immuno_workshop]	162	0	0
382	52	nuclear_sequence	DNA belonging to the nuclear genome of cell. []	382	0	0
383	52	mt_gene	A gene located in mitochondrial sequence. [SO:xp]	383	0	0
384	52	mitochondrial_sequence	DNA belonging to the genome of a mitochondria. []	384	0	0
386	52	kinetoplast	A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species. [PMID:8395055]	386	0	0
387	52	plastid_gene	A gene from plastid sequence. [SO:xp]	387	0	0
388	52	plastid_sequence	DNA belonging to the genome of a plastid such as a chloroplast. []	388	0	0
389	52	apicoplast_gene	A gene from apicoplast sequence. [SO:xp]	389	0	0
390	52	apicoplast_sequence	DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid. []	390	0	0
391	52	ct_gene	A gene from chloroplast sequence. [SO:xp]	391	0	0
392	52	chloroplast_sequence	DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis. []	392	0	0
393	52	chromoplast_gene	A gene from chromoplast_sequence. [SO:xp]	393	0	0
394	52	chromoplast_sequence	DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments. []	394	0	0
395	52	cyanelle_gene	A gene from cyanelle sequence. [SO:xp]	395	0	0
396	52	cyanelle_sequence	DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae. []	396	0	0
397	52	leucoplast_gene	A plastid gene from leucoplast sequence. [SO:xp]	397	0	0
398	52	leucoplast_sequence	DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil. []	398	0	0
399	52	proplastid_gene	A gene from proplastid sequence. [SO:ke]	399	0	0
400	52	proplastid_sequence	DNA belonging to the genome of a proplastid such as an immature chloroplast. []	400	0	0
401	52	nucleomorph_gene	A gene from nucleomorph sequence. [SO:xp]	401	0	0
402	52	nucleomorphic_sequence	DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic. []	402	0	0
403	52	plasmid_gene	A gene from plasmid sequence. [SO:xp]	403	0	0
404	52	plasmid_location	The location of DNA that has come from a plasmid sequence. []	404	0	0
405	52	proviral_gene	A gene from proviral sequence. [SO:xp]	405	0	0
406	52	proviral_location	The location of DNA that has come from a viral origin. []	406	0	0
407	52	endogenous_retroviral_gene	A proviral gene with origin endogenous retrovirus. [SO:xp]	407	0	0
408	52	endogenous_retroviral_sequence	Endogenous DNA sequence that are likely to have arisen from retroviruses. []	408	0	0
409	52	transposable_element	A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]	409	0	0
410	52	integrated_mobile_genetic_element	An MGE that is integrated into the host chromosome. [SO:ke]	410	0	0
411	52	expressed_sequence_match	A match to an EST or cDNA sequence. [SO:ke]	411	0	0
412	52	nucleotide_match	A match against a nucleotide sequence. [SO:ke]	412	0	0
413	52	clone_insert_end	The end of the clone insert. [SO:ke]	413	0	0
414	52	junction	A sequence_feature with an extent of zero. [SO:ke]	414	0	0
415	52	clone_insert	The region of sequence that has been inserted and is being propagated by the clone. [SO:ke]	415	0	0
416	52	polypeptide	A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. [SO:ma]	416	0	0
417	52	CDS	A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. [SO:ma]	418	0	0
418	52	chromosome_arm	A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. [http://www.medterms.com/script/main/art.asp?articlekey=5152]	419	0	0
419	52	chromosome_part	A region of a chromosome. [SO:ke]	420	0	0
420	52	non_capped_primary_transcript		421	1	0
421	52	sequencing_primer	A single stranded oligo used for polymerase chain reaction. []	422	0	0
422	52	primer	An oligo to which new deoxyribonucleotides can be added by DNA polymerase. [SO:ke]	423	0	0
423	52	mRNA_with_frameshift	An mRNA with a frameshift. [SO:xp]	424	0	0
424	52	frameshift	An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. [SO:ke]	425	0	0
425	52	sequence_variant_obs	A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. [SO:ke]	426	1	0
426	52	transposable_element_gene	A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. [SO:ke]	427	0	0
427	52	ss_oligo	A single stranded oligonucleotide. [SO:ke]	428	0	0
428	52	proviral_region	A viral sequence which has integrated into a host genome. [SO:ke]	429	0	0
429	52	methylated_cytosine	A methylated deoxy-cytosine. [SO:ke]	430	0	0
430	52	methylated_DNA_base_feature	A nucleotide modified by methylation. [SO:ke]	431	0	0
431	52	modified_cytosine	A modified cytosine DNA base feature. [SO:ke]	432	0	0
432	52	transcript_feature		433	1	0
433	52	edited	An attribute describing a sequence that is modified by editing. [SO:ke]	434	0	0
434	52	transcript_attribute	An attribute describing a transcript. []	435	0	0
435	52	transcript_with_readthrough_stop_codon		436	1	0
436	52	transcript_with_translational_frameshift	A transcript with a translational frameshift. [SO:xp]	437	0	0
437	52	translationally_frameshifted	Recoding by frameshifting a particular site. [SO:ke]	438	0	0
438	52	regulated	An attribute to describe a sequence that is regulated. [SO:ke]	439	0	0
439	52	protein_coding_primary_transcript	A primary transcript that, at least in part, encodes one or more proteins. [SO:ke]	440	0	0
440	52	primary_transcript	A transcript that in its initial state requires modification to be functional. [SO:ma]	441	0	0
441	52	forward_primer	A single stranded oligo used for polymerase chain reaction. [http://mged.sourceforge.net/ontologies/MGEDontology.php]	442	0	0
442	52	forward	Forward is an attribute of the feature, where the feature is in the 5' to 3' direction. [SO:ke]	443	0	0
443	52	RNA_sequence_secondary_structure	A folded RNA sequence. [SO:ke]	444	0	0
444	52	transcriptionally_regulated	An attribute describing a gene that is regulated at transcription. [SO:ma]	445	0	0
445	52	transcriptionally_constitutive	Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. [SO:ke]	446	0	0
446	52	transcriptionally_induced	An inducer molecule is required for transcription to occur. [SO:ke]	447	0	0
447	52	transcriptionally_repressed	A repressor molecule is required for transcription to stop. [SO:ke]	448	0	0
448	52	silenced_gene	A gene that is silenced. [SO:xp]	449	0	0
449	52	silenced	An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. [SO:ke]	450	0	0
450	52	gene_silenced_by_DNA_modification	A gene that is silenced by DNA modification. [SO:xp]	451	0	0
451	52	silenced_by_DNA_modification	An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. [SO:ke]	452	0	0
452	52	gene_silenced_by_DNA_methylation	A gene that is silenced by DNA methylation. [SO:xp]	453	0	0
453	52	silenced_by_DNA_methylation	An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. [SO:ke]	454	0	0
454	52	post_translationally_regulated	An attribute describing a gene that is regulated after it has been translated. [SO:ke]	455	0	0
455	52	translationally_regulated	An attribute describing a gene that is regulated as it is translated. [SO:ke]	456	0	0
456	52	reverse_primer	A single stranded oligo used for polymerase chain reaction. [http://mged.sourceforge.net/ontologies/MGEDontology.php]	457	0	0
457	52	reverse	Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer. [SO:ke]	458	0	0
458	52	epigenetically_modified	This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. [SO:ke]	459	0	0
459	52	genomically_imprinted	Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. [SO:ke]	460	0	0
460	52	maternally_imprinted	The maternal copy of the gene is modified, rendering it transcriptionally silent. [SO:ke]	461	0	0
461	52	paternally_imprinted	The paternal copy of the gene is modified, rendering it transcriptionally silent. [SO:ke]	462	0	0
462	52	allelically_excluded	Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. [SO:ke]	463	0	0
463	52	gene_rearranged_at_DNA_level	An epigenetically modified gene, rearranged at the DNA level. [SO:xp]	464	0	0
464	52	epigenetically_modified_gene	A gene that is epigenetically modified. [SO:ke]	465	0	0
465	52	rearranged_at_DNA_level	An attribute to describe the sequence of a feature, where the DNA is rearranged. [SO:ke]	466	0	0
466	52	ribosome_entry_site	Region in mRNA where ribosome assembles. [SO:ke]	467	0	0
467	52	five_prime_UTR	A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. [http://www.insdc.org/files/feature_table.html]	468	0	0
468	52	attenuator	A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. [SO:as]	469	0	0
469	52	translation_regulatory_region	A regulatory region that is involved in the control of the process of translation. [SO:ke]	470	0	0
470	52	terminator	The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. [http://www.insdc.org/files/feature_table.html]	471	0	0
471	52	DNA_sequence_secondary_structure	A folded DNA sequence. [SO:ke]	472	0	0
472	52	assembly_component	A region of known length which may be used to manufacture a longer region. [SO:ke]	473	0	0
473	52	primary_transcript_attribute		474	1	0
474	52	recoded_codon	A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. [SO:xp]	475	0	0
475	52	codon	A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. [SO:ke]	476	0	0
476	52	capped	An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. [SO:ke]	477	0	0
477	52	exon	A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. [SO:ke]	478	0	0
478	52	transcript_region	A region of a transcript. [SO:ke]	479	0	0
479	52	supercontig	One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. [SO:ls]	480	0	0
480	52	partial_genomic_sequence_assembly	A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's. [GMOD:ea]	481	0	0
558	52	aspartic_acid_tRNA_primary_transcript	A primary transcript encoding aspartyl tRNA (SO:0000257). [SO:ke]	561	0	0
2402	52	<new term>		2666	1	0
481	52	ultracontig	An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. [FB:WG]	482	0	0
482	52	sequence_assembly	A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. [SO:ma]	483	0	0
483	52	YAC	Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. [SO:ma]	484	0	0
484	52	vector_replicon	A replicon that has been modified to act as a vector for foreign sequence. [SO:ma]	485	0	0
485	52	BAC	Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. [SO:ma]	486	0	0
486	52	PAC	The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]	487	0	0
487	52	plasmid	A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. [SO:ma]	488	0	0
488	52	replicon	A region containing at least one unique origin of replication and a unique termination site. [ISBN:0716719207]	489	0	0
489	52	cosmid	A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. [SO:ma]	490	0	0
490	52	phagemid	A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. [SO:ma]	491	0	0
491	52	fosmid	A cloning vector that utilizes the E. coli F factor. [SO:ma]	492	0	0
492	52	sequence_alteration	A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. [SO:ke]	495	0	0
493	52	lambda_clone	A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. [ISBN:0-1767-2380-8]	496	1	0
494	52	methylated_adenine	A modified base in which adenine has been methylated. [SO:ke]	497	0	0
495	52	modified_adenine	A modified adenine DNA base feature. [SO:ke]	498	0	0
496	52	splice_site	Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. [SO:cjm, SO:ke]	499	0	0
497	52	primary_transcript_region	A part of a primary transcript. [SO:ke]	500	0	0
498	52	five_prime_cis_splice_site	Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	501	0	0
499	52	cis_splice_site	Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. [SO:cjm, SO:ke]	502	0	0
500	52	three_prime_cis_splice_site	Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]	503	0	0
501	52	enhancer	A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. [http://www.insdc.org/files/feature_table.html]	504	0	0
502	52	enhancer_bound_by_factor	An enhancer bound by a factor. [SO:xp]	505	0	0
503	52	bound_by_factor	An attribute describing a sequence that is bound by another molecule. [SO:ke]	506	0	0
504	52	gene_component_region	A region of a gene that has a specific function. []	507	0	0
505	52	restriction_enzyme_cut_site	A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. [SO:ma]	508	1	0
506	52	RNApol_I_promoter	A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. [SO:ke]	509	0	0
507	52	eukaryotic_promoter	A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions. []	510	0	0
508	52	RNApol_II_promoter	A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. [SO:ke]	511	0	0
509	52	RNApol_III_promoter	A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. [SO:ke]	512	0	0
510	52	CAAT_signal	Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. [http://www.insdc.org/files/feature_table.html]	513	0	0
511	52	GC_rich_promoter_region	A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. [http://www.insdc.org/files/feature_table.html]	514	0	0
512	52	promoter_element	An element that can exist within the promoter region of a gene. []	515	0	0
513	52	TATA_box	A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). [http://www.insdc.org/files/feature_table.html, PMID:16858867]	516	0	0
514	52	minus_10_signal	A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. [http://www.insdc.org/files/feature_table.html]	517	0	0
515	52	bacterial_RNApol_promoter_sigma_70_element	A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription. []	518	0	0
516	52	bacterial_RNApol_promoter_sigma_ecf_element	A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation. [Invitrogen:kc]	519	0	0
517	52	minus_35_signal	A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. [http://www.insdc.org/files/feature_table.html]	520	0	0
518	52	cross_genome_match	A nucleotide match against a sequence from another organism. [SO:ma]	521	0	0
519	52	operon	The DNA region of a group of adjacent genes whose transcription is coordinated onone or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene. [SO:ma]	522	0	0
520	52	gene_group	A collection of related genes. [SO:ma]	523	0	0
521	52	clone_insert_start	The start of the clone insert. [SO:ke]	524	0	0
522	52	retrotransposon	A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. [http://www.dddmag.com/Glossary.aspx#r]	525	0	0
523	52	translated_nucleotide_match	A match against a translated sequence. [SO:ke]	526	0	0
524	52	DNA_transposon	A transposon where the mechanism of transposition is via a DNA intermediate. [SO:ke]	527	0	0
525	52	non_transcribed_region	A region of the gene which is not transcribed. [SO:ke]	528	0	0
526	52	U2_intron	A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. [PMID:9428511]	529	0	0
527	52	spliceosomal_intron	An intron which is spliced by the spliceosome. [SO:ke]	530	0	0
528	52	LTR_retrotransposon	A retrotransposon flanked by long terminal repeat sequences. [SO:ke]	531	0	0
529	52	repeat_family	A group of characterized repeat sequences. [SO:ke]	532	1	0
530	52	intron	A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [http://www.insdc.org/files/feature_table.html]	533	0	0
531	52	non_LTR_retrotransposon	A retrotransposon without long terminal repeat sequences. [SO:ke]	534	0	0
532	52	five_prime_intron	An intron that is the most 5-prime in a given transcript. []	535	0	0
533	52	interior_intron	An intron that is not the most 3-prime or the most 5-prime in a given transcript. []	536	0	0
534	52	three_prime_intron	An intron that is the most 3-prime in a given transcript. []	537	0	0
535	52	RFLP_fragment	A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. [GOC:pj]	538	0	0
536	52	restriction_fragment	A region of polynucleotide sequence produced by digestion with a restriction endonuclease. [SO:ke]	539	0	0
537	52	LINE_element	A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]	540	0	0
538	52	five_prime_coding_exon_coding_region	The sequence of the five_prime_coding_exon that codes for protein. [SO:cjm]	541	0	0
539	52	coding_region_of_exon	The region of an exon that encodes for protein sequence. [SO:ke]	542	0	0
540	52	five_prime_coding_exon	The 5' most coding exon. [SO:ke]	543	0	0
541	52	three_prime_coding_exon_coding_region	The sequence of the three_prime_coding_exon that codes for protein. [SO:cjm]	544	0	0
542	52	three_prime_coding_exon	The coding exon that is most 3-prime on a given transcript. [SO:ma]	545	0	0
543	52	noncoding_exon	An exon that does not contain any codons. [SO:ke]	546	0	0
544	52	translocation	A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. [NCBI:th, SO:ke]	547	0	0
545	52	structural_alteration	An alteration of the genome that leads to a change in the structure of one or more chromosomes. []	548	0	0
546	52	interior_exon	An exon that is bounded by 5' and 3' splice sites. [PMID:10373547]	549	0	0
547	52	UTR	Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. [SO:ke]	550	0	0
548	52	three_prime_UTR	A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. [http://www.insdc.org/files/feature_table.html]	551	0	0
549	52	SINE_element	A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. [SO:ke]	552	0	0
550	52	simple_sequence_length_variation	SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ. [SO:ke]	553	0	0
551	52	sequence_length_alteration	A kind of kind of sequence alteration where the copies of a region present varies across a population. [SO:ke]	554	0	0
552	52	terminal_inverted_repeat_element	A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	555	0	0
553	52	rRNA_primary_transcript	A primary transcript encoding a ribosomal RNA. [SO:ke]	556	0	0
554	52	tRNA_primary_transcript	A primary transcript encoding a transfer RNA (SO:0000253). [SO:ke]	557	0	0
555	52	alanine_tRNA_primary_transcript	A primary transcript encoding alanyl tRNA. [SO:ke]	558	0	0
556	52	arginine_tRNA_primary_transcript	A primary transcript encoding arginyl tRNA (SO:0000255). [SO:ke]	559	0	0
557	52	asparagine_tRNA_primary_transcript	A primary transcript encoding asparaginyl tRNA (SO:0000256). [SO:ke]	560	0	0
647	52	engineered_fusion_gene	A fusion gene that is engineered. [SO:xp]	651	0	0
559	52	cysteine_tRNA_primary_transcript	A primary transcript encoding cysteinyl tRNA (SO:0000258). [SO:ke]	562	0	0
560	52	glutamic_acid_tRNA_primary_transcript	A primary transcript encoding glutaminyl tRNA (SO:0000260). [SO:ke]	563	0	0
561	52	glutamine_tRNA_primary_transcript	A primary transcript encoding glutamyl tRNA (SO:0000260). [SO:ke]	564	0	0
562	52	glycine_tRNA_primary_transcript	A primary transcript encoding glycyl tRNA (SO:0000263). [SO:ke]	565	0	0
563	52	histidine_tRNA_primary_transcript	A primary transcript encoding histidyl tRNA (SO:0000262). [SO:ke]	566	0	0
564	52	isoleucine_tRNA_primary_transcript	A primary transcript encoding isoleucyl tRNA (SO:0000263). [SO:ke]	567	0	0
565	52	leucine_tRNA_primary_transcript	A primary transcript encoding leucyl tRNA (SO:0000264). [SO:ke]	568	0	0
566	52	lysine_tRNA_primary_transcript	A primary transcript encoding lysyl tRNA (SO:0000265). [SO:ke]	569	0	0
567	52	methionine_tRNA_primary_transcript	A primary transcript encoding methionyl tRNA (SO:0000266). [SO:ke]	570	0	0
568	52	phenylalanine_tRNA_primary_transcript	A primary transcript encoding phenylalanyl tRNA (SO:0000267). [SO:ke]	571	0	0
569	52	proline_tRNA_primary_transcript	A primary transcript encoding prolyl tRNA (SO:0000268). [SO:ke]	572	0	0
570	52	serine_tRNA_primary_transcript	A primary transcript encoding seryl tRNA (SO:000269). [SO:ke]	573	0	0
571	52	threonine_tRNA_primary_transcript	A primary transcript encoding threonyl tRNA (SO:000270). [SO:ke]	574	0	0
572	52	tryptophan_tRNA_primary_transcript	A primary transcript encoding tryptophanyl tRNA (SO:000271). [SO:ke]	575	0	0
573	52	tyrosine_tRNA_primary_transcript	A primary transcript encoding tyrosyl tRNA (SO:000272). [SO:ke]	576	0	0
574	52	valine_tRNA_primary_transcript	A primary transcript encoding valyl tRNA (SO:000273). [SO:ke]	577	0	0
575	52	snRNA_primary_transcript	A primary transcript encoding a small nuclear RNA (SO:0000274). [SO:ke]	578	0	0
576	52	snoRNA_primary_transcript	A primary transcript encoding one or more small nucleolar RNAs (SO:0000275). [SO:ke]	579	0	0
577	52	mature_transcript	A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. [SO:ke]	580	0	0
578	52	TF_binding_site	A DNA site where a transcription factor binds. [SO:ke]	581	0	0
579	52	ORF	The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. [SGD:rb, SO:ma]	582	0	0
580	52	reading_frame	A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. [SGD:rb]	583	0	0
581	52	feature_attribute	An attribute describing a located_sequence_feature. [SO:ke]	584	0	0
582	52	foldback_element	A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]	585	0	0
583	52	flanking_region	The sequences extending on either side of a specific region. [SO:ke]	586	0	0
584	52	topologically_defined_region	A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping. [PMID:32782014, SO:cb]	587	0	0
585	52	chromosome_variation	A deviation in chromosome structure or number. []	588	0	0
586	52	variant_collection	A collection of one or more sequences of an individual. [SO:ke]	589	0	0
587	52	chromosomally_aberrant_genome	When a genome contains an abnormal amount of chromosomes. []	590	0	0
588	52	internal_UTR	A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. [SO:cjm]	591	0	0
589	52	untranslated_region_polycistronic_mRNA	The untranslated sequence separating the 'cistrons' of multicistronic mRNA. [SO:ke]	592	0	0
590	52	internal_ribosome_entry_site	Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. [SO:ke]	593	0	0
591	52	four_cutter_restriction_site		594	1	0
592	52	mRNA_by_polyadenylation_status		595	1	0
593	52	polyadenylated	A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. [SO:ke]	596	0	0
594	52	mRNA_attribute	An attribute describing an mRNA feature. [SO:ke]	597	0	0
595	52	mRNA_not_polyadenylated		598	1	0
596	52	six_cutter_restriction_site		599	1	0
597	52	modified_RNA_base_feature	A post_transcriptionally modified base. [SO:ke]	600	0	0
598	52	base	A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. [SO:ke]	601	0	0
599	52	eight_cutter_restriction_site		602	1	0
600	52	rRNA	rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity. [http://www.insdc.org/files/feature_table.html, ISBN:0198506732]	603	0	0
601	52	tRNA	Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]	604	0	0
602	52	sncRNA	A non-coding RNA less than 200 nucleotides in length. [PMID:30069443]	605	0	0
603	52	alanyl_tRNA	A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. [SO:ke]	606	0	0
604	52	rRNA_small_subunit_primary_transcript	A primary transcript encoding a small ribosomal subunit RNA. [SO:ke]	607	0	0
605	52	asparaginyl_tRNA	A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. [SO:ke]	608	0	0
606	52	aspartyl_tRNA	A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. [SO:ke]	609	0	0
607	52	cysteinyl_tRNA	A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. [SO:ke]	610	0	0
608	52	glutaminyl_tRNA	A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. [SO:ke]	611	0	0
609	52	glutamyl_tRNA	A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. [SO:ke]	612	0	0
610	52	glycyl_tRNA	A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. [SO:ke]	613	0	0
611	52	histidyl_tRNA	A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. [SO:ke]	614	0	0
612	52	isoleucyl_tRNA	A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. [SO:ke]	615	0	0
613	52	leucyl_tRNA	A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. [SO:ke]	616	0	0
614	52	lysyl_tRNA	A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. [SO:ke]	617	0	0
615	52	methionyl_tRNA	A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. [SO:ke]	618	0	0
616	52	phenylalanyl_tRNA	A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. [SO:ke]	619	0	0
617	52	prolyl_tRNA	A tRNA sequence that has a proline anticodon, and a 3' proline binding region. [SO:ke]	620	0	0
618	52	seryl_tRNA	A tRNA sequence that has a serine anticodon, and a 3' serine binding region. [SO:ke]	621	0	0
619	52	threonyl_tRNA	A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. [SO:ke]	622	0	0
620	52	tryptophanyl_tRNA	A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. [SO:ke]	623	0	0
621	52	tyrosyl_tRNA	A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. [SO:ke]	624	0	0
622	52	valyl_tRNA	A tRNA sequence that has a valine anticodon, and a 3' valine binding region. [SO:ke]	625	0	0
623	52	snRNA	A small nuclear RNA molecule involved in pre-mRNA splicing and processing. [http://www.insdc.org/files/feature_table.html, PMID:11733745, WB:ems]	626	0	0
624	52	snoRNA	Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing. [GOC:kgc, PMID:31828325]	627	0	0
625	52	miRNA	Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. [PMID:11081512, PMID:12592000]	628	0	0
626	52	small_regulatory_ncRNA	A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others). [PMID:28541282, PomBase:al, SO:ma]	630	0	0
627	52	pre_miRNA	The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure. [SO:ke]	631	0	0
628	52	transcript_bound_by_nucleic_acid	A transcript that is bound by a nucleic acid. [SO:xp]	632	0	0
629	52	bound_by_nucleic_acid	An attribute describing a sequence that is bound by a nucleic acid. [SO:ke]	633	0	0
630	52	transcript_bound_by_protein	A transcript that is bound by a protein. [SO:xp]	634	0	0
631	52	bound_by_protein	An attribute describing a sequence that is bound by a protein. [SO:ke]	635	0	0
632	52	engineered_gene	A gene that is engineered. [SO:xp]	636	0	0
633	52	engineered_region	A region that is engineered. [SO:xp]	637	0	0
634	52	engineered	An attribute to describe a region that was modified in vitro. [SO:ke]	638	0	0
635	52	engineered_foreign_gene	A gene that is engineered and foreign. [SO:xp]	639	0	0
636	52	foreign_gene	A gene that is foreign. [SO:xp]	640	0	0
637	52	engineered_foreign_region	A region that is engineered and foreign. [SO:xp]	641	0	0
638	52	foreign	An attribute to describe a region from another species. [SO:ke]	642	0	0
639	52	mRNA_with_minus_1_frameshift	An mRNA with a minus 1 frameshift. [SO:xp]	643	0	0
640	52	minus_1_frameshift	A frameshift caused by deleting one base. [SO:ke]	644	0	0
641	52	engineered_foreign_transposable_element_gene	A transposable_element that is engineered and foreign. [SO:xp]	645	0	0
642	52	type_I_enzyme_restriction_site	The recognition site is bipartite and interrupted. [http://www.promega.com]	646	1	0
643	52	long_terminal_repeat	A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. [http://www.insdc.org/files/feature_table.html]	647	0	0
644	52	repeat_region	A region of sequence containing one or more repeat units. [SO:ke]	648	0	0
645	52	fusion_gene	A gene that is a fusion. [SO:xp]	649	0	0
646	52	fusion	When two regions of DNA are joined together that are not normally together. []	650	0	0
648	52	microsatellite	A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]	652	0	0
649	52	dinucleotide_repeat_microsatellite_feature	A region of a repeating dinucleotide sequence (two bases). []	653	0	0
650	52	trinucleotide_repeat_microsatellite_feature	A region of a repeating trinucleotide sequence (three bases). []	654	0	0
651	52	repetitive_element		655	1	0
652	52	engineered_foreign_repetitive_element	A repetitive element that is engineered and foreign. [SO:xp]	656	0	0
653	52	inverted_repeat	The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. [SO:ke]	657	0	0
654	52	U12_intron	A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. [PMID:9428511]	658	0	0
655	52	origin_of_replication	A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites. [http://www.insdc.org/files/feature_table.html, NCBI:cf]	659	0	0
656	52	D_loop	Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. [http://www.insdc.org/files/feature_table.html]	660	0	0
657	52	recombination_feature	A feature where there has been exchange of genetic material in the event of mitosis or meiosis []	661	0	0
658	52	specific_recombination_site	A location where recombination or occurs during mitosis or meiosis. []	662	0	0
659	52	sequence_rearrangement_feature	A feature where a segment of DNA has been rearranged from what it was in the parent cell. []	663	0	0
660	52	recombination_feature_of_rearranged_gene	A location where a gene is rearranged due to recombination during mitosis or meiosis. []	664	0	0
661	52	vertebrate_immune_system_gene_recombination_feature	A feature where recombination has occurred for the purpose of generating a diversity in the immune system. []	665	0	0
662	52	J_gene_recombination_feature	Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	666	0	0
663	52	vertebrate_immune_system_gene_recombination_signal_feature	Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system. []	667	0	0
664	52	clip	Part of the primary transcript that is clipped off during processing. [SO:ke]	668	0	0
665	52	type_II_enzyme_restriction_site	The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. [http://www.promega.com]	669	1	0
666	52	modified_DNA_base	A modified nucleotide, i.e. a nucleotide other than A, T, C. G. [http://www.insdc.org/files/feature_table.html]	670	0	0
667	52	epigenetically_modified_region	A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification. [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]	671	0	0
668	52	CpG_island	Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. [SO:rd]	672	0	0
669	52	sequence_feature_locating_method		673	1	0
670	52	computed_feature		674	1	0
671	52	predicted_ab_initio_computation		675	1	0
672	52	computed_feature_by_similarity	. [SO:ma]	676	1	0
673	52	experimentally_determined	Attribute to describe a feature that has been experimentally verified. [SO:ke]	677	0	0
674	52	validated	An attribute to describe a feature that has been proven. [SO:ke]	678	0	0
675	52	stem_loop	A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. [http://www.insdc.org/files/feature_table.html]	679	0	0
676	52	direct_repeat	A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA. [SO:ke]	681	0	0
677	52	TSS	The first base where RNA polymerase begins to synthesize the RNA transcript. [SO:ke]	682	0	0
678	52	core_promoter_element	An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements. [GREEKC:rl]	683	0	0
679	52	cDNA_clone	Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	684	0	0
680	52	cDNA	DNA synthesized by reverse transcriptase using RNA as a template. [SO:ma]	685	0	0
681	52	start_codon	First codon to be translated by a ribosome. [SO:ke]	686	0	0
682	52	stop_codon	In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. [SO:ke]	687	0	0
683	52	intronic_splice_enhancer	Sequences within the intron that modulate splice site selection for some introns. [SO:ke]	688	0	0
684	52	splice_enhancer	Region of a transcript that regulates splicing. [SO:ke]	689	0	0
685	52	spliceosomal_intron_region	A region within an intron. [SO:ke]	690	0	0
686	52	mRNA_with_plus_1_frameshift	An mRNA with a plus 1 frameshift. [SO:ke]	691	0	0
687	52	plus_1_frameshift	A frameshift caused by inserting one base. [SO:ke]	692	0	0
688	52	nuclease_hypersensitive_site	A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance. []	693	0	0
689	52	nuclease_sensitive_site	A region of nucleotide sequence targeted by a nuclease enzyme. [SO:ma]	694	0	0
690	52	accessible_DNA_region	A region of DNA that is depleted of nucleosomes and accessible to DNA-binding proteins including transcription factors and nucleases. [PMID:25903461, SO:ds]	695	0	0
691	52	coding_start	The first base to be translated into protein. [SO:ke]	696	0	0
692	52	CDS_region	A region of a CDS. [SO:cb]	697	0	0
693	52	tag	A nucleotide sequence that may be used to identify a larger sequence. [SO:ke]	698	0	0
694	52	rRNA_large_subunit_primary_transcript	A primary transcript encoding a large ribosomal subunit RNA. [SO:ke]	699	0	0
695	52	SAGE_tag	A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]	700	0	0
696	52	coding_end	The last base to be translated into protein. It does not include the stop codon. [SO:ke]	701	0	0
697	52	microarray_oligo	A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. []	702	0	0
698	52	mRNA_with_plus_2_frameshift	An mRNA with a plus 2 frameshift. [SO:xp]	703	0	0
699	52	plus_2_framshift	A frameshift caused by inserting two bases. [SO:ke]	704	0	0
700	52	conserved_region	Region of sequence similarity by descent from a common ancestor. [SO:ke]	705	0	0
701	52	STS	Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. [http://www.biospace.com]	706	0	0
702	52	coding_conserved_region	Coding region of sequence similarity by descent from a common ancestor. [SO:ke]	707	0	0
703	52	exon_junction	The boundary between two exons in a processed transcript. [SO:ke]	708	0	0
704	52	nc_conserved_region	Non-coding region of sequence similarity by descent from a common ancestor. [SO:ke]	709	0	0
705	52	mRNA_with_minus_2_frameshift	A mRNA with a minus 2 frameshift. [SO:ke]	710	0	0
706	52	minus_2_frameshift	A frameshift caused by deleting two bases. [SO:ke]	711	0	0
707	52	RNAi_reagent	A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. [SO:rd]	712	0	0
708	52	ds_oligo	A double stranded oligonucleotide. [SO:ke]	713	0	0
709	52	MITE	A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. [http://www.pnas.org/cgi/content/full/97/18/10083]	714	0	0
710	52	recombination_hotspot	A region in a genome which promotes recombination. [SO:rd]	715	0	0
711	52	chromosome	Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. [SO:ma]	716	0	0
712	52	chromosome_band	A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. [SO:ma]	717	0	0
713	52	site_specific_recombination_target_region	A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis. []	718	0	0
714	52	splicing_regulatory_region	A regulatory_region that modulates splicing. [SO:ke]	719	0	0
715	52	EST	A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. [SO:ke]	720	0	0
716	52	loxP_site	Cre-Recombination target sequence. []	721	0	0
717	52	resolution_site	A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. [SO:as]	722	0	0
718	52	nucleic_acid	An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. [CHEBI:33696, RSC:cb]	723	0	0
719	52	polymer_attribute	An attribute to describe the kind of biological sequence. [SO:ke]	724	0	0
720	52	protein_match	A match against a protein sequence. [SO:ke]	725	0	0
721	52	FRT_site	An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. [SO:ma]	726	0	0
722	52	inversion_site	A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. [SO:ma]	727	0	0
723	52	synthetic_sequence	An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. [SO:ma]	728	0	0
724	52	DNA	An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. [RSC:cb]	729	0	0
725	52	assembly	A region of the genome of known length that is composed by ordering and aligning two or more different regions. [SO:ke]	730	0	0
726	52	group_1_intron_homing_endonuclease_target_region	A region of intronic nucleotide sequence targeted by a nuclease enzyme. [SO:ke]	731	0	0
727	52	haplotype_block	A region of the genome which is co-inherited as the result of the lack of historic recombination within it. [SO:ma]	732	0	0
728	52	RNA	An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. [RSC:cb]	733	0	0
729	52	flanked	An attribute describing a region that is bounded either side by a particular kind of region. [SO:ke]	734	0	0
730	52	floxed	An attribute describing sequence that is flanked by Lox-P sites. [SO:ke]	735	0	0
731	52	FRT_flanked	An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. [SO:ke]	736	0	0
732	52	invalidated_by_chimeric_cDNA	A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. [SO:ma]	737	0	0
733	52	invalidated	An attribute describing a feature that is invalidated. [SO:ke]	738	0	0
734	52	floxed_gene	A transgene that is floxed. [SO:xp]	739	0	0
735	52	transgene	A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. [SO:xp]	740	0	0
736	52	transposable_element_flanking_region	The region of sequence surrounding a transposable element. [SO:ke]	741	0	0
737	52	integron	A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. [SO:as]	742	0	0
738	52	insertion_site	The junction where an insertion occurred. [SO:ke]	743	0	0
739	52	attI_site	A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. [SO:as]	744	0	0
740	52	integration_excision_site	A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. [SO:as]	745	0	0
741	52	transposable_element_insertion_site	The junction in a genome where a transposable_element has inserted. [SO:ke]	746	0	0
742	52	integrase_coding_region		747	1	0
743	52	conjugative_transposon	A transposon that encodes function required for conjugation. [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]	748	0	0
744	52	enzymatic_RNA	An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. [RSC:cb]	749	0	0
745	52	enzymatic	An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. [RSC:cb]	750	0	0
746	52	recombinationally_inverted_gene	A recombinationally rearranged gene by inversion. [SO:xp]	751	0	0
747	52	recombinationally_rearranged_gene	A gene that is recombinationally rearranged. [SO:ke]	752	0	0
748	52	inversion	A continuous nucleotide sequence is inverted in the same position. [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	753	0	0
749	52	ribozyme	An RNA with catalytic activity. [SO:ma]	754	0	0
750	52	ribozymic	An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. [RSC:cb]	755	0	0
751	52	cytosolic_5_8S_rRNA	Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes. [https://rfam.xfam.org/family/RF00002]	756	0	0
752	52	cytosolic_LSU_rRNA	Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes. [SO:ke]	757	0	0
753	52	cytosolic_rRNA_5_8S_gene	A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes. []	758	0	0
754	52	RNA_6S	A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]	759	0	0
755	52	CsrB_RsmB_RNA	An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]	760	0	0
756	52	DsrA_RNA	DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]	761	0	0
757	52	GcvB_RNA	A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]	762	0	0
758	52	hammerhead_ribozyme	A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. [PMID:2436805]	763	0	0
759	52	group_IIA_intron	A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon. [PMID:20463000]	764	0	0
760	52	group_II_intron	Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]	765	0	0
1256	52	engineered_insert	A clone insert that is engineered. [SO:xp]	1281	0	0
761	52	group_IIB_intron	A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon. [PMID:20463000]	766	0	0
762	52	MicF_RNA	A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]	767	0	0
763	52	antisense_RNA	Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. [SO:ke]	768	0	0
764	52	OxyS_RNA	A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]	769	0	0
765	52	RNase_MRP_RNA	The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]	770	0	0
766	52	RNase_P_RNA	The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]	771	0	0
767	52	RprA_RNA	Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]	772	0	0
768	52	RRE_RNA	The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]	773	0	0
769	52	spot_42_RNA	A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]	774	0	0
770	52	telomerase_RNA	The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]	775	0	0
771	52	U1_snRNA	U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]	776	0	0
772	52	U2_snRNA	U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]	777	0	0
773	52	U4_snRNA	U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	778	0	0
774	52	U4atac_snRNA	An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). [PMID:12409455]	779	0	0
775	52	U5_snRNA	U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]	780	0	0
776	52	U6_snRNA	U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]	781	0	0
777	52	U6atac_snRNA	U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]	782	0	0
809	52	polypeptide_region	Biological sequence region that can be assigned to a specific subsequence of a polypeptide. [SO:GAR, SO:ke]	821	0	0
778	52	U11_snRNA	U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. [PMID:9622129]	783	0	0
779	52	U12_snRNA	The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]	784	0	0
780	52	sequence_attribute	An attribute describes a quality of sequence. [SO:ke]	785	0	0
781	52	enhancer_attribute		786	1	0
782	52	U14_snoRNA	U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]	787	0	0
783	52	C_D_box_snoRNA	Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	789	0	0
784	52	U14_snoRNA_primary_transcript	The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. [PMID:2251119]	790	0	0
785	52	vault_RNA	A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]	791	0	0
786	52	Y_RNA	Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]	792	0	0
787	52	twintron	An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. [PMID:1899376, PMID:7823908]	793	0	0
788	52	cytosolic_18S_rRNA	Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes. [SO:ke]	794	0	0
789	52	cytosolic_SSU_rRNA	Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes. [SO:ke]	795	0	0
790	52	cytosolic_rRNA_18S_gene	A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes. []	796	0	0
791	52	site	The interbase position where something (eg an aberration) occurred. [SO:ke]	797	1	0
792	52	binding_site	A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. [EBIBS:GAR, SO:ke]	798	0	0
793	52	protein_binding_site	A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. [SO:ke]	800	0	0
794	52	rescue_region	A region that rescues. [SO:xp]	801	0	0
795	52	rescue	An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. [SO:ke]	802	0	0
796	52	sequence_difference	A region where the sequence differs from that of a specified sequence. [SO:ke]	803	0	0
797	52	remark	A comment about the sequence. [SO:ke]	804	0	0
798	52	invalidated_by_genomic_contamination	An attribute to describe a feature that is invalidated due to genomic contamination. [SO:ke]	805	0	0
799	52	invalidated_by_genomic_polyA_primed_cDNA	An attribute to describe a feature that is invalidated due to polyA priming. [SO:ke]	806	0	0
800	52	invalidated_by_partial_processing	An attribute to describe a feature that is invalidated due to partial processing. [SO:ke]	807	0	0
801	52	polypeptide_domain	A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. [EBIBS:GAR]	808	0	0
802	52	polypeptide_structural_region	Region of polypeptide with a given structural property. [EBIBS:GAR, SO:cb]	812	0	0
803	52	polypeptide_conserved_region	A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. [EBIBS:GAR]	813	0	0
804	52	signal_peptide	The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. [http://www.insdc.org/files/feature_table.html]	814	0	0
805	52	peptide_localization_signal	A region of peptide sequence used to target the polypeptide molecule to a specific organelle. [SO:ke]	816	0	0
806	52	signal_peptide_region_of_CDS	A CDS region corresponding to a signal peptide of a polypeptide. []	817	0	0
807	52	propeptide	Part of a peptide chain which is cleaved off during the formation of the mature protein. [EBIBS:GAR]	818	0	0
808	52	mature_protein_region	The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. [EBIBS:GAR, http://www.insdc.org/files/feature_table.html, SO:cb]	819	0	0
810	52	mature_protein_region_of_CDS	A CDS region corresponding to a mature protein region of a polypeptide. []	822	0	0
811	52	immature_peptide_region	An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. [EBIBS:GAR]	823	0	0
812	52	five_prime_terminal_inverted_repeat	An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon. []	824	0	0
813	52	terminal_inverted_repeat	An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. [SO:ke]	825	0	0
814	52	three_prime_terminal_inverted_repeat	An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon. []	826	0	0
815	52	U5_LTR_region	The U5 segment of the long terminal repeats. []	827	0	0
816	52	LTR_component	The long terminal repeat found at the ends of the sequence to be inserted into the host genome. []	828	0	0
817	52	R_LTR_region	The R segment of the long terminal repeats. []	829	0	0
818	52	U3_LTR_region	The U3 segment of the long terminal repeats. []	830	0	0
819	52	five_prime_LTR	The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome. []	831	0	0
820	52	three_prime_LTR	The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome. []	832	0	0
821	52	R_five_prime_LTR_region	The R segment of the three-prime long terminal repeat. []	833	0	0
822	52	five_prime_LTR_component	A component of the five-prime long terminal repeat. [PMID:8649407]	834	0	0
823	52	U5_five_prime_LTR_region	The U5 segment of the three-prime long terminal repeat. []	835	0	0
824	52	U3_five_prime_LTR_region	The U3 segment of the three-prime long terminal repeat. []	836	0	0
825	52	R_three_prime_LTR_region	The R segment of the three-prime long terminal repeat. []	837	0	0
826	52	three_prime_LTR_component	A component of the three-prime long terminal repeat. [PMID:8649407]	838	0	0
827	52	U3_three_prime_LTR_region	The U3 segment of the three-prime long terminal repeat. []	839	0	0
828	52	U5_three_prime_LTR_region	The U5 segment of the three-prime long terminal repeat. []	840	0	0
829	52	non_LTR_retrotransposon_polymeric_tract	A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. [SO:ke]	841	0	0
830	52	repeat_component	A region of a repeated sequence. [SO:ke]	842	0	0
831	52	target_site_duplication	A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]	843	0	0
832	52	RR_tract	A polypurine tract within an LTR_retrotransposon. [SO:ke]	844	0	0
833	52	ARS	A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. [SO:ma]	845	0	0
834	52	assortment_derived_duplication		846	1	0
835	52	gene_not_polyadenylated		847	1	0
836	52	inverted_ring_chromosome	A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome. []	848	0	0
837	52	chromosomal_inversion	An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type. [SO:ke]	849	0	0
838	52	ring_chromosome	A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome. [http://en.wikipedia.org/wiki/Ring_chromosome]	850	0	0
839	52	three_prime_noncoding_exon	Non-coding exon in the 3' UTR. [SO:ke]	851	0	0
840	52	five_prime_noncoding_exon	Non-coding exon in the 5' UTR. [SO:ke]	852	0	0
841	52	UTR_intron	Intron located in the untranslated region. [SO:ke]	853	0	0
842	52	five_prime_UTR_intron	An intron located in the 5' UTR. [SO:ke]	854	0	0
843	52	three_prime_UTR_intron	An intron located in the 3' UTR. [SO:ke]	855	0	0
844	52	random_sequence	A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components. [SO:ma]	856	0	0
845	52	interband	A light region between two darkly staining bands in a polytene chromosome. [SO:ma]	857	0	0
846	52	gene_with_polyadenylated_mRNA	A gene that encodes a polyadenylated mRNA. [SO:xp]	858	0	0
847	52	protein_coding_gene	A gene that codes for an RNA that can be translated into a protein. []	859	0	0
848	52	polyadenylated_mRNA	An mRNA that is polyadenylated. [SO:xp]	860	0	0
849	52	transgene_attribute		861	1	0
850	52	chromosomal_transposition	A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. [FB:reference_manual, SO:ke]	862	0	0
851	52	rasiRNA	A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284, PMID:18032451]	863	0	0
852	52	piRNA	A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. [SO:ke]	864	0	0
853	52	gene_with_mRNA_with_frameshift	A gene that encodes an mRNA with a frameshift. [SO:xp]	865	0	0
854	52	recombinationally_rearranged	A gene that is recombinationally rearranged. []	866	0	0
855	52	interchromosomal_duplication	A chromosome duplication involving an insertion from another chromosome. [SO:ke]	867	0	0
856	52	chromosomal_duplication	An extra chromosome. [SO:ke]	868	0	0
857	52	D_gene_segment	Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	869	0	0
858	52	vertebrate_immunoglobulin_T_cell_receptor_segment	Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor. []	870	0	0
859	52	gene_with_trans_spliced_transcript	A gene with a transcript that is trans-spliced. [SO:xp]	871	0	0
860	52	trans_spliced_transcript	A transcript that is trans-spliced. [SO:xp]	872	0	0
861	52	inversion_derived_bipartite_deficiency	A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. [FB:km]	873	0	0
862	52	pseudogenic_region	A non-functional descendant of a functional entity. [SO:cjm]	874	0	0
863	52	encodes_alternately_spliced_transcripts	A gene that encodes more than one transcript. [SO:ke]	875	0	0
864	52	decayed_exon	A non-functional descendant of an exon. [SO:ke]	876	0	0
865	52	inversion_derived_deficiency_plus_duplication	A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. [FB:km]	877	0	0
866	52	intrachromosomal_duplication	A duplication that occurred within a chromosome. [SO:ke]	878	0	0
867	52	V_gene_segment	Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	879	0	0
868	52	post_translationally_regulated_by_protein_stability	An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. [SO:ke]	880	0	0
869	52	golden_path_fragment	One of the pieces of sequence that make up a golden path. [SO:rd]	881	0	0
870	52	golden_path	A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. [SO:ls]	882	0	0
871	52	post_translationally_regulated_by_protein_modification	An attribute describing a gene sequence where the resulting protein is modified to regulate it. [SO:ke]	883	0	0
872	52	J_gene_segment	Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	884	0	0
873	52	autoregulated	The gene product is involved in its own transcriptional regulation. [SO:ke]	885	0	0
874	52	tiling_path	A set of regions which overlap with minimal polymorphism to form a linear sequence. [SO:cjm]	886	0	0
875	52	negatively_autoregulated	The gene product is involved in its own transcriptional regulation where it decreases transcription. [SO:ke]	887	0	0
876	52	tiling_path_fragment	A piece of sequence that makes up a tiling_path (SO:0000472). [SO:ke]	888	0	0
877	52	positively_autoregulated	The gene product is involved in its own transcriptional regulation, where it increases transcription. [SO:ke]	889	0	0
878	52	contig_read	A DNA sequencer read which is part of a contig. [SO:ke]	890	0	0
879	52	polycistronic_gene	A gene that is polycistronic. [SO:ke]	891	1	0
880	52	C_gene_segment	Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	892	0	0
881	52	trans_spliced	An attribute describing transcript sequence that is created by splicing exons from diferent genes. [SO:ke]	893	0	0
882	52	tiling_path_clone	A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. [SO:ke]	894	0	0
883	52	vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration. []	895	0	0
884	52	three_prime_coding_exon_noncoding_region	The sequence of the 3' exon that is not coding. [SO:ke]	896	0	0
885	52	noncoding_region_of_exon	The maximal intersection of exon and UTR. [SO:ke]	897	0	0
886	52	DJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	898	0	0
887	52	vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration. []	899	0	0
888	52	DJ_gene_segment	Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	900	0	0
889	52	five_prime_coding_exon_noncoding_region	The sequence of the 5' exon preceding the start codon. [SO:ke]	901	0	0
890	52	VDJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	902	0	0
891	52	VDJ_gene_segment	Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	903	0	0
892	52	VDJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	904	0	0
893	52	VJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	905	0	0
894	52	VJ_gene_segment	Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	906	0	0
895	52	VJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	907	0	0
1063	52	repeat_unit	The simplest repeated component of a repeat region. A single repeat. [SO:ke]	1078	0	0
896	52	VJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	908	0	0
897	52	D_gene_recombination_feature	Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence. []	909	0	0
898	52	three_prime_D_heptamer	7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	910	0	0
899	52	heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	911	0	0
900	52	three_prime_D_recombination_signal_sequence	Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	912	0	0
901	52	three_prime_D_nonamer	A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	913	0	0
902	52	nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. []	914	0	0
903	52	three_prime_D_spacer	A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	915	0	0
904	52	vertebrate_immune_system_gene_recombination_spacer	A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase. []	916	0	0
905	52	five_prime_D_heptamer	7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	917	0	0
906	52	five_prime_D_recombination_signal_sequence	Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	918	0	0
907	52	five_prime_D_nonamer	9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	919	0	0
908	52	five_prime_D_spacer	12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	920	0	0
909	52	virtual_sequence	A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. [SO:ke]	921	0	0
910	52	Hoogsteen_base_pair	A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. [PMID:12177293]	922	0	0
911	52	reverse_Hoogsteen_base_pair	A type of non-canonical base-pairing. [SO:ke]	923	0	0
912	52	transcribed_region	A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. [SO:ke]	924	1	0
913	52	alternately_spliced_gene_encodeing_one_transcript		925	1	0
914	52	D_DJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	926	0	0
915	52	D_DJ_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	927	0	0
916	52	D_DJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	928	0	0
917	52	pseudogenic_exon	A non functional descendant of an exon, part of a pseudogene. [SO:ke]	929	0	0
918	52	pseudogenic_transcript	A non functional descendant of a transcript, part of a pseudogene. [SO:ke]	930	0	0
919	52	D_DJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	931	0	0
920	52	D_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	932	0	0
921	52	VD_gene_segment	Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	933	0	0
922	52	vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA. []	934	0	0
923	52	J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	935	0	0
924	52	inversion_derived_deficiency_plus_aneuploid	A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. [FB:km]	936	0	0
925	52	J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	937	0	0
1064	52	dispersed_repeat	A repeat that is located at dispersed sites in the genome. [SO:ke]	1079	0	0
926	52	J_nonamer	9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	938	0	0
927	52	J_heptamer	7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	939	0	0
928	52	J_spacer	12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	940	0	0
929	52	V_DJ_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	941	0	0
930	52	V_DJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	942	0	0
931	52	V_VDJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	943	0	0
932	52	V_VDJ_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	944	0	0
933	52	V_VDJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	945	0	0
934	52	V_VJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	946	0	0
935	52	V_VJ_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	947	0	0
936	52	V_VJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	948	0	0
937	52	V_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	949	0	0
938	52	V_D_DJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	950	0	0
939	52	V_D_DJ_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	951	0	0
940	52	V_D_DJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	952	0	0
941	52	V_D_DJ_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	953	0	0
942	52	V_D_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	954	0	0
943	52	V_D_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	955	0	0
944	52	V_heptamer	7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	956	0	0
945	52	V_gene_recombination_feature	Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	957	0	0
946	52	V_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	958	0	0
947	52	V_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	959	0	0
948	52	V_nonamer	9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	960	0	0
949	52	V_spacer	12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	961	0	0
950	52	DJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	962	0	0
951	52	DJ_J_C_cluster	Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	963	0	0
952	52	VDJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	964	0	0
953	52	V_DJ_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	965	0	0
954	52	alternately_spliced_gene_encoding_greater_than_one_transcript		966	1	0
955	52	helitron	A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. [http://www.pnas.org/cgi/content/full/100/11/6569]	967	0	0
1065	52	tmRNA_encoding	A region that can be transcribed into a transfer-messenger RNA (tmRNA). []	1080	0	0
1066	52	DNA_invertase_target_sequence		1081	1	0
956	52	recoding_pseudoknot	The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]	968	0	0
957	52	pseudoknot	A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. [RSC:cb]	969	0	0
958	52	recoding_stimulatory_region	A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]	970	0	0
959	52	designed_sequence	An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence. []	971	0	0
960	52	inversion_derived_bipartite_duplication	A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. [FB:km]	972	0	0
961	52	gene_with_edited_transcript	A gene that encodes a transcript that is edited. [SO:xp]	973	0	0
962	52	edited_transcript	A transcript that is edited. [SO:ke]	974	0	0
963	52	inversion_derived_duplication_plus_aneuploid	A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. [FB:km]	975	0	0
964	52	aneuploid_chromosome	A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. [SO:ke]	976	0	0
965	52	polyA_signal_sequence	The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. [http://www.insdc.org/files/feature_table.html]	977	0	0
966	52	Shine_Dalgarno_sequence	A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. [SO:jh]	978	0	0
967	52	polyA_site	The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. [http://www.insdc.org/files/feature_table.html]	979	0	0
968	52	assortment_derived_deficiency_plus_duplication		981	1	0
969	52	five_prime_clip	5' most region of a precursor transcript that is clipped off during processing. [http://www.insdc.org/files/feature_table.html]	982	0	0
970	52	three_prime_clip	3'-most region of a precursor transcript that is clipped off during processing. [http://www.insdc.org/files/feature_table.html]	983	0	0
971	52	C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	984	0	0
972	52	D_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	985	0	0
973	52	D_J_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	986	0	0
974	52	V_DJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	987	0	0
975	52	V_VDJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	988	0	0
976	52	V_VJ_J_C_cluster	Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]	989	0	0
977	52	inversion_derived_aneuploid_chromosome	A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. [FB:km]	990	0	0
978	52	bidirectional_promoter	A promoter that can allow for transcription in both directions. [PMID:21601935, SO:ke]	991	0	0
979	52	retrotransposed	An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. [SO:ke]	992	0	0
980	52	miRNA_encoding	A region that can be transcribed into a microRNA (miRNA). []	994	0	0
981	52	rRNA_encoding	A region that can be transcribed into a ribosomal RNA (rRNA). []	995	0	0
982	52	scRNA_encoding	A region that can be transcribed into a small cytoplasmic RNA (scRNA). []	996	0	0
983	52	centromere	A region of chromosome where the spindle fibers attach during mitosis and meiosis. [SO:ke]	997	0	0
984	52	chromosomal_structural_element	Regions of the chromosome that are important for structural elements. []	998	0	0
985	52	snoRNA_encoding	A region that can be transcribed into a small nucleolar RNA (snoRNA). []	999	0	0
986	52	edited_transcript_feature	A locatable feature on a transcript that is edited. [SO:ma]	1000	0	0
987	52	methylation_guide_snoRNA_primary_transcript	A primary transcript encoding a methylation guide small nucleolar RNA. [SO:ke]	1001	0	0
988	52	cap	A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]	1002	0	0
989	52	rRNA_cleavage_snoRNA_primary_transcript	A primary transcript encoding an rRNA cleavage snoRNA. [SO:ke]	1003	0	0
990	52	pre_edited_region	The region of a transcript that will be edited. [http://dna.kdna.ucla.edu/rna/index.aspx]	1004	0	0
991	52	tmRNA	A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]	1005	0	0
992	52	C_D_box_snoRNA_encoding	snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end. []	1006	0	0
993	52	tmRNA_primary_transcript	A primary transcript encoding a tmRNA (SO:0000584). [SO:ke]	1007	0	0
994	52	group_I_intron	Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]	1008	0	0
995	52	autocatalytically_spliced_intron	A self spliced intron. [SO:ke]	1009	0	0
996	52	SRP_RNA_primary_transcript	A primary transcript encoding a signal recognition particle RNA. [SO:ke]	1010	0	0
997	52	SRP_RNA	The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]	1011	0	0
998	52	H_pseudoknot	A pseudoknot which contains two stems and at least two loops. [http://www.ncbi.nlm.nih.gov\\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]	1012	0	0
999	52	C_D_box_snoRNA_primary_transcript	A primary transcript encoding a small nucleolar RNA of the box C/D family. [SO:ke]	1013	0	0
1000	52	H_ACA_box_snoRNA	Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]	1014	0	0
1001	52	H_ACA_box_snoRNA_primary_transcript	A primary transcript encoding a small nucleolar RNA of the box H/ACA family. [SO:ke]	1015	0	0
1002	52	transcript_edited_by_U_insertion/deletion	The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. [http://www.rna.ucla.edu/index.html]	1016	1	0
1003	52	edited_by_C_insertion_and_dinucleotide_insertion		1017	1	0
1004	52	edited_by_C_to_U_substitution		1018	1	0
1005	52	edited_by_A_to_I_substitution		1019	1	0
1006	52	edited_by_G_addition		1020	1	0
1007	52	guide_RNA	A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. [http://www.rna.ucla.edu/index.html]	1021	0	0
1008	52	editing_block	Edited mRNA sequence mediated by a single guide RNA (SO:0000602). [http://dna.kdna.ucla.edu/rna/index.aspx]	1022	0	0
1009	52	intergenic_region	A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. [SO:cjm]	1023	0	0
1010	52	editing_domain	Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). [http://dna.kdna.ucla.edu/rna/index.aspx]	1024	0	0
1011	52	unedited_region	The region of an edited transcript that will not be edited. [http://dna.kdna.ucla.edu/rna/index.aspx]	1025	0	0
1012	52	H_ACA_box_snoRNA_encoding	snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA). []	1026	0	0
1013	52	oligo_U_tail	The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). [http://www.rna.ucla.edu/]	1027	0	0
1014	52	polyA_sequence	Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. [SO:ke]	1028	0	0
1015	52	branch_site	A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. [SO:ke]	1029	0	0
1016	52	polypyrimidine_tract	The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. [http://nar.oupjournals.org/cgi/content/full/25/4/888]	1030	0	0
1017	52	bacterial_RNApol_promoter	A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. [SO:ke]	1031	0	0
1018	52	prokaryotic_promoter	A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous. [PMID:32665585]	1032	0	0
1019	52	bacterial_terminator	A terminator signal for bacterial transcription. [SO:ke]	1033	0	0
1020	52	terminator_of_type_2_RNApol_III_promoter	A terminator signal for RNA polymerase III transcription. [SO:ke]	1034	0	0
1021	52	eukaryotic_terminator	A signal for RNA polymerase to terminate transcription. []	1035	0	0
1022	52	transcription_end_site	The base where transcription ends. [SO:ke]	1036	0	0
1023	52	RNApol_III_promoter_type_1	This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species. [PMID:12381659]	1037	0	0
1024	52	RNApol_III_promoter_type_2	This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box. [PMID:12381659]	1038	0	0
1025	52	A_box	A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. [SO:ke]	1039	0	0
1026	52	B_box	A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. [SO:ke]	1040	0	0
1027	52	RNApol_III_promoter_type_3	This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream.  [PMID:12381659]	1041	0	0
1028	52	C_box	An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. [SO:ke]	1042	0	0
1029	52	snRNA_encoding	A region that can be transcribed into a small nuclear RNA (snRNA). []	1043	0	0
1030	52	telomere	A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. [SO:ma]	1044	0	0
1031	52	silencer	A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. [SO:ke]	1045	0	0
1032	52	insulator	A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region. [NCBI:cf, PMID:12154228, SO:regcreative]	1046	0	0
1033	52	five_prime_open_reading_frame	An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame. [PMID:12890013]	1047	0	0
1034	52	upstream_AUG_codon	A start codon upstream of the ORF. [SO:ke]	1048	0	0
1035	52	UTR_region	A region of UTR. [SO:ke]	1049	0	0
1036	52	polycistronic_primary_transcript	A primary transcript encoding for more than one gene product. [SO:ke]	1050	0	0
1037	52	monocistronic_primary_transcript	A primary transcript encoding for one gene product. [SO:ke]	1051	0	0
1038	52	monocistronic_transcript	A transcript that is monocistronic. [SO:xp]	1052	0	0
1039	52	monocistronic	An attribute describing a sequence that contains the code for one gene product. [SO:ke]	1053	0	0
1040	52	monocistronic_mRNA	An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. [SO:rd]	1054	0	0
1041	52	polycistronic_mRNA	An mRNA that encodes multiple proteins from at least two non-overlapping regions. [SO:rd]	1055	0	0
1042	52	mini_exon_donor_RNA	A primary transcript that donates the spliced leader to other mRNA. [SO:ke]	1056	0	0
1043	52	spliced_leader_RNA	Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes. [PMID:24130571]	1057	0	0
1044	52	engineered_plasmid	A plasmid that is engineered. [SO:xp]	1058	0	0
1045	52	transcribed_spacer_region	Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. [http://oregonstate.edu/instruction/bb492/general/glossary.html]	1059	0	0
1046	52	rRNA_primary_transcript_region	A region of an rRNA primary transcript. [SO:ke]	1060	0	0
1047	52	internal_transcribed_spacer_region	Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. [SO:ke]	1061	0	0
1048	52	external_transcribed_spacer_region	Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. [SO:ke]	1062	0	0
1049	52	tetranucleotide_repeat_microsatellite_feature	A region of a repeating tetranucleotide sequence (four bases). []	1063	0	0
1050	52	SRP_RNA_encoding	A region that can be transcribed into a signal recognition particle RNA (SRP RNA). []	1064	0	0
1051	52	minisatellite	A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. [http://www.informatics.jax.org/silver/glossary.shtml]	1065	0	0
1052	52	antisense_primary_transcript	The reverse complement of the primary transcript. [SO:ke]	1066	0	0
1053	52	siRNA	A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules. [PMID:12592000]	1067	0	0
1054	52	miRNA_primary_transcript	A primary transcript encoding a micro RNA. [SO:ke]	1068	0	0
1055	52	cytosolic_rRNA	Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes. [PMID:3044395]	1070	0	0
1056	52	cytosolic_5S_rRNA	Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]	1071	0	0
1057	52	cytosolic_rRNA_5S_gene	A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes. []	1072	0	0
1058	52	cytosolic_28S_rRNA	Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes. [SO:ke]	1073	0	0
1059	52	cytosolic_rRNA_28S_gene	A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes. []	1074	0	0
1060	52	maxicircle_gene	A mitochondrial gene located in a maxicircle. [SO:xp]	1075	0	0
1061	52	maxicircle	A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. [PMID:8395055]	1076	0	0
1062	52	stRNA_encoding	A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development. []	1077	0	0
1067	52	intron_attribute		1082	1	0
1068	52	tRNA_encoding	A region that can be transcribed into a transfer RNA (tRNA). []	1083	0	0
1069	52	introgressed_chromosome_region	A region of a chromosome that has been introduced by backcrossing with a separate species. [PMID:11454782]	1084	0	0
1070	52	mobile_intron	An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. [SO:ke]	1085	0	0
1071	52	mobile_genetic_element	A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. [PMID:14681355]	1086	0	0
1072	52	mobile	An attribute describing a feature that has either intra-genome or intracellular mobility. [RSC:cb]	1087	0	0
1073	52	insertion	The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. [SO:ke]	1088	0	0
1074	52	EST_match	A match against an EST sequence. [SO:ke]	1091	0	0
1075	52	chromosome_breakage_sequence	A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. [SO:ma]	1092	0	0
1076	52	internal_eliminated_sequence	A sequence eliminated from the genome of ciliates during nuclear differentiation. [SO:ma]	1093	0	0
1077	52	macronucleus_destined_segment	A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. [SO:ma]	1094	0	0
1078	52	gene_member_region	A region of a gene. [SO:ke]	1095	0	0
1079	52	unit_of_gene_expression	Transcription units or transcribed coding sequences. [Bacterial_regulation_working_group:CMA, PMID:32665585]	1096	0	0
1080	52	non_canonical_splice_site	A splice site where the donor and acceptor sites differ from the canonical form. [SO:ke]	1097	1	0
1081	52	canonical_splice_site	The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. [SO:ke]	1098	1	0
1082	52	canonical_three_prime_splice_site	The canonical 3' splice site has the sequence \\"AG\\". [SO:ke]	1099	0	0
1083	52	canonical_five_prime_splice_site	The canonical 5' splice site has the sequence \\"GT\\". [SO:ke]	1100	0	0
1084	52	non_canonical_three_prime_splice_site	A 3' splice site that does not have the sequence \\"AG\\". [SO:ke]	1101	0	0
1085	52	non_canonical_five_prime_splice_site	A 5' splice site which does not have the sequence \\"GT\\". [SO:ke]	1102	0	0
1086	52	non_canonical_start_codon	A start codon that is not the usual AUG sequence. [SO:ke]	1103	0	0
1087	52	aberrant_processed_transcript	A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons. [SO:ke]	1104	0	0
1088	52	splicing_feature		1105	1	0
1089	52	exonic_splice_enhancer	Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. [http://www.ncbi.nlm.nih.gov\\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]	1106	0	0
1090	52	DNaseI_hypersensitive_site	DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I. []	1107	0	0
1091	52	translocation_element	A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. [SO:ma]	1108	0	0
1092	52	chromosomal_translocation	A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations. [FB:reference_manual]	1109	0	0
1093	52	deletion_junction	The space between two bases in a sequence which marks the position where a deletion has occurred. [SO:ke]	1110	0	0
1094	52	cDNA_match	A match against cDNA sequence. [SO:ke]	1111	0	0
1095	52	gene_with_polycistronic_transcript	A gene that encodes a polycistronic transcript. [SO:xp]	1112	0	0
1096	52	cleaved_initiator_methionine	The initiator methionine that has been cleaved from a mature polypeptide sequence. [EBIBS:GAR]	1113	0	0
1097	52	cleaved_peptide_region	The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. [EBIBS:GAR]	1115	0	0
1098	52	gene_with_dicistronic_transcript	A gene that encodes a dicistronic transcript. [SO:xp]	1116	0	0
1099	52	gene_with_recoded_mRNA	A gene that encodes an mRNA that is recoded. [SO:xp]	1117	0	0
1100	52	recoded	An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. [SO:ke]	1118	0	0
1101	52	SNP	SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. [SO:cb]	1119	0	0
1102	52	SNV	SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. [SO:bm]	1120	0	0
1103	52	biomaterial_region	A region which is intended for use in an experiment. [SO:cb]	1121	0	0
1104	52	gene_with_stop_codon_read_through	A gene that encodes a transcript with stop codon readthrough. [SO:xp]	1122	0	0
1105	52	stop_codon_read_through	A stop codon redefined to be a new amino acid. [SO:ke]	1123	0	0
1106	52	gene_with_stop_codon_redefined_as_pyrrolysine	A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. [SO:xp]	1124	0	0
1107	52	stop_codon_redefined_as_pyrrolysine	A stop codon redefined to be the new amino acid, pyrrolysine. [SO:ke]	1125	0	0
1108	52	possible_base_call_error	A region of sequence where the validity of the base calling is questionable. [SO:ke]	1126	0	0
1109	52	possible_assembly_error	A region of sequence where there may have been an error in the assembly. [SO:ke]	1127	0	0
1110	52	experimental_result_region	A region of sequence implicated in an experimental result. [SO:ke]	1128	0	0
1111	52	trans_splice_acceptor_site	The 3' splice site of the acceptor primary transcript. [SO:ke]	1129	0	0
1112	52	trans_splice_site	Primary transcript region bordering trans-splice junction. [SO:ke]	1130	0	0
1113	52	trans_splice_donor_site	The 5' five prime splice site region of the donor RNA. [SO:ke]	1131	0	0
1114	52	SL1_acceptor_site	A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. [SO:nlw]	1132	0	0
1115	52	SL2_acceptor_site	A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	1133	0	0
1116	52	gene_with_stop_codon_redefined_as_selenocysteine	A gene encoding an mRNA that has the stop codon redefined as selenocysteine. [SO:xp]	1134	0	0
1117	52	stop_codon_redefined_as_selenocysteine	A stop codon redefined to be the new amino acid, selenocysteine. [SO:ke]	1135	0	0
1118	52	gene_with_mRNA_recoded_by_translational_bypass	A gene with mRNA recoded by translational bypass. [SO:xp]	1136	0	0
1119	52	recoded_by_translational_bypass	Recoded mRNA where a block of nucleotides is not translated. [SO:ke]	1137	0	0
1120	52	gene_with_transcript_with_translational_frameshift	A gene encoding a transcript that has a translational frameshift. [SO:xp]	1138	0	0
1121	52	nucleotide_motif	A region of nucleotide sequence corresponding to a known motif. [SO:ke]	1139	0	0
1122	52	sequence_motif	A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. [http://en.wikipedia.org/wiki/Sequence_motif]	1140	0	0
1123	52	dicistronic_mRNA	An mRNA that has the quality dicistronic. [SO:ke]	1141	0	0
1124	52	blocked_reading_frame	A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons. [SGD:rb]	1142	0	0
1125	52	foreign_transposable_element	A transposable element that is foreign. [SO:ke]	1143	0	0
1126	52	gene_with_dicistronic_primary_transcript	A gene that encodes a dicistronic primary transcript. [SO:xp]	1144	0	0
1127	52	dicistronic_primary_transcript	A primary transcript that has the quality dicistronic. [SO:xp]	1145	0	0
1128	52	gene_with_dicistronic_mRNA	A gene that encodes a polycistronic mRNA. [SO:xp]	1146	0	0
1129	52	iDNA	Genomic sequence removed from the genome, as a normal event, by a process of recombination. [SO:ma]	1147	0	0
1130	52	oriT	A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. [http://www.insdc.org/files/feature_table.html]	1148	0	0
1131	52	transit_peptide	The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). [http://www.insdc.org/files/feature_table.html]	1149	0	0
1132	52	transit_peptide_region_of_CDS	CDS region corresponding to a transit peptide region of a polypeptide. []	1151	0	0
1133	52	intein	A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. [SO:ke]	1152	0	0
1134	52	intein_containing	An attribute of protein-coding genes where the initial protein product contains an intein. [SO:ke]	1153	0	0
1135	52	gap	A gap in the sequence of known length. The unknown bases are filled in with N's. [SO:ke]	1154	0	0
1136	52	fragmentary	An attribute to describe a feature that is incomplete. [SO:ke]	1155	0	0
1137	52	status	An attribute describing the status of a feature, based on the available evidence. [SO:ke]	1156	0	0
1138	52	predicted	An attribute describing an unverified region. [SO:ke]	1157	0	0
1139	52	exemplar_mRNA	An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. [http://mged.sourceforge.net/ontologies/MGEDontology.php]	1158	0	0
1140	52	exemplar	An attribute describing a sequence is representative of a class of similar sequences. [SO:ke]	1159	0	0
1141	52	sequence_location	The location of a sequence. []	1160	0	0
1142	52	genome	A genome is the sum of genetic material within a cell or virion. [SO:immuno_workshop]	1162	0	0
1143	52	minicircle	A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. [PMID:8395055]	1163	0	0
1144	52	amplification_origin	An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. [SO:ma]	1165	0	0
1145	52	gene_group_regulatory_region	A region that is involved in the regulation of transcription of a group of regulated genes. []	1166	1	0
1146	52	lambda_vector	The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. [ISBN:0-1767-2380-8]	1167	0	0
1147	52	plasmid_vector	A plasmid that has been generated to act as a vector for foreign sequence. []	1168	0	0
1148	52	single_stranded_cDNA	DNA synthesized from RNA by reverse transcriptase, single stranded. []	1169	0	0
1149	52	double_stranded_cDNA	DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded. []	1170	0	0
1150	52	plasmid_clone		1171	1	0
1151	52	YAC_clone		1172	1	0
1152	52	phagemid_clone		1173	1	0
1153	52	PAC_clone		1174	1	0
1154	52	fosmid_clone		1175	1	0
1155	52	BAC_clone		1176	1	0
1156	52	cosmid_clone		1177	1	0
1157	52	pyrrolysyl_tRNA	A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. [SO:ke]	1178	0	0
1158	52	pyrrolysine_tRNA_primary_transcript	A primary transcript encoding pyrrolysyl tRNA (SO:0000766). [RSC:cb]	1179	0	0
1159	52	clone_insert_start(SO:0000767)		1180	1	0
1160	52	episome	A plasmid that may integrate with a chromosome. [SO:ma]	1181	0	0
1161	52	tmRNA_coding_piece	The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]	1182	0	0
1162	52	tmRNA_region	A region of a tmRNA. [SO:cb]	1183	0	0
1163	52	tmRNA_acceptor_piece	The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. [doi:10.1093/nar/gkh795, Indiana:kw]	1184	0	0
1164	52	genomic_island	A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. [Phigo:at, SO:ke]	1185	0	0
1165	52	pathogenic_island	Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. [SO:ke]	1186	0	0
1166	52	metabolic_island	A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. [SO:ke]	1187	0	0
1167	52	adaptive_island	An adaptive island is a genomic island that provides an adaptive advantage to the host. [SO:ke]	1188	0	0
1168	52	symbiosis_island	A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. [SO:ke]	1189	0	0
1169	52	pseudogenic_rRNA	A non functional descendant of an rRNA. [SO:ke]	1190	0	0
1170	52	pseudogenic_tRNA	A non functional descendent of a tRNA. [SO:ke]	1191	0	0
1171	52	engineered_episome	An episome that is engineered. [SO:xp]	1192	0	0
1172	52	transposable_element_attribute		1193	1	0
1173	52	transgenic	Attribute describing sequence that has been integrated with foreign sequence. [SO:ke]	1194	0	0
1174	52	natural	An attribute describing a feature that occurs in nature. [SO:ke]	1195	0	0
1175	52	cloned_region	The region of sequence that has been inserted and is being propagated by the clone. []	1196	0	0
1176	52	reagent_attribute		1197	1	0
1177	52	clone_attribute		1198	1	0
1178	52	cloned		1199	1	0
1179	52	cloned_genomic		1200	1	0
1180	52	cloned_cDNA		1201	1	0
1181	52	engineered_DNA		1202	1	0
1182	52	engineered_rescue_region	A rescue region that is engineered. [SO:xp]	1203	0	0
1183	52	rescue_mini_gene	A mini_gene that rescues. [SO:xp]	1204	0	0
1184	52	mini_gene	By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. [PMID:15992143]	1205	0	0
1185	52	transgenic_transposable_element	TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. [FB:mc]	1206	0	0
1186	52	natural_transposable_element	TE that exists (or existed) in nature. [FB:mc]	1207	0	0
1187	52	extrachromosomal_mobile_genetic_element	An MGE that is not integrated into the host chromosome. [SO:ke]	1208	0	0
1188	52	engineered_transposable_element	TE that has been modified by manipulations in vitro. [FB:mc]	1209	0	0
1189	52	engineered_foreign_transposable_element	A transposable_element that is engineered and foreign. [FB:mc]	1210	0	0
1190	52	assortment_derived_duplication(SO:0000800)	A multi-chromosome duplication aberration generated by reassortment of other aberration components. [FB:gm]	1211	0	0
1191	52	assortment_derived_variation	A chromosome variation derived from an event during meiosis. [SO:ke]	1212	0	0
1192	52	assortment_derived_deficiency_plus_duplication(SO:0000801)	A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication. [FB:gm]	1213	0	0
1193	52	assortment_derived_deficiency(SO:0000802)	A multi-chromosome deficiency aberration generated by reassortment of other aberration components. [FB:gm]	1214	0	0
1194	52	assortment_derived_aneuploid(SO:0000803)	A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication. [FB:gm]	1215	0	0
1195	52	engineered_tag	A tag that is engineered. [SO:xp]	1216	0	0
1196	52	validated_cDNA_clone	A cDNA clone that has been validated. [SO:xp]	1217	0	0
1197	52	invalidated_cDNA_clone	A cDNA clone that is invalid. [SO:xp]	1218	0	0
1198	52	chimeric_cDNA_clone	A cDNA clone invalidated because it is chimeric. [SO:xp]	1219	0	0
1199	52	genomically_contaminated_cDNA_clone	A cDNA clone invalidated by genomic contamination. [SO:xp]	1220	0	0
1200	52	polyA_primed_cDNA_clone	A cDNA clone invalidated by polyA priming. [SO:xp]	1221	0	0
1201	52	partially_processed_cDNA_clone	A cDNA invalidated clone by partial processing. [SO:xp]	1222	0	0
1202	52	rescue_gene	A gene that rescues. [SO:xp]	1223	0	0
1203	52	wild_type	An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. [SO:ke]	1224	0	0
1204	52	wild_type_rescue_gene	A gene that rescues. [SO:xp]	1226	0	0
1205	52	mitochondrial_chromosome	A chromosome originating in a mitochondria. [SO:xp]	1227	0	0
1206	52	chloroplast_chromosome	A chromosome originating in a chloroplast. [SO:xp]	1228	0	0
1207	52	chromoplast_chromosome	A chromosome originating in a chromoplast. [SO:xp]	1229	0	0
1208	52	cyanelle_chromosome	A chromosome originating in a cyanelle. [SO:xp]	1230	0	0
1209	52	leucoplast_chromosome	A chromosome with origin in a leucoplast. [SO:xp]	1231	0	0
1210	52	macronuclear_chromosome	A chromosome originating in a macronucleus. [SO:xp]	1232	0	0
1211	52	micronuclear_chromosome	A chromosome originating in a micronucleus. [SO:xp]	1233	0	0
1212	52	nuclear_chromosome	A chromosome originating in a nucleus. [SO:xp]	1234	0	0
1213	52	nucleomorphic_chromosome	A chromosome originating in a nucleomorph. [SO:xp]	1235	0	0
1214	52	promoter_region	A region of sequence which is part of a promoter. [SO:ke]	1236	1	0
1215	52	mature_transcript_region	A region of a mature transcript. [SO:ke]	1237	0	0
1216	52	bacterial_RNApol_promoter_region	A region which is part of a bacterial RNA polymerase promoter. [SO:ke]	1240	1	0
1217	52	RNApol_II_promoter_region	A region of sequence which is a promoter for RNA polymerase II. [SO:ke]	1241	1	0
1218	52	RNApol_III_promoter_type_1_region	A region of sequence which is a promoter for RNA polymerase III type 1. [SO:ke]	1242	1	0
1219	52	RNApol_III_promoter_type_2_region	A region of sequence which is a promoter for RNA polymerase III type 2. [SO:ke]	1243	1	0
1220	52	exon_region	A region of an exon. [RSC:cb]	1244	0	0
1221	52	homologous_region	A region that is homologous to another region. [SO:ke]	1245	0	0
1222	52	homologous	Similarity due to common ancestry. [SO:ke]	1246	0	0
1223	52	paralogous_region	A homologous_region that is paralogous to another region. [SO:ke]	1247	0	0
1224	52	paralogous	An attribute describing a kind of homology where divergence occurred after a duplication event. [SO:ke]	1248	0	0
1225	52	orthologous_region	A homologous_region that is orthologous to another region. [SO:ke]	1249	0	0
1226	52	orthologous	An attribute describing a kind of homology where divergence occurred after a speciation event. [SO:ke]	1250	0	0
1227	52	conserved	A region that is similar or identical across more than one species. []	1251	0	0
1228	52	syntenic	Attribute describing sequence regions occurring in same order on chromosome of different species. [SO:ke]	1252	0	0
1229	52	capped_primary_transcript	A primary transcript that is capped. [SO:xp]	1253	0	0
1230	52	capped_mRNA	An mRNA that is capped. [SO:xp]	1254	0	0
1231	52	trans_spliced_mRNA	An mRNA that is trans-spliced. [SO:xp]	1255	0	0
1232	52	anchor_binding_site		1256	0	0
1233	52	edited_transcript_by_A_to_I_substitution	A transcript that has been edited by A to I substitution. [SO:ke]	1257	0	0
1234	52	alternatively_spliced	An attribute describing a situation where a gene may encode for more than 1 transcript. [SO:ke]	1258	0	0
1235	52	codon_redefined	An attribute describing the alteration of codon meaning. [SO:ke]	1259	0	0
1236	52	maternally_imprinted_gene	A gene that is maternally_imprinted. [SO:xp]	1260	0	0
1237	52	paternally_imprinted_gene	A gene that is paternally imprinted. [SO:xp]	1261	0	0
1238	52	post_translationally_regulated_gene	A gene that is post translationally regulated. [SO:xp]	1262	0	0
1239	52	negatively_autoregulated_gene	A gene that is negatively autoreguated. [SO:xp]	1263	0	0
1240	52	positively_autoregulated_gene	A gene that is positively autoregulated. [SO:xp]	1264	0	0
1241	52	translationally_regulated_gene	A gene that is translationally regulated. [SO:xp]	1265	0	0
1242	52	allelically_excluded_gene	A gene that is allelically_excluded. [SO:xp]	1266	0	0
1243	52	nuclear_mitochondrial	An attribute describing a nuclear pseudogene of a mitochndrial gene. [SO:ke]	1267	1	0
1244	52	processed	An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail. [SO:ke]	1268	1	0
1245	52	unequally_crossed_over	An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. [SO:ke]	1269	1	0
1246	52	independently_known	Attribute to describe a feature that is independently known - not predicted. [SO:ke]	1270	0	0
1247	52	supported_by_sequence_similarity	An attribute to describe a feature that has been predicted using sequence similarity techniques. [SO:ke]	1271	0	0
1248	52	supported_by_domain_match	An attribute to describe a feature that has been predicted using sequence similarity of a known domain. [SO:ke]	1272	0	0
1249	52	supported_by_EST_or_cDNA	An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. [SO:ke]	1273	0	0
1250	52	orphan	A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. []	1274	0	0
1251	52	predicted_by_ab_initio_computation	An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. [SO:ke]	1275	0	0
1252	52	asx_turn	A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). [http://www.ebi.ac.uk/msd-srv/msdmotif/]	1276	0	0
1253	52	polypeptide_turn_motif	A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. [EBIBS:GAR, uniprot:feature_type]	1278	0	0
1254	52	cloned_cDNA_insert	A clone insert made from cDNA. [SO:xp]	1279	0	0
1255	52	cloned_genomic_insert	A clone insert made from genomic DNA. [SO:xp]	1280	0	0
1259	52	delete_U	An edit to delete a uridine. [SO:ke]	1284	1	0
1260	52	substitute_A_to_I	An edit to substitute an I for an A. [SO:ke]	1285	1	0
1261	52	insert_C	An edit to insert a cytidine. [SO:ke]	1286	1	0
1262	52	insert_dinucleotide	An edit to insert a dinucleotide. [SO:ke]	1287	1	0
1263	52	substitute_C_to_U	An edit to substitute an U for a C. [SO:ke]	1288	1	0
1264	52	insert_G	An edit to insert a G. [SO:ke]	1289	1	0
1265	52	insert_GC	An edit to insert a GC dinucleotide. [SO:ke]	1290	1	0
1266	52	insert_GU	An edit to insert a GU dinucleotide. [SO:ke]	1291	1	0
1267	52	insert_CU	An edit to insert a CU dinucleotide. [SO:ke]	1292	1	0
1268	52	insert_AU	An edit to insert a AU dinucleotide. [SO:ke]	1293	1	0
1269	52	insert_AA	An edit to insert a AA dinucleotide. [SO:ke]	1294	1	0
1270	52	edited_mRNA	An mRNA that is edited. [SO:xp]	1295	0	0
1271	52	guide_RNA_region	A region of guide RNA. [SO:ma]	1296	0	0
1272	52	anchor_region	A region of a guide_RNA that base-pairs to a target mRNA. [SO:jk]	1297	0	0
1273	52	pre_edited_mRNA	A primary transcript that, at least in part, encodes one or more proteins that has not been edited. []	1298	0	0
1274	52	intermediate	An attribute to describe a feature between stages of processing. [SO:ke]	1299	0	0
1275	52	miRNA_target_site	A miRNA target site is a binding site where the molecule is a micro RNA. [FB:cds]	1300	0	0
1276	52	nucleotide_binding_site	A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. [SO:cb]	1301	0	0
1277	52	edited_CDS	A CDS that is edited. [SO:xp]	1302	0	0
1278	52	vertebrate_immune_system_feature		1303	1	0
1279	52	recombinationally_rearranged_vertebrate_immune_system_gene	A recombinationally rearranged gene of the vertebrate immune system. [SO:xp]	1304	0	0
1280	52	attP_site	An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome. [SO:as]	1305	0	0
1281	52	phage_sequence	The nucleotide sequence of a virus that infects bacteria. [SO:ke]	1306	0	0
1282	52	attB_site	An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. [SO:as]	1307	0	0
1283	52	attL_site	A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site. [SO:as]	1308	0	0
1284	52	attR_site	A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site. [SO:as]	1309	0	0
1285	52	dif_site	A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. [SO:as]	1310	0	0
1286	52	attC_site	An attC site is a sequence required for the integration of a DNA of an integron. [SO:as]	1311	0	0
1287	52	oriV	An origin of vegetative replication in plasmids and phages. [SO:as]	1312	0	0
1288	52	oriC	An origin of bacterial chromosome replication. [SO:as]	1313	0	0
1289	52	DNA_chromosome	Structural unit composed of a self-replicating, DNA molecule. [SO:ma]	1314	0	0
1290	52	double_stranded_DNA_chromosome	Structural unit composed of a self-replicating, double-stranded DNA molecule. [SO:ma]	1315	0	0
1291	52	double	When a nucleotide polymer has two strands that are reverse-complement to one another and pair together. []	1316	0	0
1292	52	single_stranded_DNA_chromosome	Structural unit composed of a self-replicating, single-stranded DNA molecule. [SO:ma]	1317	0	0
1293	52	single	When a nucleotide polymer has only one strand. []	1318	0	0
1294	52	linear_double_stranded_DNA_chromosome	Structural unit composed of a self-replicating, double-stranded, linear DNA molecule. [SO:ma]	1319	0	0
1295	52	linear	A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. [SO:cb]	1320	0	0
1296	52	circular_double_stranded_DNA_chromosome	Structural unit composed of a self-replicating, double-stranded, circular DNA molecule. [SO:ma]	1321	0	0
1297	52	circular	A quality of a nucleotide polymer that has no terminal nucleotide residues. [SO:cb]	1322	0	0
1298	52	linear_single_stranded_DNA_chromosome	Structural unit composed of a self-replicating, single-stranded, linear DNA molecule. [SO:ma]	1323	0	0
1299	52	circular_single_stranded_DNA_chromosome	Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. [SO:ma]	1324	0	0
1300	52	RNA_chromosome	Structural unit composed of a self-replicating, RNA molecule. [SO:ma]	1325	0	0
1301	52	single_stranded_RNA_chromosome	Structural unit composed of a self-replicating, single-stranded RNA molecule. [SO:ma]	1326	0	0
1302	52	linear_single_stranded_RNA_chromosome	Structural unit composed of a self-replicating, single-stranded, linear RNA molecule. [SO:ma]	1327	0	0
1303	52	linear_double_stranded_RNA_chromosome	Structural unit composed of a self-replicating, double-stranded, linear RNA molecule. [SO:ma]	1328	0	0
1304	52	double_stranded_RNA_chromosome	Structural unit composed of a self-replicating, double-stranded RNA molecule. [SO:ma]	1329	0	0
1305	52	circular_single_stranded_RNA_chromosome	Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. [SO:ma]	1330	0	0
1306	52	circular_double_stranded_RNA_chromosome	Structural unit composed of a self-replicating, double-stranded, circular RNA molecule. [SO:ma]	1331	0	0
1307	52	sequence_replication_mode		1332	1	0
1308	52	rolling_circle		1333	1	0
1309	52	theta_replication		1334	1	0
1310	52	DNA_replication_mode		1335	1	0
1311	52	RNA_replication_mode		1336	1	0
1312	52	insertion_sequence	A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats. [SO:as]	1337	0	0
1313	52	minicircle_gene	A gene found within a minicircle. []	1338	0	0
1314	52	cryptic	A feature_attribute describing a feature that is not manifest under normal conditions. [SO:ke]	1339	0	0
1315	52	template_region	A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. [SO:jk]	1340	0	0
1316	52	gRNA_encoding	A non-protein_coding gene that encodes a guide_RNA. [SO:ma]	1341	0	0
1317	52	rho_dependent_bacterial_terminator	A transcription terminator that is dependent upon Rho. []	1343	0	0
1318	52	rho_independent_bacterial_terminator	A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure. []	1344	0	0
1319	52	strand_attribute	The attribute of how many strands are present in a nucleotide polymer. []	1345	0	0
1320	52	topology_attribute	The attribute of whether a nucleotide polymer is linear or circular. []	1346	0	0
1321	52	class_II_RNA	Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. [PMID:15333696]	1347	0	0
1322	52	class_I_RNA	Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. [PMID:15333696]	1348	0	0
1323	52	BAC_cloned_genomic_insert	A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome. []	1349	0	0
1324	52	consensus	A sequence produced from an aligment algorithm that uses multiple sequences as input. []	1350	0	0
1325	52	consensus_region	A region that has a known consensus sequence. []	1351	0	0
1326	52	consensus_mRNA	An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input. []	1352	0	0
1327	52	predicted_gene	A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments. []	1353	0	0
1328	52	gene_fragment	A portion of a gene that is not the complete gene. []	1354	0	0
1329	52	recursive_splice_site	A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. [http://www.genetics.org/cgi/content/full/170/2/661]	1355	0	0
1330	52	BAC_end	A region of sequence from the end of a BAC clone that may provide a highly specific marker. [SO:ke]	1356	0	0
1331	52	cytosolic_16S_rRNA	Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes. [SO:ke]	1357	0	0
1332	52	cytosolic_rRNA_16S_gene	A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes. []	1358	0	0
1333	52	cytosolic_23S_rRNA	Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes. [SO:ke]	1359	0	0
1334	52	cytosolic_rRNA_23S_gene	A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes. []	1360	0	0
1335	52	cytosolic_25S_rRNA	Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes. [PMID:15493135, PMID:2100998, RSC:cb]	1361	0	0
1336	52	cytosolic_rRNA_25S_gene	A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes. []	1362	0	0
1337	52	solo_LTR	A recombination product between the 2 LTR of the same element. [SO:ke]	1363	0	0
1338	52	low_complexity	When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases. []	1364	0	0
1339	52	low_complexity_region	A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides. []	1365	0	0
1340	52	prophage	A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\". [GOC:jl]	1366	0	0
1341	52	cryptic_prophage	A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes. [GOC:jl]	1367	0	0
1342	52	tetraloop	A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. [SO:ke]	1368	0	0
1343	52	DNA_constraint_sequence	A double-stranded DNA used to control macromolecular structure and function. [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50]	1369	0	0
1344	52	i_motif	A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. [PMID:9753739]	1370	0	0
1345	52	PNA_oligo	Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. [SO:ke]	1371	0	0
1346	52	PNA	An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. [RSC:cb]	1372	0	0
1347	52	DNAzyme	A DNA sequence with catalytic activity. [SO:cb]	1373	0	0
1348	52	MNP	A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]	1374	0	0
1349	52	MNV	An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence. [NCBI:th]	1375	0	0
1350	52	intron_domain	An intronic region that has an attribute. []	1376	0	0
1351	52	wobble_base_pair	A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. [PMID:11256617]	1377	0	0
1352	52	internal_guide_sequence	A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. [SO:cb]	1378	0	0
1353	52	silent_mutation	A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation. [SO:ke]	1379	0	0
1354	52	feature_variant	A sequence variant that falls entirely or partially within a genomic feature. [EBI:fc, SO:ke]	1381	0	0
1355	52	epitope	A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. [http://en.wikipedia.org/wiki/Epitope, SO:cb]	1382	0	0
1356	52	copy_number_variation	A variation that increases or decreases the copy number of a given region. [SO:ke]	1383	0	0
1357	52	sequence_variant_affecting_copy_number		1384	1	0
1358	52	chromosome_breakpoint	A chromosomal region that may sustain a double-strand break, resulting in a recombination event. []	1385	0	0
1359	52	inversion_breakpoint	The point within a chromosome where an inversion begins or ends. [SO:cb]	1387	0	0
1360	52	allele	An allele is one of a set of coexisting sequence variants of a gene. [SO:immuno_workshop]	1388	0	0
1361	52	haplotype	A haplotype is one of a set of coexisting sequence variants of a haplotype block. [SO:immuno_workshop]	1389	0	0
1362	52	polymorphic_sequence_variant	A sequence variant that is segregating in one or more natural populations of a species. [SO:immuno_workshop]	1390	0	0
1363	52	sequence_collection	A collection of discontinuous sequences. [SO:ke]	1391	0	0
1364	52	genotype	A genotype is a variant genome, complete or incomplete. [SO:immuno_workshop]	1392	0	0
1365	52	diplotype	A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. [SO:immuno_workshop]	1393	0	0
1366	52	direction_attribute	The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse). []	1394	0	0
1367	52	mitochondrial_DNA	DNA belonging to the genome of a mitochondria. []	1395	0	0
1368	52	chloroplast_DNA	DNA belonging to the genome of a chloroplast, a photosynthetic plastid. []	1396	0	0
1369	52	miRtron	A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. [PMID:17589500, SO:ma]	1397	0	0
1370	52	arginyl_tRNA	A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. [SO:ke]	1398	0	0
1371	52	integrated_plasmid	A plasmid sequence that is integrated within the host chromosome. [SO:ke]	1399	0	0
1372	52	viral_sequence	The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. [SO:ke]	1400	0	0
1373	52	attCtn_site	An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. [Phigo:at]	1401	0	0
1374	52	nuclear_mt_pseudogene	A nuclear pseudogene of either coding or non-coding mitochondria derived sequence. [SO:xp]	1402	0	0
1375	52	cointegrated_plasmid	A MGE region consisting of two fused plasmids resulting from a replicative transposition event. [phigo:at]	1403	0	0
1376	52	IRLinv_site	Component of the inversion site located at the left of a region susceptible to site-specific inversion. [Phigo:at]	1404	0	0
1377	52	inversion_site_part	A region located within an inversion site. [SO:ke]	1405	0	0
1378	52	IRRinv_site	Component of the inversion site located at the right of a region susceptible to site-specific inversion. [Phigo:at]	1406	0	0
1379	52	defective_conjugative_transposon	An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon. [Phigo:ariane]	1407	0	0
1380	52	repeat_fragment	A portion of a repeat, interrupted by the insertion of another element. [SO:ke]	1408	0	0
1381	52	nested_repeat(SO:0001649)	A repeat that is disrupted by the insertion of another element. [SO:ke]	1409	0	0
1382	52	nested_region		1410	1	0
1383	52	nested_repeat		1411	1	0
1384	52	nested_transposon		1412	1	0
1385	52	transposon_fragment	A portion of a transposon, interrupted by the insertion of another element. [SO:ke]	1413	0	0
1386	52	nested_transposon(SO:0001648)	A transposon that is disrupted by the insertion of another element. [SO:ke]	1414	0	0
1387	52	regulatory_region	A region of sequence that is involved in the control of a biological process. [SO:ke]	1415	0	0
1388	52	enhanceosome		1416	1	0
1389	52	promoter_targeting_sequence	A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. [SO:regcreative]	1417	1	0
1390	52	sequence_comparison	A position or feature where two sequences have been compared. []	1420	0	0
1391	52	propeptide_cleavage_site	The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs. [EBIBS:GAR]	1421	0	0
1392	52	propeptide_region_of_CDS	A CDS region corresponding to a propeptide of a polypeptide. []	1424	0	0
1393	52	active_peptide	Active peptides are proteins which are biologically active, released from a precursor molecule. [EBIBS:GAR, UniProt:curation_manual]	1426	0	0
1394	52	compositionally_biased_region_of_peptide	Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length. [EBIBS:GAR, UniProt:curation_manual]	1428	0	0
1395	52	polypeptide_motif	A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.). [EBIBS:GAR, UniProt:curation_manual]	1430	0	0
1396	52	polypeptide_repeat	A polypeptide_repeat is a single copy of an internal sequence repetition. [EBIBS:GAR]	1432	0	0
1397	52	membrane_structure	Arrangement of the polypeptide with respect to the lipid bilayer. [EBIBS:GAR]	1435	0	0
1398	52	extramembrane_polypeptide_region	Polypeptide region that is localized outside of a lipid bilayer. [EBIBS:GAR, SO:cb]	1437	0	0
1399	52	cytoplasmic_polypeptide_region	Polypeptide region that is localized inside the cytoplasm. [EBIBS:GAR, SO:cb]	1439	0	0
1400	52	non_cytoplasmic_polypeptide_region	Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. [EBIBS:GAR, SO:cb]	1441	0	0
1401	52	intramembrane_polypeptide_region	Polypeptide region present in the lipid bilayer. [EBIBS:GAR]	1443	0	0
1402	52	membrane_peptide_loop	Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. [EBIBS:GAR, SO:cb]	1445	0	0
1403	52	transmembrane_polypeptide_region	Polypeptide region traversing the lipid bilayer. [EBIBS:GAR, UniProt:curator_manual]	1447	0	0
1404	52	polypeptide_secondary_structure	A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. [EBIBS:GAR]	1449	0	0
1405	52	polypeptide_structural_motif	Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. [EBIBS:GAR]	1451	0	0
1406	52	coiled_coil	A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. [EBIBS:GAR, UniProt:curation_manual]	1453	0	0
1407	52	helix_turn_helix	A motif comprising two helices separated by a turn. [EBIBS:GAR]	1455	0	0
1408	52	peptide_helix	A helix is a secondary_structure conformation where the peptide backbone forms a coil. [EBIBS:GAR]	1457	0	0
1409	52	polypeptide_sequencing_information	Incompatibility in the sequence due to some experimental problem. [EBIBS:GAR]	1458	0	0
1410	52	non_adjacent_residues	Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. [EBIBS:GAR, UniProt:curation_manual]	1460	0	0
1411	52	non_terminal_residue	The residue at an extremity of the sequence is not the terminal residue. [EBIBS:GAR, UniProt:curation_manual]	1462	0	0
1412	52	sequence_conflict	Different sources report differing sequences. [EBIBS:GAR, UniProt:curation_manual]	1464	0	0
1413	52	sequence_uncertainty	Describes the positions in a sequence where the authors are unsure about the sequence assignment. [EBIBS:GAR, UniProt:curation_manual]	1466	0	0
1414	52	cross_link	Posttranslationally formed amino acid bonds. [EBIBS:GAR, UniProt:curation_manual]	1468	1	0
1415	52	disulfide_bond	The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules. [EBIBS:GAR, UniProt:curation_manual]	1470	1	0
1416	52	post_translationally_modified_region	A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein. [EBIBS:GAR, UniProt:curation_manual]	1472	0	0
1417	52	biochemical_region_of_peptide	A region of a peptide that is involved in a biochemical function. [EBIBS:GAR]	1474	0	0
1418	52	covalent_binding_site	Binding involving a covalent bond. [EBIBS:GAR]	1475	1	0
1419	52	non_covalent_binding_site	Binding site for any chemical group (co-enzyme, prosthetic group, etc.). [EBIBS:GAR]	1477	1	0
1420	52	polypeptide_metal_contact	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions. [EBIBS:GAR, SO:cb, UniProt:curation_manual]	1479	0	0
1421	52	metal_binding_site	A binding site that, in the molecule, interacts selectively and non-covalently with metal ions. [SO:cb]	1481	0	0
1422	52	molecular_contact_region	A region that is involved a contact with another molecule. [EBIBS:GAR]	1482	0	0
1423	52	protein_protein_contact	A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues. [EBIBS:GAR, UniProt:Curation_manual]	1483	0	0
1424	52	polypeptide_calcium_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions. [EBIBS:GAR]	1485	0	0
1425	52	polypeptide_cobalt_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions. [EBIBS:GAR, SO:cb]	1487	0	0
1426	52	polypeptide_copper_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions. [EBIBS:GAR, SO:cb]	1489	0	0
1427	52	polypeptide_iron_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions. [EBIBS:GAR, SO:cb]	1491	0	0
1428	52	polypeptide_magnesium_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions. [EBIBS:GAR, SO:cb]	1493	0	0
1429	52	polypeptide_manganese_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions. [EBIBS:GAR, SO:cb]	1495	0	0
1430	52	polypeptide_molybdenum_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions. [EBIBS:GAR, SO:cb]	1497	0	0
1431	52	polypeptide_nickel_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions. [EBIBS:GAR]	1499	0	0
1577	52	apicoplast_chromosome	A chromosome originating in an apicoplast. [SO:xp]	1697	0	0
1432	52	polypeptide_tungsten_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions. [EBIBS:GAR, SO:cb]	1501	0	0
1433	52	polypeptide_zinc_ion_contact_site	A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions. [EBIBS:GAR, SO:cb]	1503	0	0
1434	52	catalytic_residue	Amino acid involved in the activity of an enzyme. [EBIBS:GAR, UniProt:curation_manual]	1505	0	0
1435	52	amino_acid	A sequence feature that corresponds to a single amino acid residue in a polypeptide. [RSC:cb]	1507	0	0
1436	52	polypeptide_catalytic_motif	A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues. [EBIBS:GAR]	1508	0	0
1437	52	polypeptide_ligand_contact	Residues which interact with a ligand. [EBIBS:GAR]	1509	0	0
1438	52	ligand_binding_site	A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone. [SO:ke]	1511	0	0
1439	52	asx_motif	A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1512	0	0
1440	52	beta_bulge	A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1514	0	0
1441	52	beta_bulge_loop	A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]	1516	0	0
1442	52	beta_bulge_loop_five	A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1518	0	0
1443	52	beta_bulge_loop_six	A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1520	0	0
1444	52	beta_strand	A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. [EBIBS:GAR, UniProt:curation_manual]	1522	0	0
1445	52	antiparallel_beta_strand	A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. [EBIBS:GAR, UniProt:curation_manual]	1524	0	0
1446	52	parallel_beta_strand	A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. [EBIBS:GAR, UniProt:curation_manual]	1526	0	0
1447	52	left_handed_peptide_helix	A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. [EBIBS:GAR]	1529	0	0
1448	52	right_handed_peptide_helix	A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. [EBIBS:GAR]	1531	0	0
1449	52	alpha_helix	The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. [EBIBS:GAR]	1533	0	0
1450	52	pi_helix	The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. [EBIBS:GAR]	1535	0	0
1451	52	three_ten_helix	The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. [EBIBS:GAR]	1537	0	0
1452	52	polypeptide_nest_motif	A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1539	0	0
1453	52	polypeptide_nest_left_right_motif	A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1541	0	0
1623	52	N6_hydroxynorvalylcarbamoyladenosine	N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1774	0	0
1454	52	polypeptide_nest_right_left_motif	A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1543	0	0
1455	52	schellmann_loop	A motif of six or seven consecutive residues that contains two H-bonds. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1545	0	0
1456	52	schellmann_loop_seven	Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1547	0	0
1457	52	schellmann_loop_six	Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1549	0	0
1458	52	serine_threonine_motif	A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1551	0	0
1459	52	serine_threonine_staple_motif	A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1553	0	0
1460	52	asx_turn_left_handed_type_one	Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1556	0	0
1461	52	asx_turn_left_handed_type_two	Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1558	0	0
1462	52	asx_turn_right_handed_type_two	Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1560	0	0
1463	52	asx_turn_right_handed_type_one	Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1562	0	0
1464	52	beta_turn	A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1564	0	0
1465	52	beta_turn_left_handed_type_one	Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1566	0	0
1466	52	beta_turn_left_handed_type_two	Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1568	0	0
1467	52	beta_turn_right_handed_type_one	Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1570	0	0
1468	52	beta_turn_right_handed_type_two	Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1572	0	0
1469	52	gamma_turn	Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1574	0	0
1470	52	gamma_turn_classic	Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1576	0	0
1471	52	gamma_turn_inverse	Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1578	0	0
1472	52	serine_threonine_turn	A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1580	0	0
1473	52	st_turn_left_handed_type_one	The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1582	0	0
1474	52	st_turn_left_handed_type_two	The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1584	0	0
1475	52	st_turn_right_handed_type_one	The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1586	0	0
1476	52	st_turn_right_handed_type_two	The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	1588	0	0
1477	52	polypeptide_variation_site	A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis. [EBIBS:GAR, SO:ke]	1590	0	0
1478	52	natural_variant_site	Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars. [EBIBS:GAR, UniProt:curation_manual]	1592	0	0
1479	52	mutated_variant_site	Site which has been experimentally altered. [EBIBS:GAR, UniProt:curation_manual]	1594	0	0
1480	52	alternate_sequence_site	Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. [EBIBS:GAR, UniProt:curation_manual]	1596	0	0
1481	52	beta_turn_type_six	A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. [SO:cb]	1599	0	0
1482	52	beta_turn_type_six_a	A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. [PMID:2371257, SO:cb]	1600	0	0
1483	52	beta_turn_type_six_a_one	A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees. [PMID:27428516]	1601	0	0
1484	52	beta_turn_type_six_a_two	A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees. [PMID:27428516]	1602	0	0
1485	52	beta_turn_type_six_b	A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. [PMID:2371257, SO:cb]	1603	0	0
1486	52	beta_turn_type_eight	A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. [PMID:2371257, SO:cb]	1604	0	0
1487	52	DRE_motif	A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. [PMID:12537576]	1605	0	0
1488	52	DMv4_motif	A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). [PMID:16827941\\:12537576]	1606	0	0
1489	52	E_box_motif	A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015). [PMID:12537576\\:16827941]	1607	0	0
1490	52	DMv5_motif	A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). [PMID:12537576\\:16827941]	1608	0	0
1491	52	DMv3_motif	A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162). [PMID:12537576\\:16827941]	1609	0	0
1492	52	DMv2_motif	A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). [PMID:12537576\\:16827941]	1610	0	0
1493	52	MTE	A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159). [PMID:12537576\\:15231738, PMID:16858867]	1611	0	0
1494	52	INR1_motif	A promoter motif with consensus sequence TCATTCG. [PMID:16827941]	1612	0	0
1495	52	DPE1_motif	A promoter motif with consensus sequence CGGACGT. [PMID:16827941]	1613	0	0
1496	52	DMv1_motif	A promoter motif with consensus sequence CARCCCT. [PMID:16827941]	1614	0	0
1497	52	GAGA_motif	A non directional promoter motif with consensus sequence GAGAGCG. [PMID:16827941]	1615	0	0
1498	52	NDM2_motif	A non directional promoter motif with consensus CGMYGYCR. [PMID:16827941]	1616	0	0
1499	52	NDM3_motif	A non directional promoter motif with consensus sequence GAAAGCT. [PMID:16827941]	1617	0	0
1500	52	ds_RNA_viral_sequence	A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA. [SO:ke]	1618	0	0
1501	52	polinton	A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements. [PMID:16537396]	1619	0	0
1502	52	rRNA_21S	A component of the large ribosomal subunit in mitochondrial rRNA. [RSC:cb]	1620	1	0
1503	52	tRNA_region	A region of a tRNA. [RSC:cb]	1621	0	0
1504	52	anticodon_loop	A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3. [ISBN:0716719207]	1622	0	0
1505	52	anticodon	A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. [RSC:cb]	1623	0	0
1506	52	CCA_tail	Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. [ISBN:0716719207]	1624	0	0
1507	52	DHU_loop	Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. [ISBN:071671920]	1625	0	0
1508	52	T_loop	Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. [ISBN:0716719207]	1626	0	0
1509	52	U3_snoRNA	U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]	1627	0	0
1510	52	AU_rich_element	A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. [PMID:7892223]	1628	0	0
1511	52	Bruno_response_element	A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. [PMID:10893231]	1629	0	0
1512	52	iron_responsive_element	A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. [PMID:3198610, PMID:8710843]	1630	0	0
1513	52	pseudouridylation_guide_snoRNA	A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. [GOC:mah, PMID:12457565]	1631	0	0
1514	52	LNA	An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link. [CHEBI:48010]	1632	0	0
1515	52	LNA_oligo	An oligo composed of LNA residues. [RSC:cb]	1633	0	0
1516	52	TNA	An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. [CHEBI:48019]	1634	0	0
1517	52	TNA_oligo	An oligo composed of TNA residues. [RSC:cb]	1635	0	0
1518	52	GNA	An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. [CHEBI:48015]	1636	0	0
1519	52	GNA_oligo	An oligo composed of GNA residues. [RSC:cb]	1637	0	0
1520	52	R_GNA	An attribute describing a GNA sequence in the (R)-GNA enantiomer. [CHEBI:48016]	1638	0	0
1521	52	R_GNA_oligo	An oligo composed of (R)-GNA residues. [RSC:cb]	1639	0	0
1522	52	S_GNA	An attribute describing a GNA sequence in the (S)-GNA enantiomer. [CHEBI:48017]	1640	0	0
1523	52	S_GNA_oligo	An oligo composed of (S)-GNA residues. [RSC:cb]	1641	0	0
1524	52	ds_DNA_viral_sequence	A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA. [SO:ke]	1642	0	0
1525	52	ss_RNA_viral_sequence	A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA. [SO:ke]	1643	0	0
1526	52	negative_sense_ssRNA_viral_sequence	A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation. [SO:ke]	1644	0	0
1527	52	positive_sense_ssRNA_viral_sequence	A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host. [SO:ke]	1645	0	0
1528	52	ambisense_ssRNA_viral_sequence	A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity. [SO:ke]	1646	0	0
1529	52	RNA_polymerase_promoter	A region (DNA) to which RNA polymerase binds, to begin transcription. [xenbase:jb]	1647	1	0
1530	52	Phage_RNA_Polymerase_Promoter	A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. [xenbase:jb]	1648	0	0
1531	52	viral_promoter	A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses. [GREEKC:cl]	1649	0	0
1532	52	SP6_RNA_Polymerase_Promoter	A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. [xenbase:jb]	1650	0	0
1533	52	T3_RNA_Polymerase_Promoter	A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. [xenbase:jb]	1651	0	0
1534	52	T7_RNA_Polymerase_Promoter	A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. [xenbase:jb]	1652	0	0
1535	52	five_prime_EST	An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	1653	0	0
1536	52	three_prime_EST	An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs). [http://www.ncbi.nlm.nih.gov/About/primer/est.html]	1654	0	0
1537	52	translational_frameshift	The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. [http://www.insdc.org/files/feature_table.html, SO:ke]	1655	0	0
1538	52	plus_1_translational_frameshift	The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. [SO:ke]	1656	0	0
1539	52	plus_2_translational_frameshift	The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. [SO:ke]	1657	0	0
1540	52	group_III_intron	Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. [PMID:11377794]	1658	0	0
1541	52	endonuclease_spliced_intron	An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. [SO:ke]	1659	0	0
1542	52	transgenic_insertion	An insertion that derives from another organism, via the use of recombinant DNA technology. [SO:bm]	1660	0	0
1543	52	retrogene	A gene that has been produced as the product of a reverse transcriptase mediated event. []	1661	0	0
1544	52	silenced_by_RNA_interference	An attribute describing an epigenetic process where a gene is inactivated by RNA interference. [RSC:cb]	1662	0	0
1545	52	silenced_by_histone_modification	An attribute describing an epigenetic process where a gene is inactivated by histone modification. [RSC:cb]	1663	0	0
1546	52	silenced_by_histone_methylation	An attribute describing an epigenetic process where a gene is inactivated by histone methylation. [RSC:cb]	1664	0	0
1547	52	silenced_by_histone_deacetylation	An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. [RSC:cb]	1665	0	0
1548	52	gene_silenced_by_RNA_interference	A gene that is silenced by RNA interference. [SO:xp]	1666	0	0
1549	52	gene_silenced_by_histone_modification	A gene that is silenced by histone modification. [SO:xp]	1667	0	0
1550	52	gene_silenced_by_histone_methylation	A gene that is silenced by histone methylation. [SO:xp]	1668	0	0
1551	52	gene_silenced_by_histone_deacetylation	A gene that is silenced by histone deacetylation. [SO:xp]	1669	0	0
1552	52	dihydrouridine	A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. [RSC:cb]	1670	0	0
1553	52	modified_uridine	A uridine base that has been modified. []	1672	0	0
1554	52	pseudouridine	A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. [RSC:cb]	1673	0	0
1555	52	inosine	A modified RNA base in which hypoxanthine is bound to the ribose ring. [http://library.med.utah.edu/RNAmods/, RSC:cb]	1675	0	0
1556	52	seven_methylguanine	A modified RNA base in which guanine is methylated at the 7- position. [RSC:cb]	1676	0	0
1557	52	ribothymidine	A modified RNA base in which thymine is bound to the ribose ring. [RSC:cb]	1677	0	0
1558	52	methylinosine	A modified RNA base in which methylhypoxanthine is bound to the ribose ring. [RSC:cb]	1678	0	0
1559	52	modified_inosine	A modified inosine is an inosine base feature that has been altered. [SO:ke]	1679	0	0
1560	52	major_TSS	The tanscription start site that is most frequently used for transcription of a gene. []	1680	0	0
1561	52	minor_TSS	A tanscription start site that is not the most frequently used for transcription of a gene. []	1681	0	0
1562	52	TSS_region	The region of a gene from the 5' most TSS to the 3' TSS. [BBOP:nw]	1682	1	0
1563	52	encodes_alternate_transcription_start_sites	A gene that has multiple possible transcription start sites. []	1683	0	0
1564	52	miRNA_primary_transcript_region	A part of an miRNA primary_transcript. [SO:ke]	1684	0	0
1565	52	miRNA_stem	The stem of the hairpin loop formed by folding of the pre-miRNA. [SO:ke]	1685	0	0
1566	52	miRNA_loop	The loop of the hairpin loop formed by folding of the pre-miRNA. [SO:ke]	1686	0	0
1567	52	fragment_assembly	A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. [SO:ke]	1687	0	0
1568	52	fingerprint_map	A fingerprint_map is a physical map composed of restriction fragments. [SO:ke]	1688	0	0
1569	52	STS_map	An STS map is a physical map organized by the unique STS landmarks. [SO:ke]	1689	0	0
1570	52	RH_map	A radiation hybrid map is a physical map. [SO:ke]	1690	0	0
1571	52	sonicate_fragment	A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments. [SO:ke]	1691	0	0
1572	52	polyploid	A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. [SO:ke]	1692	0	0
1573	52	autopolyploid	A polyploid where the multiple chromosome set was derived from the same organism. [SO:ke]	1693	0	0
1574	52	allopolyploid	A polyploid where the multiple chromosome set was derived from a different organism. [SO:ke]	1694	0	0
1575	52	homing_endonuclease_binding_site	The binding site (recognition site) of a homing endonuclease. The binding site is typically large. [SO:ke]	1695	0	0
1576	52	octamer_motif	A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors. [GOC:dh, PMID:3095662]	1696	0	0
2622	52	plastid_LSU_rRNA_gene	A gene that codes for plastid LSU rRNA. []	2893	0	0
1578	52	overlapping_feature_set	A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature. [SO:ke]	1698	0	0
1579	52	overlapping_EST_set	A continous experimental result region extending the length of multiple overlapping EST's. [SO:ke]	1699	0	0
1580	52	ncRNA_gene	A gene that encodes a non-coding RNA. []	1700	0	0
1581	52	gRNA_gene	A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system. []	1701	0	0
1582	52	miRNA_gene	A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression. []	1702	0	0
1583	52	sncRNA_gene	A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length. [PMID:28449079, PMID:30069443, PMID:30937442]	1704	0	0
1584	52	scRNA_gene	A gene encoding a small noncoding RNA that is generally found only in the cytoplasm. []	1705	0	0
1585	52	snoRNA_gene	A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs. []	1706	0	0
1586	52	snRNA_gene	A gene that encodes a small nuclear RNA. [http://en.wikipedia.org/wiki/Small_nuclear_RNA]	1707	0	0
1587	52	SRP_RNA_gene	A gene that encodes a signal recognition particle (SRP) RNA. []	1708	0	0
1588	52	tmRNA_gene	A bacterial RNA with both tRNA and mRNA like properties. []	1709	0	0
1589	52	tRNA_gene	A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA. []	1710	0	0
1590	52	modified_adenosine	A modified adenine is an adenine base feature that has been altered. [SO:ke]	1711	0	0
1591	52	modified_cytidine	A modified cytidine is a cytidine base feature which has been altered. [SO:ke]	1712	0	0
1592	52	modified_guanosine	A guanosine base that has been modified. []	1713	0	0
1593	52	one_methylinosine	1-methylinosine is a modified inosine. [http://library.med.utah.edu/RNAmods/]	1714	0	0
1594	52	one_two_prime_O_dimethylinosine	1,2'-O-dimethylinosine is a modified inosine. [http://library.med.utah.edu/RNAmods/]	1716	0	0
1595	52	two_prime_O_methylinosine	2'-O-methylinosine is a modified inosine. [http://library.med.utah.edu/RNAmods/]	1718	0	0
1596	52	three_methylcytidine	3-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1720	0	0
1597	52	five_methylcytidine	5-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1722	0	0
1598	52	two_prime_O_methylcytidine	2'-O-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1724	0	0
1599	52	two_thiocytidine	2-thiocytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1726	0	0
1600	52	N4_acetylcytidine	N4-acetylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1728	0	0
1601	52	five_formylcytidine	5-formylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1730	0	0
1602	52	five_two_prime_O_dimethylcytidine	5,2'-O-dimethylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1732	0	0
1603	52	N4_acetyl_2_prime_O_methylcytidine	N4-acetyl-2'-O-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1734	0	0
1604	52	lysidine	Lysidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1736	0	0
1605	52	N4_methylcytidine	N4-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1738	0	0
1606	52	N4_2_prime_O_dimethylcytidine	N4,2'-O-dimethylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1740	0	0
1607	52	five_hydroxymethylcytidine	5-hydroxymethylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1742	0	0
1608	52	five_formyl_two_prime_O_methylcytidine	5-formyl-2'-O-methylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1744	0	0
1609	52	N4_N4_2_prime_O_trimethylcytidine	N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. [http://library.med.utah.edu/RNAmods/]	1746	0	0
1610	52	one_methyladenosine	1_methyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1748	0	0
1611	52	two_methyladenosine	2_methyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1750	0	0
1612	52	N6_methyladenosine	N6_methyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1752	0	0
1613	52	two_prime_O_methyladenosine	2prime_O_methyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1754	0	0
1614	52	two_methylthio_N6_methyladenosine	2_methylthio_N6_methyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1756	0	0
1615	52	N6_isopentenyladenosine	N6_isopentenyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1758	0	0
1616	52	two_methylthio_N6_isopentenyladenosine	2_methylthio_N6_isopentenyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1760	0	0
1617	52	N6_cis_hydroxyisopentenyl_adenosine	N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1762	0	0
1618	52	two_methylthio_N6_cis_hydroxyisopentenyl_adenosine	2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1764	0	0
1619	52	N6_glycinylcarbamoyladenosine	N6_glycinylcarbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1766	0	0
1620	52	N6_threonylcarbamoyladenosine	N6_threonylcarbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1768	0	0
1621	52	two_methylthio_N6_threonyl_carbamoyladenosine	2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1770	0	0
1622	52	N6_methyl_N6_threonylcarbamoyladenosine	N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1772	0	0
1624	52	two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine	2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1776	0	0
1625	52	two_prime_O_ribosyladenosine_phosphate	2prime_O_ribosyladenosine_phosphate is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1778	0	0
1626	52	N6_N6_dimethyladenosine	N6_N6_dimethyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1780	0	0
1627	52	N6_2_prime_O_dimethyladenosine	N6_2prime_O_dimethyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1782	0	0
1628	52	N6_N6_2_prime_O_trimethyladenosine	N6_N6_2prime_O_trimethyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1784	0	0
1629	52	one_two_prime_O_dimethyladenosine	1,2'-O-dimethyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1786	0	0
1630	52	N6_acetyladenosine	N6_acetyladenosine is a modified adenosine. [http://library.med.utah.edu/RNAmods/]	1788	0	0
1631	52	seven_deazaguanosine	7-deazaguanosine is a modified guanosine. [http://library.med.utah.edu/RNAmods/]	1790	0	0
1632	52	queuosine	Queuosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1791	0	0
1633	52	epoxyqueuosine	Epoxyqueuosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1793	0	0
1634	52	galactosyl_queuosine	Galactosyl_queuosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1795	0	0
1635	52	mannosyl_queuosine	Mannosyl_queuosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1797	0	0
1636	52	seven_cyano_seven_deazaguanosine	7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1799	0	0
1637	52	seven_aminomethyl_seven_deazaguanosine	7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1801	0	0
1638	52	archaeosine	Archaeosine is a modified 7-deazoguanosine. [http://library.med.utah.edu/RNAmods/]	1803	0	0
1639	52	one_methylguanosine	1_methylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1805	0	0
1640	52	N2_methylguanosine	N2_methylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1807	0	0
1641	52	seven_methylguanosine	7_methylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1809	0	0
1642	52	two_prime_O_methylguanosine	2prime_O_methylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1811	0	0
1643	52	N2_N2_dimethylguanosine	N2_N2_dimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1813	0	0
1644	52	N2_2_prime_O_dimethylguanosine	N2_2prime_O_dimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1815	0	0
1645	52	N2_N2_2_prime_O_trimethylguanosine	N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1817	0	0
1646	52	two_prime_O_ribosylguanosine_phosphate	2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1819	0	0
1647	52	wybutosine	Wybutosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1821	0	0
1648	52	peroxywybutosine	Peroxywybutosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1823	0	0
1649	52	hydroxywybutosine	Hydroxywybutosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1825	0	0
1650	52	undermodified_hydroxywybutosine	Undermodified_hydroxywybutosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1827	0	0
1651	52	wyosine	Wyosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1829	0	0
1652	52	methylwyosine	Methylwyosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1831	0	0
1653	52	N2_7_dimethylguanosine	N2_7_dimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1833	0	0
1654	52	N2_N2_7_trimethylguanosine	N2_N2_7_trimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1835	0	0
1655	52	one_two_prime_O_dimethylguanosine	1_2prime_O_dimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1837	0	0
1656	52	four_demethylwyosine	4_demethylwyosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1839	0	0
1657	52	isowyosine	Isowyosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1841	0	0
1658	52	N2_7_2prirme_O_trimethylguanosine	N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. [http://library.med.utah.edu/RNAmods/]	1843	0	0
1659	52	five_methyluridine	5_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1845	0	0
1660	52	two_prime_O_methyluridine	2prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1847	0	0
1661	52	five_two_prime_O_dimethyluridine	5_2_prime_O_dimethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1849	0	0
1662	52	one_methylpseudouridine	1_methylpseudouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1851	0	0
1663	52	two_prime_O_methylpseudouridine	2prime_O_methylpseudouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1853	0	0
1664	52	two_thiouridine	2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1855	0	0
1665	52	four_thiouridine	4_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1857	0	0
1666	52	five_methyl_2_thiouridine	5_methyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1859	0	0
1667	52	two_thio_two_prime_O_methyluridine	2_thio_2prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1861	0	0
1668	52	three_three_amino_three_carboxypropyl_uridine	3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1863	0	0
1669	52	five_hydroxyuridine	5_hydroxyuridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1865	0	0
1670	52	five_methoxyuridine	5_methoxyuridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1866	0	0
1671	52	uridine_five_oxyacetic_acid	Uridine_5_oxyacetic_acid is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1868	0	0
1672	52	uridine_five_oxyacetic_acid_methyl_ester	Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1870	0	0
1673	52	five_carboxyhydroxymethyl_uridine	5_carboxyhydroxymethyl_uridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1872	0	0
1674	52	five_carboxyhydroxymethyl_uridine_methyl_ester	5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1874	0	0
1675	52	five_methoxycarbonylmethyluridine	Five_methoxycarbonylmethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1876	0	0
1676	52	five_methoxycarbonylmethyl_two_prime_O_methyluridine	Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1878	0	0
1677	52	five_methoxycarbonylmethyl_two_thiouridine	5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1880	0	0
1678	52	five_aminomethyl_two_thiouridine	5_aminomethyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1882	0	0
1679	52	five_methylaminomethyluridine	5_methylaminomethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1884	0	0
1680	52	five_methylaminomethyl_two_thiouridine	5_methylaminomethyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1886	0	0
1681	52	five_methylaminomethyl_two_selenouridine	5_methylaminomethyl_2_selenouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1888	0	0
1682	52	five_carbamoylmethyluridine	5_carbamoylmethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1890	0	0
1683	52	five_carbamoylmethyl_two_prime_O_methyluridine	5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1892	0	0
1684	52	five_carboxymethylaminomethyluridine	5_carboxymethylaminomethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1894	0	0
1685	52	five_carboxymethylaminomethyl_two_prime_O_methyluridine	5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1896	0	0
1686	52	five_carboxymethylaminomethyl_two_thiouridine	5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1898	0	0
1687	52	three_methyluridine	3_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1900	0	0
1688	52	one_methyl_three_three_amino_three_carboxypropyl_pseudouridine	1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1902	0	0
1689	52	five_carboxymethyluridine	5_carboxymethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1904	0	0
1690	52	three_two_prime_O_dimethyluridine	3_2prime_O_dimethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1906	0	0
1691	52	five_methyldihydrouridine	5_methyldihydrouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1908	0	0
1692	52	three_methylpseudouridine	3_methylpseudouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1910	0	0
1693	52	five_taurinomethyluridine	5_taurinomethyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1912	0	0
1694	52	five_taurinomethyl_two_thiouridine	5_taurinomethyl_2_thiouridineis a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1914	0	0
1695	52	five_isopentenylaminomethyl_uridine	5_isopentenylaminomethyl_uridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1916	0	0
1696	52	five_isopentenylaminomethyl_two_thiouridine	5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1918	0	0
1697	52	five_isopentenylaminomethyl_two_prime_O_methyluridine	5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. [http://library.med.utah.edu/RNAmods/]	1920	0	0
1698	52	histone_binding_site	A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone. [SO:ke]	1922	0	0
1699	52	CDS_fragment	A portion of a CDS that is not the complete CDS. []	1923	0	0
1700	52	modified_amino_acid_feature	A post translationally modified amino acid feature. [SO:ke]	1924	0	0
1701	52	modified_glycine	A post translationally modified glycine amino acid feature. [SO:ke]	1925	0	0
1702	52	modified_L_alanine	A post translationally modified alanine amino acid feature. [SO:ke]	1927	0	0
1703	52	modified_L_asparagine	A post translationally modified asparagine amino acid feature. [SO:ke]	1929	0	0
1704	52	modified_L_aspartic_acid	A post translationally modified aspartic acid amino acid feature. [SO:ke]	1931	0	0
1705	52	modified_L_cysteine	A post translationally modified cysteine amino acid feature. [SO:ke]	1933	0	0
1706	52	modified_L_glutamic_acid	A post translationally modified glutamic acid. []	1935	0	0
1707	52	modified_L_threonine	A post translationally modified threonine amino acid feature. [SO:ke]	1937	0	0
1708	52	modified_L_tryptophan	A post translationally modified tryptophan amino acid feature. [SO:ke]	1939	0	0
1709	52	modified_L_glutamine	A post translationally modified glutamine amino acid feature. [SO:ke]	1941	0	0
1710	52	modified_L_methionine	A post translationally modified methionine amino acid feature. [SO:ke]	1943	0	0
1711	52	modified_L_isoleucine	A post translationally modified isoleucine amino acid feature. [SO:ke]	1945	0	0
1712	52	modified_L_phenylalanine	A post translationally modified phenylalanine amino acid feature. [SO:ke]	1947	0	0
1713	52	modified_L_histidine	A post translationally modified histidine amino acid feature. [SO:ke]	1949	0	0
1714	52	modified_L_serine	A post translationally modified serine amino acid feature. [SO:ke]	1951	0	0
1715	52	modified_L_lysine	A post translationally modified lysine amino acid feature. [SO:ke]	1953	0	0
1716	52	modified_L_leucine	A post translationally modified leucine amino acid feature. [SO:ke]	1955	0	0
1717	52	modified_L_selenocysteine	A post translationally modified selenocysteine amino acid feature. [SO:ke]	1957	0	0
1718	52	modified_L_valine	A post translationally modified valine amino acid feature. [SO:ke]	1959	0	0
1719	52	modified_L_proline	A post translationally modified proline amino acid feature. [SO:ke]	1961	0	0
1720	52	modified_L_tyrosine	A post translationally modified tyrosine amino acid feature. [SO:ke]	1963	0	0
1721	52	modified_L_arginine	A post translationally modified arginine amino acid feature. [SO:ke]	1965	0	0
1722	52	peptidyl	An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds. [SO:ke]	1967	0	0
1723	52	cleaved_for_gpi_anchor_region	The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor. [EBI:rh]	1968	0	0
1724	52	translocation_breakpoint	The point within a chromosome where a translocation begins or ends. [SO:cb]	1969	0	0
1725	52	insertion_breakpoint	The point within a chromosome where a insertion begins or ends. [SO:cb]	1970	0	0
1726	52	deletion_breakpoint	The point within a chromosome where a deletion begins or ends. [SO:cb]	1971	0	0
1727	52	five_prime_flanking_region	A flanking region located five prime of a specific region. [SO:chado]	1972	0	0
1728	52	three_prime_flanking_region	A flanking region located three prime of a specific region. [SO:chado]	1973	0	0
1729	52	transcribed_fragment	An experimental region, defined by a tiling array experiment to be transcribed at some level. [SO:ke]	1974	0	0
1730	52	splice_junction	The boundary between an intron and an exon. [SO:ke]	1975	0	0
1731	52	conformational_switch	A region of a polypeptide, involved in the transition from one conformational state to another. [SO:ke]	1976	0	0
1732	52	dye_terminator_read	A read produced by the dye terminator method of sequencing. [SO:ke]	1977	0	0
1733	52	pyrosequenced_read	A read produced by pyrosequencing technology. [SO:ke]	1978	0	0
1734	52	ligation_based_read	A read produced by ligation based sequencing technologies. [SO:ke]	1979	0	0
1735	52	polymerase_synthesis_read	A read produced by the polymerase based sequence by synthesis method. [SO:ke]	1980	0	0
1736	52	cis_regulatory_frameshift_element	A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence. [RFAM:jd]	1981	0	0
1737	52	expressed_sequence_assembly	A sequence assembly derived from expressed sequences. [SO:ke]	1982	0	0
1738	52	DNA_binding_site	A binding site that, in the molecule, interacts selectively and non-covalently with DNA. [SO:ke]	1983	0	0
1739	52	cryptic_gene	A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. [SO:ke]	1984	0	0
1740	52	sequence_variant_affecting_polyadenylation		1985	1	0
1741	52	three_prime_RACE_clone	A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host. [modENCODE:nlw]	1986	0	0
1742	52	cassette_pseudogene	A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy. [SO:ke]	1987	0	0
1743	52	alanine	A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG). []	1988	0	0
1744	52	valine	A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG). []	1989	0	0
1745	52	leucine	A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG. []	1990	0	0
1746	52	isoleucine	A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA). []	1991	0	0
1747	52	proline	A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG). []	1992	0	0
1748	52	tryptophan	A non-polar, hydorophobic amino acid encoded by the codon TGG. []	1993	0	0
1749	52	phenylalanine	A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC. []	1994	0	0
1750	52	methionine	A non-polar, hydorophobic amino acid encoded by the codon ATG. []	1995	0	0
1751	52	glycine	A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG). []	1996	0	0
1752	52	serine	A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC. []	1997	0	0
1753	52	threonine	A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG). []	1998	0	0
1754	52	tyrosine	A polar, hydorophilic amino acid encoded by the codons TAT and TAC. []	1999	0	0
1755	52	cysteine	A polar amino acid encoded by the codons TGT and TGC. []	2000	0	0
1756	52	glutamine	A polar, hydorophilic amino acid encoded by the codons CAA and CAG.  []	2001	0	0
1757	52	asparagine	A polar, hydorophilic amino acid encoded by the codons AAT and AAC. []	2002	0	0
1758	52	lysine	A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG. []	2003	0	0
1759	52	arginine	A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG. []	2004	0	0
1760	52	histidine	A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC. []	2005	0	0
1761	52	aspartic_acid	A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC. []	2006	0	0
1762	52	glutamic_acid	A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG. []	2007	0	0
1763	52	selenocysteine	A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts. [PMID:23275319]	2008	0	0
1764	52	pyrrolysine	A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts. [PMID:15788401]	2009	0	0
1765	52	transcribed_cluster	A region defined by a set of transcribed sequences from the same gene or expressed pseudogene. [SO:ke]	2010	0	0
1766	52	unigene_cluster	A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene. [SO:ke]	2011	0	0
1767	52	CRISPR	Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences. [RFAM:jd]	2012	0	0
1768	52	insulator_binding_site	A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. [SO:ke]	2013	0	0
1769	52	enhancer_binding_site	A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. [SO:ke]	2014	0	0
1770	52	contig_collection	A collection of contigs. [SO:ke]	2015	0	0
1771	52	lincRNA	Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand. [http://www.gencodegenes.org/gencode_biotypes.html, PMID:19182780, PMID:23463798, SO:ke]	2016	0	0
1772	52	lncRNA	A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced." [HGNC:mw] {comment="PMID:33353982}	2017	0	0
1773	52	UST	An EST spanning part or all of the untranslated regions of a protein-coding transcript. [SO:nlw]	2018	0	0
1774	52	three_prime_UST	A UST located in the 3'UTR of a protein-coding transcript. [SO:nlw]	2019	0	0
1775	52	five_prime_UST	An UST located in the 5'UTR of a protein-coding transcript. [SO:nlw]	2020	0	0
1776	52	RST	A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long. [SO:nlw]	2021	0	0
1777	52	three_prime_RST	A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long. [SO:nlw]	2022	0	0
1778	52	five_prime_RST	A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long. [SO:nlw]	2023	0	0
1779	52	UST_match	A match against an UST sequence. [SO:nlw]	2024	0	0
1780	52	RST_match	A match against an RST sequence. [SO:nlw]	2025	0	0
1781	52	primer_match	A nucleotide match to a primer sequence. [SO:nlw]	2026	0	0
1782	52	miRNA_antiguide	A region of the pri miRNA that base pairs with the guide to form the hairpin. [SO:ke]	2027	0	0
1783	52	trans_splice_junction	The boundary between the spliced leader and the first exon of the mRNA. [SO:ke]	2028	0	0
1784	52	outron	A region of a primary transcript, that is removed via trans splicing. [PMID:16401417, SO:ke]	2029	0	0
1785	52	natural_plasmid	A plasmid that occurs naturally. [SO:xp]	2030	0	0
1786	52	gene_trap_construct	A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. [ZFIN:dh]	2031	0	0
1787	52	promoter_trap_construct	A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. [ZFIN:dh]	2032	0	0
1788	52	enhancer_trap_construct	An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. [ZFIN:dh]	2033	0	0
1789	52	PAC_end	A region of sequence from the end of a PAC clone that may provide a highly specific marker. [ZFIN:mh]	2034	0	0
1790	52	RAPD	RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers. [ZFIN:mh]	2035	0	0
1791	52	shadow_enhancer	An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene. [PMID:22083793]	2036	0	0
1792	52	substitution	A sequence alteration where the length of the change in the variant is the same as that of the reference. [SO:ke]	2037	0	0
1793	52	X_element_combinatorial_repeat	An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element. [http://www.yeastgenome.org/help/glossary.html]	2038	0	0
1794	52	Y_prime_element	A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. [http:http\\://www.yeastgenome.org/help/glossary.html]	2039	0	0
1795	52	standard_draft	The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete. [DOI:10.1126]	2040	0	0
1796	52	whole_genome_sequence_status	The status of whole genome sequence. [DOI:10.1126]	2041	0	0
1797	52	high_quality_draft	The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome. [DOI:10.1126]	2042	0	0
1798	52	improved_high_quality_draft	The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution. [DOI:10.1126]	2043	0	0
1799	52	annotation_directed_improved_draft	The status of a whole genome sequence,where annotation, and verification of coding regions has occurred. [DOI:10.1126]	2044	0	0
1800	52	noncontiguous_finished	The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions. [DOI:10.1126]	2045	0	0
1801	52	finished_genome	The status of a whole genome sequence, with less than 1 error per 100,000 base pairs. [DOI:10.1126]	2046	0	0
1802	52	intronic_regulatory_region	A regulatory region that is part of an intron. [SO:ke]	2047	0	0
1803	52	centromere_DNA_Element_I	A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p). [PMID:11222754]	2048	0	0
1804	52	point_centromere	A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae. [PMID:7502067, SO:vw]	2049	0	0
1805	52	centromere_DNA_Element_II	A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length. [PMID:11222754]	2050	0	0
1806	52	centromere_DNA_Element_III	A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex. [PMID:11222754]	2051	0	0
1807	52	telomeric_repeat	The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. [PMID:8720065]	2052	0	0
1808	52	X_element	The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site. [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]	2053	0	0
1809	52	YAC_end	A region of sequence from the end of a YAC clone that may provide a highly specific marker. [SO:ke]	2054	0	0
1810	52	peptide_collection	A collection of peptide sequences. [BBOP:nlw]	2055	0	0
1811	52	high_identity_region	An experimental feature with high sequence identity to another sequence. [SO:ke]	2056	0	0
1812	52	processed_transcript	A transcript for which no open reading frame has been identified and for which no other function has been determined. [MGI:hdeen]	2057	0	0
1813	52	reference_genome	A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. [SO:ke]	2058	0	0
1814	52	variant_genome	A collection of sequences (often chromosomes) of an individual. [SO:ke]	2059	0	0
1815	52	alteration_attribute	An attribute of alteration of one or more chromosomes. []	2060	0	0
1816	52	chromosomal_variation_attribute	An attribute of a change in the structure or number of a chromosomes. []	2061	0	0
1817	52	intrachromosomal	A change in chromosomes that occurs between two separate chromosomes. []	2062	0	0
1818	52	interchromosomal	A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes. []	2063	0	0
1819	52	insertion_attribute	A quality of a chromosomal insertion,. [SO:ke]	2064	0	0
1820	52	tandem	An insertion of extension of a tandem repeat. []	2065	0	0
1821	52	direct	A quality of an insertion where the insert is not in a cytologically inverted orientation. [SO:ke]	2066	0	0
1822	52	inverted	A quality of an insertion where the insert is in a cytologically inverted orientation. [SO:ke]	2067	0	0
1823	52	free	The quality of a duplication where the new region exists independently of the original. [SO:ke]	2068	0	0
1824	52	duplication_attribute	An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. []	2069	0	0
1825	52	inversion_attribute	When a region of a chromosome is changed to the reverse order without duplication or deletion. []	2070	0	0
1826	52	pericentric	An inversion event that includes the centromere. []	2071	0	0
1827	52	paracentric	An inversion event that does not include the centromere. []	2072	0	0
1828	52	translocaton_attribute	An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. []	2073	0	0
1829	52	reciprocal	When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials. []	2074	0	0
1830	52	insertional	When a translocation is simply moving genetic material from one chromosome to another. []	2075	0	0
1831	52	assembly_error_correction	A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake. [SO:ke]	2076	0	0
1832	52	base_call_error_correction	A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake. [SO:ke]	2077	0	0
1833	52	nuclear_localization_signal	A polypeptide region that targets a polypeptide to the nucleus. [SO:ke]	2078	0	0
1834	52	endosomal_localization_signal	A polypeptide region that targets a polypeptide to the endosome. [SO:ke]	2079	0	0
1835	52	lysosomal_localization_signal	A polypeptide region that targets a polypeptide to the lysosome. [SO:ke]	2080	0	0
1836	52	nuclear_export_signal	A polypeptide region that targets a polypeptide to he cytoplasm. [SO:ke]	2081	0	0
1837	52	recombination_signal_sequence	A region recognized by a recombinase. [SO:ke]	2082	0	0
1838	52	cryptic_splice_site	A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. [SO:ke]	2083	0	0
1839	52	nuclear_rim_localization_signal	A polypeptide region that targets a polypeptide to the nuclear rim. [SO:ke]	2084	0	0
1840	52	P_TIR_transposon	A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain. [PMID:6309410, SO:ke]	2086	0	0
1841	52	functional_effect_variant	A variant whereby the effect is evaluated with respect to a reference. [SO:ke]	2087	0	0
1842	52	structural_variant	A sequence variant that changes one or more structural features. [SO:ke]	2088	0	0
1843	52	transcript_function_variant	A sequence variant which alters the functioning of a transcript with respect to a reference sequence. [SO:ke]	2089	0	0
1844	52	functionally_abnormal	A sequence variant in which the function of a gene product is altered with respect to a reference. []	2090	0	0
1845	52	translational_product_function_variant	A sequence variant that affects the functioning of a translational product with respect to a reference sequence. [SO:ke]	2091	0	0
1846	52	level_of_transcript_variant	A sequence variant which alters the level of a transcript. [SO:ke]	2092	0	0
1847	52	decreased_transcript_level_variant	A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence. [SO:ke]	2093	0	0
1848	52	increased_transcript_level_variant	A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. [SO:ke]	2094	0	0
1849	52	transcript_processing_variant	A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence. [SO:ke]	2095	0	0
1850	52	editing_variant	A transcript processing variant whereby the process of editing is disrupted with respect to the reference. [SO:ke]	2096	0	0
1851	52	polyadenylation_variant	A sequence variant that changes polyadenylation with respect to a reference sequence. [SO:ke]	2097	0	0
1852	52	transcript_stability_variant	A variant that changes the stability of a transcript with respect to a reference sequence. [SO:ke]	2098	0	0
1853	52	decreased_transcript_stability_variant	A sequence variant that decreases transcript stability with respect to a reference sequence. [SO:ke]	2099	0	0
1854	52	increased_transcript_stability_variant	A sequence variant that increases transcript stability with respect to a reference sequence. [SO:ke]	2100	0	0
1855	52	transcription_variant	A variant that changes alters the transcription of a transcript with respect to a reference sequence. [SO:ke]	2101	0	0
1856	52	rate_of_transcription_variant	A sequence variant that changes the rate of transcription with respect to a reference sequence. [SO:ke]	2102	0	0
1857	52	increased_transcription_rate_variant	A sequence variant that increases the rate of transcription with respect to a reference sequence. [SO:ke]	2103	0	0
1858	52	decreased_transcription_rate_variant	A sequence variant that decreases the rate of transcription with respect to a reference sequence. [SO:ke]	2104	0	0
1859	52	translational_product_level_variant	A functional variant that changes the translational product level with respect to a reference sequence. [SO:ke]	2105	0	0
1860	52	polypeptide_function_variant	A sequence variant which changes polypeptide functioning with respect to a reference sequence. [SO:ke]	2106	0	0
1861	52	decreased_translational_product_level	A sequence variant which decreases the translational product level with respect to a reference sequence. [SO:ke]	2107	0	0
1862	52	increased_translational_product_level	A sequence variant which increases the translational product level with respect to a reference sequence. [SO:ke]	2108	0	0
1863	52	polypeptide_gain_of_function_variant	A sequence variant which causes gain of polypeptide function with respect to a reference sequence. [SO:ke]	2109	0	0
1864	52	polypeptide_localization_variant	A sequence variant which changes the localization of a polypeptide with respect to a reference sequence. [SO:ke]	2110	0	0
1865	52	polypeptide_loss_of_function_variant	A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence. [SO:ke]	2111	0	0
1866	52	inactive_ligand_binding_site	A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence. [SO:ke]	2112	0	0
1867	52	polypeptide_partial_loss_of_function	A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. [SO:ke]	2113	0	0
1868	52	polypeptide_post_translational_processing_variant	A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence. [SO:ke]	2114	0	0
1869	52	copy_number_change	A sequence variant where copies of a feature (CNV) are either increased or decreased. [SO:ke]	2115	0	0
1870	52	sequence_length_variant	A sequence variant that changes the length of one or more sequence features. []	2116	0	0
1871	52	gene_variant	A sequence variant where the structure of the gene is changed. [SO:ke]	2117	0	0
1872	52	gene_fusion	A sequence variant whereby a two genes have become joined. [SO:ke]	2118	0	0
1873	52	feature_fusion	A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features. [SO:ke]	2119	0	0
1874	52	regulatory_region_variant	A sequence variant located within a regulatory region. [SO:ke]	2120	0	0
1875	52	stop_retained_variant	A sequence variant where at least one base in the terminator codon is changed, but the terminator remains. [SO:ke]	2121	0	0
1876	52	terminator_codon_variant	A sequence variant whereby at least one of the bases in the terminator codon is changed. [SO:ke]	2122	0	0
1877	52	synonymous_variant	A sequence variant where there is no resulting change to the encoded amino acid. [SO:ke]	2123	0	0
1878	52	splicing_variant	A sequence variant that changes the process of splicing. [SO:ke]	2124	0	0
1879	52	transcript_variant	A sequence variant that changes the structure of the transcript. [SO:ke]	2126	0	0
1880	52	cryptic_splice_site_variant	A sequence variant causing a new (functional) splice site. [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	2127	0	0
1881	52	cryptic_splice_acceptor	A sequence variant whereby a new splice site is created due to the activation of a new acceptor. [SO:ke]	2128	0	0
1882	52	cryptic_splice_donor	A sequence variant whereby a new splice site is created due to the activation of a new donor. [SO:ke]	2129	0	0
1883	52	exon_loss_variant	A sequence variant whereby an exon is lost from the transcript. [SO:ke]	2130	0	0
1884	52	intron_gain_variant	A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor. [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]	2131	0	0
1885	52	splice_acceptor_variant	A splice variant that changes the 2 base region at the 3' end of an intron. [SO:ke]	2132	0	0
1886	52	splice_site_variant	A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript. [http://ensembl.org/info/docs/variation/index.html]	2133	0	0
1887	52	splice_donor_variant	A splice variant that changes the 2 base pair region at the 5' end of an intron. [SO:ke]	2134	0	0
1888	52	complex_transcript_variant	A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. [http://ensembl.org/info/docs/variation/index.html]	2135	0	0
1889	52	stop_lost	A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. [SO:ke]	2136	0	0
1890	52	feature_elongation	A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence. [SO:ke]	2137	0	0
1891	52	nonsynonymous_variant	A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change. [SO:ke]	2138	0	0
1892	52	transcript_sequence_variant		2139	1	0
1893	52	coding_sequence_variant	A sequence variant that changes the coding sequence. [SO:ke]	2140	0	0
1894	52	exon_variant	A sequence variant that changes exon sequence. [SO:ke]	2142	0	0
1895	52	coding_transcript_variant	A transcript variant of a protein coding gene. [SO:ke]	2143	0	0
1896	52	initiator_codon_variant	A codon variant that changes at least one base of the first codon of a transcript. [SO:ke]	2144	0	0
1897	52	missense_variant	A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. [EBI:fc, EBI:gr, SO:ke]	2146	0	0
1898	52	conservative_missense_variant	A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious. [SO:ke]	2150	0	0
1899	52	non_conservative_missense_variant	A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties. [SO:ke]	2151	0	0
1900	52	stop_gained	A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide. [SO:ke]	2152	0	0
1901	52	feature_truncation	A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence. [SO:ke]	2154	0	0
1902	52	frameshift_variant	A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. [SO:ke]	2155	0	0
1903	52	protein_altering_variant	A sequence_variant which is predicted to change the protein encoded in the coding sequence. [EBI:gr]	2157	0	0
1904	52	frame_restoring_variant	A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame. [SO:ke]	2160	0	0
1905	52	minus_1_frameshift_variant	A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	2161	0	0
1906	52	minus_2_frameshift_variant	A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward. []	2162	0	0
1907	52	plus_1_frameshift_variant	A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]	2163	0	0
1908	52	plus_2_frameshift_variant	A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward. []	2164	0	0
1909	52	transcript_secondary_structure_variant	A sequence variant within a transcript that changes the secondary structure of the RNA product. [SO:ke]	2165	0	0
1910	52	compensatory_transcript_secondary_structure_variant	A secondary structure variant that compensate for the change made by a previous variant. [SO:ke]	2166	0	0
1911	52	translational_product_structure_variant	A sequence variant within the transcript that changes the structure of the translational product. [SO:ke]	2167	0	0
1912	52	3D_polypeptide_structure_variant	A sequence variant that changes the resulting polypeptide structure. [SO:ke]	2168	0	0
1913	52	complex_3D_structural_variant	A sequence variant that changes the resulting polypeptide structure. [SO:ke]	2169	0	0
1914	52	conformational_change_variant	A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence. [SO:ke]	2170	0	0
1915	52	complex_change_of_translational_product_variant	A variant that changes the translational product with respect to the reference. []	2171	0	0
1916	52	polypeptide_sequence_variant	A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence. [SO:ke]	2172	0	0
1917	52	amino_acid_deletion	A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide. [SO:ke]	2173	0	0
1918	52	amino_acid_insertion	A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide. [SO:ke]	2174	0	0
1919	52	amino_acid_substitution	A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide. [SO:ke]	2175	0	0
1920	52	conservative_amino_acid_substitution	A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide. [SO:ke]	2176	0	0
1921	52	non_conservative_amino_acid_substitution	A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide. [SO:ke]	2177	0	0
1922	52	elongated_polypeptide	An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS. [SO:ke]	2178	0	0
1923	52	elongated_polypeptide_C_terminal	An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS. [SO:ke]	2179	0	0
1924	52	CDS_three_prime_extension	A sequence variant extending the CDS at the 3' end, that causes elongation of the resulting polypeptide sequence at the C terminus. [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195]	2180	0	0
1925	52	elongated_polypeptide_N_terminal	An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS. [SO:ke]	2181	0	0
1926	52	CDS_five_prime_extension	A sequence variant extending the CDS at the 5' end, that causes elongation of the resulting polypeptide sequence at the N terminus. [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195]	2182	0	0
1927	52	elongated_in_frame_polypeptide_C_terminal	A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus. [SO:ke]	2183	0	0
1928	52	elongated_out_of_frame_polypeptide_C_terminal	A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus. [SO:ke]	2184	0	0
1929	52	elongated_in_frame_polypeptide_N_terminal_elongation	A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus. [SO:ke]	2185	0	0
1930	52	elongated_out_of_frame_polypeptide_N_terminal	A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus. [SO:ke]	2186	0	0
1931	52	polypeptide_fusion	A sequence variant that causes a fusion of two polypeptide sequences. [SO:ke]	2187	0	0
1932	52	polypeptide_truncation	A sequence variant of the CD that causes a truncation of the resulting polypeptide. [SO:ke]	2188	0	0
1933	52	inactive_catalytic_site	A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence. [SO:ke]	2189	0	0
1934	52	non_coding_transcript_variant	A transcript variant of a non coding RNA gene. [SO:ke]	2190	0	0
1935	52	mature_miRNA_variant	A transcript variant located with the sequence of the mature miRNA. [SO:ke]	2191	0	0
1936	52	NMD_transcript_variant	A variant in a transcript that is the target of nonsense-mediated mRNA decay. [SO:ke]	2193	0	0
1937	52	UTR_variant	A transcript variant that is located within the UTR. [SO:ke]	2194	0	0
1938	52	5_prime_UTR_variant	A UTR variant of the 5' UTR. [SO:ke]	2195	0	0
1939	52	3_prime_UTR_variant	A UTR variant of the 3' UTR. [SO:ke]	2196	0	0
1940	52	incomplete_terminal_codon_variant	A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. [SO:ke]	2197	0	0
1941	52	inframe_variant	A sequence variant which does not cause a disruption of the translational reading frame. [SO:ke]	2198	0	0
1942	52	intron_variant	A transcript variant occurring within an intron. [SO:ke]	2199	0	0
1943	52	intergenic_variant	A sequence variant located in the intergenic region, between genes. [SO:ke]	2200	0	0
1944	52	splice_region_variant	A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. [http://ensembl.org/info/docs/variation/index.html]	2201	0	0
1945	52	upstream_gene_variant	A sequence variant located 5' of a gene. [SO:ke]	2202	0	0
1946	52	downstream_gene_variant	A sequence variant located 3' of a gene. [SO:ke]	2203	0	0
1947	52	5KB_downstream_variant	A sequence variant located within 5 KB of the end of a gene. [SO:ke]	2204	0	0
1948	52	500B_downstream_variant	A sequence variant located within a half KB of the end of a gene. [SO:ke]	2205	0	0
1949	52	5KB_upstream_variant	A sequence variant located within 5KB 5' of a gene. [SO:ke]	2206	0	0
1950	52	2KB_upstream_variant	A sequence variant located within 2KB 5' of a gene. [SO:ke]	2207	0	0
1951	52	rRNA_gene	A gene that encodes for ribosomal RNA. [SO:ke]	2208	0	0
1952	52	piRNA_gene	A gene that encodes for an piwi associated RNA. [SO:ke]	2209	0	0
1953	52	RNase_P_RNA_gene	A gene that encodes an RNase P RNA. [SO:ke]	2210	0	0
1954	52	enzymatic_RNA_gene	A gene that encodes an enzymatic RNA. []	2211	0	0
1955	52	RNase_MRP_RNA_gene	A gene that encodes a RNase_MRP_RNA. [SO:ke]	2212	0	0
1956	52	lincRNA_gene	A gene that encodes a long, intervening non-coding RNA. [http://www.gencodegenes.org/gencode_biotypes.html, PMID:23463798, SO:ke]	2213	0	0
1957	52	lncRNA_gene	A gene that encodes a long non-coding RNA. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2214	0	0
1958	52	mathematically_defined_repeat	A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness. [SO:jestill]	2215	0	0
1959	52	telomerase_RNA_gene	A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. [SO:ke]	2216	0	0
2623	52	plastid_SSU_rRNA_gene	A gene that codes for plastid SSU rRNA. []	2894	0	0
1960	52	targeting_vector	An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications. [MGD:tm, PMID:10354467]	2217	0	0
1961	52	DArT_marker	A genetic marker, discovered using Diversity Arrays Technology (DArT) technology. [SO:ke]	2218	0	0
1962	52	kozak_sequence	A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. [SO:ke]	2219	0	0
1963	52	retinoic_acid_responsive_element	A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. [PMID:11327309, PMID:19917671]	2220	0	0
1964	52	nested_tandem_repeat	An NTR is a nested repeat of two distinct tandem motifs interspersed with each other. [SO:AF]	2221	0	0
1965	52	RNA_polymerase_II_TATA_box	A TATA box core promoter of a gene transcribed by RNA polymerase II. [PMID:16858867]	2222	0	0
1966	52	RNA_polymerase_III_TATA_box	A TATA box core promoter of a gene transcribed by RNA polymerase III. [SO:ke]	2223	0	0
1967	52	BREd_motif	A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G). [PMID:16858867]	2224	0	0
1968	52	DCE	A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII. [PMID:16858867]	2225	0	0
1969	52	DCE_SI	A sub element of the DCE core promoter element, with consensus sequence CTTC. [PMID:16858867, SO:ke]	2226	0	0
1970	52	DCE_SII	A sub element of the DCE core promoter element with consensus sequence CTGT. [PMID:16858867, SO:ke]	2227	0	0
1971	52	DCE_SIII	A sub element of the DCE core promoter element with consensus sequence AGC. [PMID:16858867, SO:ke]	2228	0	0
1972	52	proximal_promoter_element	DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor). [PMID:12515390, PMID:9679020, SO:ml]	2229	0	0
1973	52	regulatory_promoter_element	A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region. [PMID:12381659]	2230	0	0
1974	52	distal_promoter_element	A regulatory promoter element that is distal from the TSS. []	2231	0	0
1975	52	bacterial_RNApol_promoter_sigma54_element	A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription. []	2232	0	0
1976	52	minus_12_signal	A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. [PMID:18331472]	2233	0	0
1977	52	minus_24_signal	A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. [PMID:18331472]	2234	0	0
1978	52	A_box_type_1	An A box within an RNA polymerase III type 1 promoter. [SO:ke]	2235	0	0
1979	52	A_box_type_2	An A box within an RNA polymerase III type 2 promoter. [SO:ke]	2236	0	0
1980	52	intermediate_element	A core promoter region of RNA polymerase III type 1 promoters. [PMID:12381659]	2237	0	0
1981	52	transcription_regulatory_region	A regulatory region that is involved in the control of the process of transcription. [SO:ke]	2238	1	0
1982	52	recombination_regulatory_region	A regulatory region that is involved in the control of the process of recombination. [SO:ke]	2239	0	0
1983	52	replication_regulatory_region	A regulatory region that is involved in the control of the process of nucleotide replication. [SO:ke]	2240	0	0
1984	52	experimental_feature_attribute	An attribute of an experimentally derived feature. [SO:ke]	2241	0	0
1985	52	score	The score of an experimentally derived feature such as a p-value. [SO:ke]	2242	0	0
1986	52	quality_value	An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score. [SO:ke]	2243	0	0
1987	52	restriction_enzyme_recognition_site	The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. [SO:ke]	2244	0	0
1988	52	restriction_enzyme_region	A region related to restriction enzyme function. [SO:ke]	2245	0	0
1989	52	restriction_enzyme_cleavage_junction	The boundary at which a restriction enzyme breaks the nucleotide sequence. [SO:ke]	2246	0	0
1990	52	nucleotide_cleavage_site	A point in nucleic acid where a cleavage event occurs. []	2247	0	0
1991	52	five_prime_restriction_enzyme_junction	The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence. [SO:ke]	2248	0	0
1992	52	single_strand_restriction_enzyme_cleavage_site	A restriction enzyme cleavage site whereby only one strand is cut. [SO:ke]	2249	0	0
1993	52	sticky_end_restriction_enzyme_cleavage_site	A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'. []	2250	0	0
1994	52	three_prime_restriction_enzyme_junction	The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence. []	2251	0	0
1995	52	blunt_end_restriction_enzyme_cleavage_site	A restriction enzyme recognition site that, when cleaved, results in no overhangs. [SBOL:jgquinn, SO:ke]	2252	0	0
1996	52	blunt_end_restriction_enzyme_cleavage_junction	A restriction enzyme cleavage site where both strands are cut at the same position. [SO:ke]	2253	0	0
1997	52	restriction_enzyme_single_strand_overhang	A terminal region of DNA sequence where the end of the region is not blunt ended. [SO:ke]	2254	0	0
1998	52	experimentally_defined_binding_region	A region that has been implicated in binding although the exact coordinates of binding may be unknown. [SO:ke]	2255	0	0
1999	52	ChIP_seq_region	A region of sequence identified by CHiP seq technology to contain a protein binding site. [SO:ke]	2256	0	0
2000	52	ASPE_primer	\\"A primer containing an SNV at the 3' end for accurate genotyping. [http://www.ncbi.nlm.nih.gov/pubmed/11252801]	2257	0	0
2001	52	dCAPS_primer	A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site. [http://www.ncbi.nlm.nih.gov/pubmed/9628033]	2258	0	0
2002	52	histone_modification	Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation. [http:en.wikipedia.org/wiki/Histone]	2259	0	0
2003	52	histone_methylation_site	A histone modification site where the modification is the methylation of the residue. [SO:ke]	2260	0	0
2004	52	histone_acetylation_site	A histone modification where the modification is the acylation of the residue. [SO:ke]	2261	0	0
2005	52	H3K9_acetylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated. [http://en.wikipedia.org/wiki/Histone]	2262	0	0
2006	52	histone_3_acetylation_site	A histone 3 modification where the modification is the acetylation of the residue. [EBI:nj, ISBN:0815341059, SO:ke]	2263	0	0
2007	52	H3K14_acetylation_site	A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated. [http://en.wikipedia.org/wiki/Histone]	2264	0	0
2008	52	H3K4_monomethylation_site	A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. [http://en.wikipedia.org/wiki/Histone]	2265	0	0
2009	52	H3K4_methylation_site	A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. [SO:ke]	2266	0	0
2010	52	H3K4_trimethylation	A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. [http://en.wikipedia.org/wiki/Histone]	2267	0	0
2011	52	H3K9_trimethylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. [http://en.wikipedia.org/wiki/Histone]	2268	0	0
2012	52	H3K9_methylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. [SO:ke]	2269	0	0
2013	52	H3K27_monomethylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. [http://en.wikipedia.org/wiki/Histone]	2270	0	0
2014	52	H3K27_methylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated. [SO:ke]	2271	0	0
2015	52	H3K27_trimethylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. [http://en.wikipedia.org/wiki/Histone]	2272	0	0
2016	52	H3K79_monomethylation_site	A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. [http://en.wikipedia.org/wiki/Histone]	2273	0	0
2017	52	H3K79_methylation_site	A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. [SO:ke]	2274	0	0
2018	52	H3K79_dimethylation_site	A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. [http://en.wikipedia.org/wiki/Histone]	2275	0	0
2019	52	H3K79_trimethylation_site	A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. [http://en.wikipedia.org/wiki/Histone]	2276	0	0
2020	52	H4K20_monomethylation_site	A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated. [http://en.wikipedia.org/wiki/Histone]	2277	0	0
2021	52	H2BK5_monomethylation_site	A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. [http://en.wikipedia.org/wiki/Histone]	2278	0	0
2022	52	ISRE	An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. [http://genesdev.cshlp.org/content/2/4/383.abstrac]	2279	0	0
2023	52	histone_ubiqitination_site	A histone modification site where ubiquitin may be added. [SO:ke]	2280	0	0
2024	52	H2B_ubiquitination_site	A histone modification site on H2B where ubiquitin may be added. [SO:ke]	2281	0	0
2025	52	H3K18_acetylation_site	A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated. [SO:ke]	2282	0	0
2026	52	H3K23_acetylation_site	A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated. [SO:ke]	2283	0	0
2027	52	H3K27_acylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated. [SO:ke]	2284	1	0
2028	52	H3K36_monomethylation_site	A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. [SO:ke]	2285	0	0
2029	52	H3K36_methylation_site	A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. [SO:ke]	2286	0	0
2030	52	H3K36_dimethylation_site	A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. [SO:ke]	2287	0	0
2031	52	H3K36_trimethylation_site	A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. [SO:ke]	2288	0	0
2032	52	H3K4_dimethylation_site	A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. [SO:ke]	2289	0	0
2033	52	H3K27_dimethylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. [SO:ke]	2290	0	0
2034	52	H3K9_monomethylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. [SO:ke]	2291	0	0
2035	52	H3K9_dimethylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. [SO:ke]	2292	0	0
2036	52	H4K16_acetylation_site	A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated. [SO:ke]	2293	0	0
2037	52	histone_4_acetylation_site	A histone 4 modification where the modification is the acetylation of the residue. [EBI:nj, ISBN:0815341059, SO:ke]	2294	0	0
2038	52	H4K5_acetylation_site	A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated. [SO:ke]	2295	0	0
2039	52	H4K8_acetylation_site	A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated. [SO:KE]	2296	0	0
2040	52	histone_acylation_region	A histone modification, whereby the histone protein is acylated at multiple sites in a region. [SO:ke]	2297	0	0
2041	52	H4K_acylation_region	A region of the H4 histone whereby multiple lysines are acylated. [SO:ke]	2298	0	0
2042	52	gene_with_non_canonical_start_codon	A gene with a start codon other than AUG. [SO:xp]	2299	0	0
2043	52	gene_with_start_codon_CUG	A gene with a translational start codon of CUG. [SO:mc]	2300	0	0
2044	52	pseudogenic_gene_segment	A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. [SO:hd]	2301	0	0
2045	52	gene_segment	A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. [GOC:add]	2302	0	0
2046	52	copy_number_gain	A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. [SO:ke]	2303	0	0
2047	52	copy_number_loss	A sequence alteration whereby the copy number of a given region is less than the reference sequence. [SO:ke]	2304	0	0
2048	52	UPD	Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. [SO:BM]	2305	0	0
2049	52	maternal_uniparental_disomy	Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. [SO:bm]	2306	0	0
2050	52	paternal_uniparental_disomy	Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. [SO:bm]	2307	0	0
2051	52	open_chromatin_region	A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. [SO:cb]	2308	0	0
2052	52	SL3_acceptor_site	A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2309	0	0
2053	52	SL4_acceptor_site	A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2310	0	0
2054	52	SL5_acceptor_site	A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2311	0	0
2055	52	SL6_acceptor_site	A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2312	0	0
2056	52	SL7_acceptor_site	A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2313	0	0
2057	52	SL8_acceptor_site	A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2314	0	0
2058	52	SL9_acceptor_site	A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2315	0	0
2059	52	SL10_acceptor_site	A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2316	0	0
2060	52	SL11_acceptor_site	A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2317	0	0
2061	52	SL12_acceptor_site	A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. [SO:nlw]	2318	0	0
2062	52	duplicated_pseudogene	A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence. [http://en.wikipedia.org/wiki/Pseudogene]	2319	0	0
2063	52	unitary_pseudogene	A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, http://en.wikipedia.org/wiki/Pseudogene, SO:ke]	2320	0	0
2064	52	variant_quality	A dependent entity that inheres in a bearer, a sequence variant. [PMID:17597783, SO:ke]	2321	0	0
2065	52	variant_origin	A quality inhering in a variant by virtue of its origin. [PMID:17597783, SO:ke]	2322	0	0
2066	52	variant_frequency	A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. [PMID:17597783, SO:ke]	2323	0	0
2067	52	unique_variant	A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. [SO:ke]	2324	0	0
2068	52	rare_variant	When a variant from the genomic sequence is rarely found in the general population. The threshold for 'rare' varies between studies. []	2325	0	0
2069	52	polymorphic_variant	A variant that affects one of several possible alleles at that location, such as the major histocompatibility complex (MHC) genes. []	2326	0	0
2070	52	common_variant	When a variant from the genomic sequence is commonly found in the general population. []	2327	0	0
2071	52	fixed_variant	When a variant has become fixed in the population so that it is now the only variant. []	2328	0	0
2072	52	variant_phenotype	A quality inhering in a variant by virtue of its phenotype. [PMID:17597783, SO:ke]	2329	0	0
2073	52	benign_variant	A variant that does not affect the function of the gene or cause disease. []	2330	0	0
2074	52	disease_associated_variant	A variant that has been found to be associated with disease. []	2331	0	0
2075	52	disease_causing_variant	A variant that has been found to cause disease. []	2332	0	0
2076	52	lethal_variant	A sequence variant where the mutated gene product does not allow for one or more basic functions necessary for survival. []	2333	0	0
2077	52	quantitative_variant	A variant within a gene that contributes to a quantitative trait such as height or weight. []	2334	0	0
2078	52	maternal_variant	A variant in the genetic material inherited from the mother. []	2335	0	0
2079	52	paternal_variant	A variant in the genetic material inherited from the father. []	2336	0	0
2080	52	somatic_variant	A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body. []	2337	0	0
2081	52	germline_variant	A variant present in the embryo that is carried by every cell in the body. []	2338	0	0
2082	52	pedigree_specific_variant	A variant that is found only by individuals that belong to the same pedigree. []	2339	0	0
2083	52	population_specific_variant	A variant found within only speficic populations. []	2340	0	0
2084	52	de_novo_variant	A variant arising in the offspring that is not found in either of the parents. []	2341	0	0
2085	52	TF_binding_site_variant	A sequence variant located within a transcription factor binding site. [EBI:fc]	2342	0	0
2086	52	complex_structural_alteration	A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints. [FB:reference_manual, NCBI:th, SO:ke]	2343	0	0
2087	52	loss_of_heterozygosity	A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene. [SO:ke]	2345	0	0
2088	52	splice_donor_5th_base_variant	A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript. [EBI:gr]	2346	0	0
2089	52	U_box	An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription. [PMID:10556309, PMID:11577982, PMID:9649446]	2347	0	0
2090	52	mating_type_region	A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type. [SO:ke]	2348	0	0
2091	52	non_coding_transcript_exon_variant	A sequence variant that changes non-coding exon sequence in a non-coding transcript. [EBI:fc, SO:ke]	2349	0	0
2092	52	clone_end	A read from an end of the clone sequence. [SO:ke]	2350	0	0
2093	52	regional_centromere	A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions. [PMID:7502067, SO:vw]	2351	0	0
2094	52	regional_centromere_central_core	A conserved region within the central region of a modular centromere, where the kinetochore is formed. [SO:vw]	2352	0	0
2095	52	centromeric_repeat	A repeat region found within the modular centromere. [SO:ke]	2353	0	0
2096	52	regional_centromere_inner_repeat_region	The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm. [SO:vw]	2354	0	0
2097	52	regional_centromere_outer_repeat_region	The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms. [SO:vw]	2355	0	0
2098	52	tasiRNA	The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. [PMID:16145017]	2356	0	0
2099	52	tasiRNA_primary_transcript	A primary transcript encoding a tasiRNA. [PMID:16145017]	2357	0	0
2100	52	increased_polyadenylation_variant	A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference. [SO:ke]	2358	0	0
2101	52	decreased_polyadenylation_variant	A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference. [SO:ke]	2359	0	0
2102	52	DDB_box	A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases. [PMID:18794354, PMID:19818632]	2360	0	0
2103	52	destruction_box	A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN. [PMID:12208841, PMID:1842691]	2361	0	0
2104	52	polypeptide_conserved_motif	A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. [EBIBS:GAR]	2362	0	0
2105	52	ER_retention_signal	A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL. [doi:10.1093/jxb/50.331.157, PMID:2077689]	2363	0	0
2106	52	KEN_box	A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN. [PMID:10733526, PMID:1220884, PMID:18426916]	2364	0	0
2107	52	mitochondrial_targeting_signal	A polypeptide region that targets a polypeptide to the mitochondrion. [PomBase:mah]	2365	0	0
2108	52	signal_anchor	A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane. [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]	2366	0	0
2109	52	PIP_box	A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains. [PMID:9631646]	2367	0	0
2110	52	phosphorylation_site	A post-translationally modified region in which residues of the protein are modified by phosphorylation. [PomBase:mah]	2368	0	0
2111	52	transmembrane_helix	A region that traverses the lipid bilayer and adopts a helical secondary structure. [PomBase:mah]	2369	0	0
2112	52	vacuolar_sorting_signal	A polypeptide region that targets a polypeptide to the vacuole. [PomBase:mah]	2370	0	0
2113	52	coding_variant_quality	An attribute of a coding genomic variant. []	2371	0	0
2114	52	synonymous	A variant that does not lead to any change in the amino acid sequence. []	2372	0	0
2115	52	non_synonymous	A variant that leads to the change of an amino acid within the protein. []	2373	0	0
2116	52	inframe	An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3. [SO:ke]	2374	0	0
2117	52	inframe_indel	A coding sequence variant where the change does not alter the frame of the transcript. [SO:ke]	2376	0	0
2118	52	inframe_insertion	An inframe non synonymous variant that inserts bases into in the coding sequence. [EBI:gr]	2377	0	0
2119	52	internal_feature_elongation	A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence. [SO:ke]	2379	0	0
2120	52	inframe_deletion	An inframe non synonymous variant that deletes bases from the coding sequence. [EBI:gr]	2380	0	0
2121	52	conservative_inframe_insertion	An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons. [EBI:gr]	2382	0	0
2122	52	disruptive_inframe_insertion	An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon. [EBI:gr]	2383	0	0
2123	52	conservative_inframe_deletion	An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons. [EBI:gr]	2384	0	0
2124	52	disruptive_inframe_deletion	An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon. [EBI:gr]	2385	0	0
2125	52	mRNA_read	A sequencer read of an mRNA substrate. [SO:ke]	2386	0	0
2126	52	genomic_DNA_read	A sequencer read of a genomic DNA substrate. [SO:ke]	2387	0	0
2127	52	mRNA_contig	A contig composed of mRNA_reads. [SO:ke]	2388	0	0
2128	52	AFLP_fragment	A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments. [GMOD:ea]	2389	0	0
2129	52	protein_hmm_match	A match to a protein HMM such as pfam. [SO:ke]	2390	0	0
2130	52	immunoglobulin_region	A region of immunoglobulin sequence, either constant or variable. [SO:ke]	2391	0	0
2131	52	V_region	The variable region of an immunoglobulin polypeptide sequence. [SO:ke]	2392	0	0
2132	52	C_region	The constant region of an immunoglobulin polypeptide sequence. [SO:ke]	2393	0	0
2133	52	N_region	Extra nucleotides inserted between rearranged immunoglobulin segments. [SO:ke]	2394	0	0
2134	52	S_region	The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. [SO:ke]	2395	0	0
2135	52	mobile_element_insertion	A kind of insertion where the inserted sequence is a mobile element. [EBI:dvga]	2396	0	0
2136	52	novel_sequence_insertion	An insertion the sequence of which cannot be mapped to the reference genome. [NCBI:th]	2397	0	0
2137	52	CSL_response_element	A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors. [PMID:19101542]	2398	0	0
2138	52	GATA_box	A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G). [PMID:8321208]	2399	0	0
2139	52	polymorphic_pseudogene	A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, JAX:hd]	2400	0	0
2140	52	AP_1_binding_site	A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors. [PMID:1899230, PMID:3034432, PMID:3125983]	2401	0	0
2141	52	CRE	MERGED DEFINITION:\\nTARGET DEFINITION: A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.\\n--------------------\\nSOURCE DEFINITION: A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components. [PMID:11483355, PMID:11483993, PMID:15448137]	2402	0	0
2142	52	CuRE	A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast). [PMID:10593913, PMID:9188496, PMID:9211922]	2404	0	0
2143	52	DRE	A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis. [PMID:11073995, PMID:8668127]	2405	0	0
2144	52	FLEX_element	A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain. [PMID:10747048, PMID:14871934]	2406	0	0
2145	52	forkhead_motif	A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain. [PMID:15195092]	2407	0	0
2146	52	homol_D_box	A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence. [PMID:21673110, PMID:7501449, PMID:8458332]	2408	0	0
2147	52	homol_E_box	A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence. [PMID:7501449]	2409	0	0
2148	52	HSE	A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF. [PMID:17347150, PMID:8689565]	2410	0	0
2149	52	iron_repressed_GATA_element	A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron. [PMID:11956219, PMID:17211681]	2411	0	0
2150	52	mating_type_M_box	A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc. [PMID:9233811]	2412	0	0
2151	52	androgen_response_element	A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen. [PMID:21796522]	2413	0	0
2152	52	smFISH_probe	A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment. [PMID:18806792]	2414	0	0
2153	52	MCB	A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle. [PMID:16285853]	2415	0	0
2154	52	CCAAT_motif	A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels. [PMID:16963626]	2416	0	0
2155	52	Ace2_UAS	A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2. [PMID:16678171]	2417	0	0
2156	52	TR_box	A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis. [PMID:1657709]	2418	0	0
2157	52	STREP_motif	A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2. [PMID:11739717]	2419	0	0
2158	52	rDNA_intergenic_spacer_element	A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). The S. pombe telomeric repeat consensus is TTAC(0-1)A(0-1)G(1-8). [ISBN:978-0199638901, PMID:9016645]	2420	0	0
2159	52	sterol_regulatory_element	A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs. [GO:mah, PMID:11111080, PMID:16537923]	2421	0	0
2160	52	GT_dinucleotide_repeat	A dinucleotide repeat region composed of GT repeating elements. [SO:ke]	2422	0	0
2161	52	GTT_trinucleotide_repeat	A trinucleotide repeat region composed of GTT repeating elements. [SO:ke]	2423	0	0
2162	52	Sap1_recognition_motif	A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats. [PMID:16166653, PMID:7651412]	2424	0	0
2163	52	CDRE_motif	An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA. [PMID:16928959]	2425	0	0
2164	52	BAC_read_contig	A contig of BAC reads. [GMOD:ea]	2426	0	0
2165	52	candidate_gene	A gene suspected of being involved in the expression of a trait. [GMOD:ea]	2427	0	0
2166	52	positional_candidate_gene	A candidate gene whose association with a trait is based on the gene's location on a chromosome. [GMOD:ea]	2428	0	0
2167	52	functional_candidate_gene	A candidate gene whose function has something in common biologically with the trait under investigation. [GMOD:ea]	2429	0	0
2168	52	enhancerRNA	A short ncRNA that is transcribed from an enhancer. May have a regulatory function. [doi:10.1038/465173a, SO:cjm]	2430	0	0
2169	52	PCB	A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle. [GO:mah, PMID:12411492]	2431	0	0
2170	52	rearrangement_region	A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome. [NCBI:th, PMID:18564416]	2432	0	0
2171	52	interchromosomal_breakpoint	A rearrangement breakpoint between two different chromosomes. [NCBI:th]	2433	0	0
2172	52	intrachromosomal_breakpoint	A rearrangement breakpoint within the same chromosome. [NCBI:th]	2434	0	0
2173	52	unassigned_supercontig	A supercontig that is not been assigned to any ultracontig during a genome assembly project. [GMOD:ea]	2435	0	0
2174	52	feature_ablation	A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features. [SO:ke]	2436	0	0
2175	52	feature_amplification	A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features. [SO:ke]	2437	0	0
2176	52	feature_translocation	A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features. [SO:ke]	2438	0	0
2177	52	transcript_translocation	A feature translocation where the region contains a transcript. [SO:ke]	2439	0	0
2178	52	regulatory_region_translocation	A feature translocation where the region contains a regulatory region. [SO:ke]	2440	0	0
2179	52	TFBS_translocation	A feature translocation where the region contains a transcription factor binding site. [SO:ke]	2441	0	0
2180	52	transcript_fusion	A feature fusion where the deletion brings together transcript regions. [SO:ke]	2442	0	0
2181	52	regulatory_region_fusion	A feature fusion where the deletion brings together regulatory regions. [SO:ke]	2443	0	0
2182	52	TFBS_fusion	A fusion where the deletion brings together transcription factor binding sites. [SO:ke]	2444	0	0
2183	52	transcript_amplification	A feature amplification of a region containing a transcript. [SO:ke]	2445	0	0
2184	52	transcript_regulatory_region_fusion	A feature fusion where the deletion brings together a regulatory region and a transcript region. [SO:ke]	2446	0	0
2185	52	regulatory_region_amplification	A feature amplification of a region containing a regulatory region. [SO:ke]	2447	0	0
2186	52	TFBS_amplification	A feature amplification of a region containing a transcription factor binding site. [SO:ke]	2448	0	0
2187	52	transcript_ablation	A feature ablation whereby the deleted region includes a transcript feature. [SO:ke]	2449	0	0
2188	52	regulatory_region_ablation	A feature ablation whereby the deleted region includes a regulatory region. [SO:ke]	2450	0	0
2189	52	TFBS_ablation	A feature ablation whereby the deleted region includes a transcription factor binding site. [SO:ke]	2451	0	0
2190	52	transposable_element_CDS	A CDS that is part of a transposable element. [SO:ke]	2452	0	0
2191	52	transposable_element_pseudogene	A pseudogene contained within a transposable element. [SO:ke]	2453	0	0
2192	52	dg_repeat	A repeat region which is part of the regional centromere outer repeat region. [PMID:16407326, SO:vw]	2454	0	0
2193	52	dh_repeat	A repeat region which is part of the regional centromere outer repeat region. [PMID:16407326, SO:vw]	2455	0	0
2194	52	AACCCT_box	A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site. [PMID:17452352, PMID:4092687]	2456	0	0
2195	52	splice_region	A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. [SO:bm]	2457	0	0
2196	52	antisense_lncRNA	Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. [PMID:19638999]	2458	0	0
2197	52	regional_centromere_outer_repeat_transcript	A transcript that is transcribed from the outer repeat region of a regional centromere. [PomBase:mah]	2459	0	0
2198	52	frameshift_elongation	A frameshift variant that causes the translational reading frame to be extended relative to the reference feature. [SO:ke]	2460	0	0
2199	52	frameshift_truncation	A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature. [SO:ke]	2461	0	0
2200	52	copy_number_increase	A sequence variant where copies of a feature are increased relative to the reference. [SO:ke]	2462	0	0
2201	52	copy_number_decrease	A sequence variant where copies of a feature are decreased relative to the reference. [SO:ke]	2463	0	0
2202	52	rDNA_replication_fork_barrier	A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. [PMID:14645529]	2464	0	0
2203	52	transcription_start_cluster	A region defined by a cluster of experimentally determined transcription starting sites. [PMID:19624849, PMID:21372179, SO:andrewgibson]	2465	0	0
2204	52	CAGE_tag	A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites. [SO:andrewgibson]	2466	0	0
2205	52	CAGE_cluster	A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region. [PMID:16645617, SO:andrewgibson]	2467	0	0
2206	52	5_methylcytosine	A cytosine methylated at the 5 carbon. [SO:rtapella]	2468	0	0
2207	52	4_methylcytosine	A cytosine methylated at the 4 nitrogen. [SO:rtapella]	2469	0	0
2208	52	N6_methyladenine	An adenine methylated at the 6 nitrogen. [SO:rtapella]	2470	0	0
2209	52	mitochondrial_contig	A contig of mitochondria derived sequences. [GMOD:ea]	2471	0	0
2210	52	mitochondrial_supercontig	A scaffold composed of mitochondrial contigs. [GMOD:ea]	2472	0	0
2211	52	TERRA	A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long. [PMID:22139915]	2473	0	0
2212	52	telomeric_transcript	A non-coding transcript derived from the transcript of the telomere. [PMID:22139915]	2474	0	0
2213	52	ARRET	A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats. [PMID:2139915]	2475	0	0
2214	52	ARIA	A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats. [PMID:22139915]	2476	0	0
2215	52	anti_ARRET	A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts. [PMID:22139915]	2477	0	0
2216	52	distal_duplication	A duplication of the distal region of a chromosome. [SO:bm]	2478	0	0
2217	52	duplication	An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]	2479	0	0
2218	52	mitochondrial_DNA_read	A sequencer read of a mitochondrial DNA sample. [GMOD:ea]	2480	0	0
2219	52	chloroplast_DNA_read	A sequencer read of a chloroplast DNA sample. [GMOD:ea]	2481	0	0
2220	52	consensus_gDNA	Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input. [GMOD:ea]	2482	0	0
2221	52	restriction_enzyme_five_prime_single_strand_overhang	A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end. [SO:ke]	2483	0	0
2222	52	restriction_enzyme_three_prime_single_strand_overhang	A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end. [SO:ke]	2484	0	0
2223	52	monomeric_repeat	A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem. [SO:ke]	2485	0	0
2224	52	H3K20_trimethylation_site	A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated. [EBI:nj]	2486	0	0
2225	52	H3K36_acetylation_site	A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated. [EBI:nj]	2487	0	0
2226	52	H2BK12_acetylation_site	A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated. [EBI:nj]	2488	0	0
2227	52	histone_2B_acetylation_site	A histone 2B modification where the modification is the acetylation of the residue. [ISBN:0815341059]	2489	0	0
2228	52	H2AK5_acetylation_site	A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated. [EBI:nj]	2490	0	0
2229	52	histone_2A_acetylation_site	A histone 2A modification where the modification is the acetylation of the residue. [ISBN:0815341059]	2491	0	0
2230	52	H4K12_acetylation_site	A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated. [EBI:nj]	2492	0	0
2231	52	H2BK120_acetylation_site	A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated. [EBI:nj, http://dx.doi.org/10.4161/epi.6.5.15623]	2493	0	0
2232	52	H4K91_acetylation_site	A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated. [EBI:nj]	2494	0	0
2233	52	H2BK20_acetylation_site	A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated. [EBI:nj]	2495	0	0
2234	52	H3K4_acetylation_site	A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated. [EBI:nj]	2496	0	0
2235	52	H2AK9_acetylation_site	A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated. [EBI:nj]	2497	0	0
2236	52	H3K56_acetylation_site	A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated. [EBI:nj]	2498	0	0
2237	52	H2BK15_acetylation_site	A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated. [EBI:nj]	2499	0	0
2238	52	H3R2_monomethylation_site	A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated. [EBI:nj]	2500	0	0
2239	52	H3R2_dimethylation_site	A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated. [EBI:nj]	2501	0	0
2240	52	H4R3_dimethylation_site	A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated. [EBI:nj]	2502	0	0
2241	52	H4K4_trimethylation_site	A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated. [EBI:nj]	2503	0	0
2242	52	H3K23_dimethylation_site	A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated. [EBI:nj]	2504	0	0
2243	52	promoter_flanking_region	A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites. [EBI:nj]	2505	0	0
2244	52	restriction_enzyme_assembly_scar	A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends. [SO:ke]	2506	0	0
2245	52	protein_stability_element	A polypeptide region that proves structure in a protein that affects the stability of the protein. [SO:ke]	2507	0	0
2246	52	protease_site	A polypeptide_region that codes for a protease cleavage site. [SO:ke]	2508	0	0
2247	52	RNA_stability_element	RNA secondary structure that affects the stability of an RNA molecule. [SO:ke]	2509	1	0
2248	52	lariat_intron	A kind of intron whereby the excision is driven by lariat formation. [SO:ke]	2510	0	0
2249	52	TCT_motif	A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator. [PMID:20801935, SO:myl]	2511	0	0
2250	52	5_hydroxymethylcytosine	A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon. [SO:ke]	2512	0	0
2251	52	5_formylcytosine	A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon. [SO:ke]	2513	0	0
2252	52	modified_guanine	A modified guanine DNA base feature. [SO:ke]	2514	0	0
2253	52	8_oxoguanine	A modified DNA guanine base,at the 8 carbon, often the product of DNA damage. [SO:ke]	2515	0	0
2254	52	5_carboxylcytosine	A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon. [SO:ke]	2516	0	0
2255	52	8_oxoadenine	A modified DNA adenine base,at the 8 carbon, often the product of DNA damage. [SO:ke]	2517	0	0
2256	52	coding_transcript_intron_variant	A transcript variant occurring within an intron of a coding transcript. [SO:ke]	2518	0	0
2257	52	non_coding_transcript_intron_variant	A transcript variant occurring within an intron of a non coding transcript. [SO:ke]	2519	0	0
2258	52	zinc_finger_binding_site	A binding site to which a polypeptide will bind with a zinc finger motif, which is characterized by requiring one or more Zinc 2+ ions for stabilized folding. []	2520	0	0
2259	52	CTCF_binding_site	A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor. [EBI:nj]	2521	0	0
2260	52	five_prime_sticky_end_restriction_enzyme_cleavage_site	A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs. [SO:ke]	2522	0	0
2261	52	three_prime_sticky_end_restriction_enzyme_cleavage_site	A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs. [SO:ke]	2523	0	0
2262	52	ribonuclease_site	A region of a transcript encoding the cleavage site for a ribonuclease enzyme. [SO:ke]	2524	0	0
2263	52	signature	A region of sequence where developer information is encoded. [SO:ke]	2525	0	0
2264	52	RNA_stability_element(SO:0001979)	A motif that affects the stability of RNA. [PMID:22495308, SO:ke]	2526	0	0
2265	52	G_box	A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a. [PMID:19249238, PMID:8571452, SO:ml]	2527	0	0
2266	52	L_box	An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants. [PMID:17381552, PMID:2902624, SO:ml]	2528	0	0
2267	52	I-box	A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core). [PMID:2347304, PMID:2902624, SO:ml]	2529	0	0
2268	52	5_prime_UTR_premature_start_codon_variant	A 5' UTR variant where a premature start codon is introduced, moved or lost. [SANGER:am]	2530	0	0
2269	52	silent_mating_type_cassette_array	A gene cassette array that corresponds to a silenced version of a mating type region. [PomBase:mah]	2531	0	0
2270	52	gene_cassette_array	An array of non-functional genes whose members, when captured by recombination form functional genes. [SO:ma]	2532	0	0
2271	52	Okazaki_fragment	Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication. [ISBN:0805350152]	2533	0	0
2272	52	upstream_transcript_variant	A feature variant, where the alteration occurs upstream of the transcript TSS. [EBI:gr]	2534	0	0
2273	52	downstream_transcript_variant	A feature variant, where the alteration occurs downstream of the transcript termination site. []	2535	0	0
2274	52	5_prime_UTR_premature_start_codon_gain_variant	A 5' UTR variant where a premature start codon is gained. [Sanger:am]	2536	0	0
2275	52	5_prime_UTR_premature_start_codon_loss_variant	A 5' UTR variant where a premature start codon is lost. [SANGER:am]	2537	0	0
2276	52	five_prime_UTR_premature_start_codon_location_variant	A 5' UTR variant where a premature start codon is moved. [SANGER:am]	2538	0	0
2277	52	consensus_AFLP_fragment	A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input. [GMOD:ea]	2539	0	0
2278	52	extended_cis_splice_site	Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after. [SANGER:am]	2540	0	0
2279	52	intron_base_5	Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron. [SANGER:am]	2541	0	0
2280	52	extended_intronic_splice_region_variant	A sequence variant occurring in the intron, within 10 bases of exon. [sanger:am]	2542	0	0
2281	52	extended_intronic_splice_region	Region of intronic sequence within 10 bases of an exon. [SANGER:am]	2543	0	0
2282	52	subtelomere	A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed. [POMBE:al]	2544	0	0
2283	52	sgRNA	A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method. [PMID:23934893]	2545	0	0
2284	52	mating_type_region_motif	DNA motif that is a component of a mating type region. [SO:ke]	2546	0	0
2285	52	Y_region	A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha). [SGD:jd]	2547	0	0
2286	52	Z1_region	A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR). [SGD:jd]	2548	0	0
2287	52	Z2_region	A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR). [SGD:jd]	2549	0	0
2288	52	ARS_consensus_sequence	The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS. [SGD:jd]	2550	0	0
2289	52	DSR_motif	The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome. [PMID:22645662]	2551	0	0
2290	52	zinc_repressed_element	A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc. [PMID:24003116, POMBE:mh]	2552	0	0
2291	52	rare_amino_acid_variant	A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid. [SO:ke]	2553	0	0
2292	52	selenocysteine_loss	A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid. [SO:ke]	2554	0	0
2293	52	pyrrolysine_loss	A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid. [SO:ke]	2555	0	0
2294	52	intragenic_variant	A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence. [SO:ke]	2556	0	0
2295	52	start_lost	A codon variant that changes at least one base of the canonical start codon. [SO:ke]	2557	0	0
2296	52	5_prime_UTR_truncation	A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence. [SO:ke]	2558	0	0
2297	52	5_prime_UTR_elongation	A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence. [SO:ke]	2559	0	0
2374	52	3_prime_UTR_exon_variant	A UTR variant of exonic sequence of the 3' UTR. [SO:ke]	2638	0	0
2298	52	3_prime_UTR_truncation	A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence. [SO:ke]	2560	0	0
2299	52	3_prime_UTR_elongation	A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence. [SO:ke]	2561	0	0
2300	52	conserved_intergenic_variant	A sequence variant located in a conserved intergenic region, between genes. [SO:ke]	2562	0	0
2301	52	conserved_intron_variant	A transcript variant occurring within a conserved region of an intron. [SO:ke]	2563	0	0
2302	52	start_retained_variant	A sequence variant where at least one base in the start codon is changed, but the start remains. [SO:ke]	2564	0	0
2303	52	boundary_element	Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions. [PMID:24013502]	2565	0	0
2304	52	mating_type_region_replication_fork_barrier	A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. [PMID:17614787]	2566	0	0
2305	52	priRNA	A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts. [PMID:20178743, PMID:24095277, PomBase:al]	2567	0	0
2306	52	multiplexing_sequence_identifier	A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library. [OBO:prs, PMID:22574170]	2568	0	0
2307	52	W_region	The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR. [SGD:jd]	2569	0	0
2308	52	cis_acting_homologous_chromosome_pairing_region	A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I. [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]	2571	0	0
2309	52	intein_encoding_region	The nucleotide sequence which encodes the intein portion of the precursor gene. [PMID:8165123]	2572	0	0
2310	52	uORF	A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation. [PMID:12890013, PMID:16153175, POMBASE:mah]	2573	0	0
2311	52	sORF	An open reading frame that encodes a peptide of less than 100 amino acids. [PMID:23970561, PMID:24705786, POMBASE:mah]	2575	0	0
2312	52	tnaORF	A translated ORF encoded entirely within the antisense strand of a known protein coding gene. [POMBASE:vw]	2576	0	0
2313	52	X_region	One of two segments of homology found at all three mating loci (HML, MAT and HMR). [SGD:jd]	2577	0	0
2314	52	shRNA	A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference. [PMID:6699500, SO:ke]	2578	0	0
2315	52	moR	A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA. [SO:ke]	2579	0	0
2316	52	loR	A short, non coding transcript of loop-derived sequences encoded in precursor miRNA. [SO:ke]	2580	0	0
2317	52	miR_encoding_snoRNA_primary_transcript	A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2581	0	0
2318	52	lncRNA_primary_transcript	A primary transcript encoding a lncRNA. [SO:ke]	2582	0	0
2319	52	miR_encoding_lncRNA_primary_transcript	A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2583	0	0
2320	52	miR_encoding_tRNA_primary_transcript	A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2584	0	0
2321	52	shRNA_primary_transcript	A primary transcript encoding an shRNA. [SO:ke]	2585	0	0
2322	52	miR_encoding_shRNA_primary_transcript	A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2586	0	0
2323	52	vaultRNA_primary_transcript	A primary transcript encoding a vaultRNA. [SO:ke]	2587	0	0
2324	52	miR_encoding_vaultRNA_primary_transcript	A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2588	0	0
2325	52	Y_RNA_primary_transcript	A primary transcript encoding a Y-RNA. [SO:ke]	2589	0	0
2326	52	miR_encoding_Y_RNA_primary_transcript	A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. [SO:ke]	2590	0	0
2327	52	TCS_element	A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT. [PMID:1489142, PMID:20118212, SO:ke]	2591	0	0
2328	52	pheromone_response_element	A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]. [PMID:1489142, SO:ke]	2592	0	0
2329	52	FRE	A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae. [PMID:1489142, SO:ke]	2593	0	0
2330	52	transcription_pause_site	Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli. [PMID:24789973, SO:ke]	2594	0	0
2331	52	disabled_reading_frame	A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons). [SGD:se]	2595	0	0
2332	52	H3K27_acetylation_site	A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated. [SO:rs]	2596	0	0
2333	52	constitutive_promoter	A promoter that allows for continual transcription of gene. [SO:ke]	2597	0	0
2334	52	inducible_promoter	A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors. [SO:ke]	2598	0	0
2335	52	dominant_negative_variant	A variant where the mutated gene product adversely affects the other (wild type) gene product. [SO:ke]	2599	0	0
2336	52	gain_of_function_variant	A sequence variant whereby new or enhanced function is conferred on the gene product. [SO:ke]	2600	0	0
2337	52	loss_of_function_variant	A sequence variant whereby the gene product has diminished or abolished function. [SO:ke]	2601	0	0
2338	52	null_mutation	A variant whereby the gene product is not functional or the gene product is not produced. [SO:ke]	2602	0	0
2339	52	intronic_splicing_silencer	An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control. [PMID:23241926, SO:ke]	2603	0	0
2340	52	intronic_splicing_enhancer		2604	1	0
2341	52	exonic_splicing_silencer	An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control. [PMID:23241926, SO:ke]	2605	0	0
2342	52	recombination_enhancer	A regulatory_region that promotes or induces the process of recombination. [PMID:8861911, SGD:se]	2606	0	0
2343	52	interchromosomal_translocation	A translocation where the regions involved are from different chromosomes. [NCBI:th]	2607	0	0
2344	52	intrachromosomal_translocation	A translocation where the regions involved are from the same chromosome. [NCBI:th]	2608	0	0
2345	52	complex_chromosomal_rearrangement	A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis. [NCBI:th]	2609	0	0
2346	52	Alu_insertion	An insertion of sequence from the Alu family of mobile elements. [NCBI:th]	2610	0	0
2347	52	LINE1_insertion	An insertion from the Line1 family of mobile elements. [NCBI:th]	2611	0	0
2348	52	L1_LINE_retrotransposon	Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs. [PMID:31709017]	2612	0	0
2349	52	SVA_insertion	An insertion of sequence from the SVA family of mobile elements. [NCBI:th]	2613	0	0
2350	52	mobile_element_deletion	A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element). [NCBI:th]	2614	0	0
2351	52	HERV_deletion	A deletion of the HERV mobile element with respect to a reference. [NCBI:th]	2615	0	0
2352	52	Endogenous_Retrovirus_LTR_retrotransposon	Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses. [PMID:17984973]	2616	0	0
2353	52	SVA_deletion	A deletion of an SVA mobile element. [NCBI:th]	2617	0	0
2354	52	LINE1_deletion	A deletion of a LINE1 mobile element with respect to a reference. [NCBI:th]	2618	0	0
2355	52	Alu_deletion	A deletion of an Alu mobile element with respect to a reference. [NCBI:th]	2619	0	0
2356	52	CDS_supported_by_peptide_spectrum_match	A CDS that is supported by proteomics data. [SO:ke]	2620	0	0
2357	52	CDS_supported_by_sequence_similarity_data	A CDS that is supported by sequence similarity data. [SO:xp]	2621	0	0
2358	52	no_sequence_alteration	A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence. [SO:ke]	2622	0	0
2359	52	intergenic_1kb_variant	A variant that falls in an intergenic region that is 1 kb or less between 2 genes. [SO:ke]	2623	0	0
2360	52	incomplete_transcript_variant	A sequence variant that intersects an incompletely annotated transcript. [SO:ke]	2624	0	0
2361	52	incomplete_transcript_3UTR_variant	A sequence variant that intersects the 3' UTR of an incompletely annotated transcript. [SO:ke]	2625	0	0
2362	52	incomplete_transcript_5UTR_variant	A sequence variant that intersects the 5' UTR of an incompletely annotated transcript. [SO:ke]	2626	0	0
2363	52	incomplete_transcript_intronic_variant	A sequence variant that intersects the intron of an incompletely annotated transcript. [SO:ke]	2627	0	0
2364	52	incomplete_transcript_splice_region_variant	A sequence variant that intersects the splice region of an incompletely annotated transcript. [SO:ke]	2628	0	0
2365	52	incomplete_transcript_exonic_variant	A sequence variant that intersects the exon of an incompletely annotated transcript. [SO:ke]	2629	0	0
2366	52	incomplete_transcript_CDS	A sequence variant that intersects the coding regions of an incompletely annotated transcript. [SO:ke]	2630	0	0
2367	52	incomplete_transcript_coding_splice_variant	A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript. [SO:ke]	2631	0	0
2368	52	2KB_downstream_variant	A sequence variant located within 2KB 3' of a gene. [SO:ke]	2632	0	0
2369	52	exonic_splice_region_variant	A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary. [SO:ke]	2633	0	0
2370	52	unidirectional_gene_fusion	A sequence variant whereby two genes, on the same strand have become joined. [SO:ke]	2634	0	0
2371	52	bidirectional_gene_fusion	A sequence variant whereby two genes, on alternate strands have become joined. [SO:ke]	2635	0	0
2372	52	pseudogenic_CDS	A non functional descendant of the coding portion of a coding transcript, part of a pseudogene. [SO:ke]	2636	0	0
2373	52	non_coding_transcript_splice_region_variant	A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript. [SO:ke]	2637	0	0
2375	52	3_prime_UTR_intron_variant	A UTR variant of intronic sequence of the 3' UTR. [SO:ke]	2639	0	0
2376	52	5_prime_UTR_intron_variant	A UTR variant of intronic sequence of the 5' UTR. [SO:ke]	2640	0	0
2377	52	5_prime_UTR_exon_variant	A UTR variant of exonic sequence of the 5' UTR. [SO:ke]	2641	0	0
2378	52	structural_interaction_variant	A variant that impacts the internal interactions of the resulting polypeptide structure. [SO:ke]	2642	0	0
2379	52	non_allelic_homologous_recombination_region	A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination. []	2643	0	0
2380	52	scaRNA	A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs). [PMC:126017, PMID:27775477, PMID:28869095, SO:nrs]	2644	0	0
2381	52	short_tandem_repeat_variation	A variation that expands or contracts a tandem repeat with regard to a reference. [SO:ke]	2645	0	0
2382	52	vertebrate_immune_system_pseudogene	A pseudogene derived from a vertebrate immune system gene. [SO:ke]	2646	0	0
2383	52	immunoglobulin_pseudogene	A pseudogene derived from an immunoglobulin gene. [SO:ke]	2647	0	0
2384	52	T_cell_receptor_pseudogene	A pseudogene derived from a T-cell receptor gene. [SO:ke]	2648	0	0
2385	52	IG_C_pseudogene	A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2649	0	0
2386	52	IG_J_pseudogene	A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2650	0	0
2387	52	IG_V_pseudogene	A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2651	0	0
2388	52	TR_V_pseudogene	A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2652	0	0
2389	52	TR_J_pseudogene	A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2653	0	0
2390	52	translated_processed_pseudogene	A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2654	0	0
2391	52	translated_unprocessed_pseudogene	A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2655	0	0
2392	52	transcribed_unprocessed_pseudogene	A unprocessed pseudogene supported by locus-specific evidence of transcription. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2656	0	0
2393	52	transcribed_unitary_pseudogene	A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2657	0	0
2394	52	transcribed_processed_pseudogene	A processed_pseudogene overlapped by locus-specific evidence of transcription. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2658	0	0
2395	52	polymorphic_pseudogene_with_retained_intron	A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2659	0	0
2396	52	pseudogene_processed_transcript	A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus). [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2660	0	0
2397	52	coding_transcript_with_retained_intron	A protein coding transcript containing a retained intron. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2661	0	0
2398	52	lncRNA_with_retained_intron	A lncRNA transcript containing a retained intron. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2662	0	0
2399	52	NMD_transcript	A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2663	0	0
2400	52	pseudogenic_transcript_with_retained_intron	A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2664	0	0
2431	52	H2AZK15_acetylation_site	A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated. [PMID:19385636, PMID:24316985, PMID:27087541]	2697	0	0
2432	52	AUG_initiated_uORF	A uORF beginning with the canonical start codon AUG. [PMID:26684391, PMID:27313038]	2698	0	0
2403	52	NMD_polymorphic_pseudogene_transcript	A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2667	0	0
2404	52	allelic_frequency	A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population. [SO:ke]	2668	0	0
2405	52	three_prime_overlapping_ncrna	Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2670	0	0
2406	52	vertebrate_immune_system_gene	The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci). [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2671	0	0
2407	52	immunoglobulin_gene	A germline immunoglobulin gene. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2672	0	0
2408	52	IG_C_gene	A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2673	0	0
2409	52	IG_D_gene	A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2674	0	0
2410	52	IG_J_gene	A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2675	0	0
2411	52	IG_V_gene	A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2676	0	0
2412	52	mt_rRNA	Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2677	0	0
2413	52	mt_tRNA	Mitochondrial transfer RNA. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2678	0	0
2414	52	NSD_transcript	A transcript that contains a CDS but has no stop codon before the polyA site is reached. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2679	0	0
2415	52	sense_intronic_lncRNA	A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence. [GENECODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2680	0	0
2416	52	sense_overlap_lncRNA	A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence. [GENECODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2682	0	0
2417	52	T_cell_receptor_gene	A T-cell receptor germline gene. []	2683	0	0
2418	52	TR_C_Gene	A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2684	0	0
2419	52	TR_D_Gene	A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2685	0	0
2420	52	TR_J_Gene	A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2686	0	0
2421	52	TR_V_Gene	A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php]	2687	0	0
2422	52	predicted_transcript	A transcript feature that has been predicted but is not yet validated. [SO:ke]	2688	0	0
2423	52	unconfirmed_transcript	This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies. [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html]	2689	0	0
2424	52	early_origin_of_replication	An origin of replication that initiates early in S phase. [PMID:23348837, PMID:9115207]	2690	0	0
2425	52	late_origin_of_replication	An origin of replication that initiates late in S phase. [PMID:23348837, PMID:9115207]	2691	0	0
2426	52	histone_2AZ_acetylation_site	A histone 2AZ modification where the modification is the acetylation of the residue. [PMID:19385636, PMID:24316985, PMID:27087541]	2692	0	0
2427	52	H2AZK4_acetylation_site	A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated. [PMID:19385636, PMID:24316985, PMID:27087541]	2693	0	0
2428	52	H2AZK7_acetylation_site	A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated. [PMID:19385636, PMID:24316985, PMID:27087541]	2694	0	0
2429	52	H2AZK11_acetylation_site	A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated. [PMID:19385636, PMID:24316985, PMID:27087541]	2695	0	0
2430	52	H2AZK13_acetylation_site	A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated. [PMID:19385636, PMID:24316985, PMID:27087541]	2696	0	0
2433	52	non_AUG_initiated_uORF	A uORF beginning with a codon other than AUG. [PMID:26684391, PMID:27313038]	2699	0	0
2434	52	genic_downstream_transcript_variant	A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms. [NCBI:dm, SO:ke]	2700	0	0
2435	52	genic_upstream_transcript_variant	A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms. [NCBI:dm, SO:ke]	2701	0	0
2436	52	mitotic_recombination_region	A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells. [NCBI:cf, SO:ke]	2702	0	0
2437	52	meiotic_recombination_region	A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase. [NCBI:cf, SO:ke]	2703	0	0
2438	52	CArG_box	A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'. [PMID:1748287, PMID:7623803]	2704	0	0
2439	52	Mat2P	A gene cassette array containing H+ mating type specific information. [PMID:18354497]	2705	0	0
2440	52	Mat3M	A gene cassette array containing H- mating type specific information. [PMID:18354497]	2706	0	0
2441	52	SHP_box	A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG. [PMID:17083136, PMID:27655872]	2707	0	0
2442	52	short_tandem_repeat_change	A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded. []	2708	0	0
2443	52	short_tandem_repeat_expansion	A short tandem repeat variant containing more repeat units than the reference sequence. []	2709	0	0
2444	52	short_tandem_repeat_contraction	A short tandem repeat variant containing fewer repeat units than the reference sequence. []	2710	0	0
2445	52	H2BK5_acetylation_site	A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated. [http://www.actrec.gov.in/histome/ptm_sp.php?ptm_sp=H2BK5ac, PMID:18552846]	2711	0	0
2446	52	trinucleotide_repeat_expansion	A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence. []	2712	0	0
2447	52	ref_miRNA	A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA. [PMID:26453491]	2713	0	0
2448	52	isomiR	IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA. [PMID:26453491]	2714	0	0
2449	52	RNA_thermometer	An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression. [PMID:22421878]	2715	0	0
2450	52	splice_polypyrimidine_tract_variant	A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17). []	2717	0	0
2451	52	splice_donor_region_variant	A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron). []	2718	0	0
2452	52	telomeric_D_loop	A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus. [PMID:10338204, PMID:15071557, PMID:24012755]	2719	0	0
2453	52	sequence_alteration_artifact	A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process. []	2720	0	0
2454	52	indel_artifact	An indel that is the result of base-calling or assembly error. []	2721	0	0
2455	52	deletion_artifact	A deletion that is the result of base-calling or assembly error. []	2722	0	0
2456	52	insertion_artifact	An insertion that is the result of base-calling or assembly error. []	2723	0	0
2457	52	substitution_artifact	A substitution that is the result of base-calling or assembly error. []	2724	0	0
2458	52	duplication_artifact	A duplication that is the result of base-calling or assembly error. []	2725	0	0
2459	52	SNV_artifact	An SNV that is the result of base-calling or assembly error. []	2726	0	0
2460	52	MNV_artifact	An MNV that is the result of base-calling or assembly error. []	2727	0	0
2461	52	ribozyme_gene	A gene that encodes a ribozyme. []	2728	0	0
2462	52	antisense_lncRNA_gene	A gene that encodes an antisense long, non-coding RNA. []	2729	0	0
2463	52	sense_overlap_lncRNA_gene	A gene that encodes a sense overlap long non-coding RNA. []	2730	0	0
2464	52	sense_intronic_lncRNA_gene	A gene that encodes a sense intronic long non-coding RNA. []	2731	0	0
2465	52	bidirectional_promoter_lncRNA_gene	A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand. [https://www.gencodegenes.org/pages/biotypes.html]	2732	0	0
2466	52	mutational_hotspot	A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance. []	2733	0	0
2467	52	HERV_insertion	An insertion of sequence from the HERV family of mobile elements with respect to a reference. [NCBI:th]	2734	0	0
2468	52	functional_gene_region	A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product. [Clingen:mb]	2735	0	0
2469	52	allelic_pseudogene	A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. []	2736	0	0
2470	52	enhancer_blocking_element	A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator. [NCBI:cf]	2737	0	0
2471	52	imprinting_control_region	A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs. []	2738	0	0
2472	52	flanking_repeat	A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites). []	2739	0	0
2473	52	processed_pseudogenic_rRNA	The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. []	2740	0	0
2474	52	unprocessed_pseudogenic_rRNA	The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. []	2741	0	0
2475	52	unitary_pseudogenic_rRNA	The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. []	2742	0	0
2476	52	allelic_pseudogenic_rRNA	A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. []	2743	0	0
2477	52	processed_pseudogenic_tRNA	The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. []	2744	0	0
2478	52	unprocessed_pseudogenic_tRNA	The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. []	2745	0	0
2479	52	unitary_pseudogenic_tRNA	The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. []	2746	0	0
2480	52	allelic_pseudogenic_tRNA	A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. []	2747	0	0
2481	52	terminal_repeat	A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat. []	2748	0	0
2482	52	repeat_instability_region	A repeat region that is prone to expansions and/or contractions. []	2749	0	0
2483	52	replication_start_site	A nucleotide site from which replication initiates. [NCBI:cf]	2750	0	0
2484	52	response_element	A regulatory element that acts in response to a stimulus, usually via transcription factor binding. []	2751	0	0
2485	52	sequence_source	Identifies the biological source of the specified span of the sequence [NCBI:tm]	2752	0	0
2486	52	UNAAAC_motif	A hexameric RNA motif consisting of nucleotides UNAAAC (where N can be any nucleotide) that targets the RNA for degradation. [PMID:22645662, PMID:28765164, PomBase:al]	2753	0	0
2487	52	long_terminal_repeat_transcript	An RNA that is transcribed from a long terminal repeat. [PMID:24256266, PomBase:mh]	2754	0	0
2488	52	genomic_DNA_contig	A contig composed of genomic DNA derived sequences. [BCS:etrwz]	2755	0	0
2489	52	presence_absence_variation	A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome. [BCS:bbean, PMID:19956538, PMID:25881062]	2756	0	0
2490	52	circular_plasmid	A self replicating circular nucleic acid molecule that is distinct from a chromosome in the organism. [PMID:21719542, SBOL:jb]	2757	0	0
2491	52	linear_plasmid	A self replicating linear nucleic acid molecule that is distinct from a chromosome in the organism. They are capped by terminal proteins covalently bound to the 5' ends of the DNA. [PMID:21719542, SBOL:jb]	2758	0	0
2492	52	transcription_termination_signal	Termination signal preferentially observed downstream of polyadenylation signal [PMID:28367989]	2759	0	0
2493	52	redundant_inserted_stop_gained	A sequence variant whereby at least one base of a codon is changed, resulting in a stop codon inserted next to an existing stop codon. This leads to a polypeptide of the same length. []	2760	0	0
2494	52	Zas1_recognition_motif	A DNA motif to which the S. pombe Zas1 protein binds. The consensus sequence is 5'-(Y)CCCCAY-3'. [PMID:29735745, PomBase:vw]	2761	0	0
2495	52	Pho7_binding_site	A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7. [PMID:28811350]	2762	0	0
2496	52	unspecified_indel	A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category. [ZFIN:st]	2763	0	0
2497	52	functionally_normal	A sequence variant in which the function of a gene product is retained with respect to a reference. []	2764	0	0
2498	52	function_uncertain_variant	A sequence variant in which the function of a gene product is unknown with respect to a reference. []	2765	0	0
2499	52	inert_DNA_spacer	Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes. [PMID:20843779, PMID:24933158, PMID:27034378, PMID:28422998]	2766	0	0
2500	52	2A_self_cleaving_peptide_region	A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction. [PMID:22301656, PMID:28526819]	2768	0	0
2764	52	sequence_variant_causing_gain_of_function_of_polypeptide		3045	1	0
2501	52	LOZ1_response_element	A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc. []	2769	0	0
2502	52	group_IIC_intron	A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA. [PMID:20463000]	2770	0	0
2503	52	CDS_extension	A sequence variant extending the CDS, that causes elongation of the resulting polypeptide sequence. [PMID:14732127, PMID:15864293, PMID:27984720, PMID:31216041, PMID:32020195]	2771	0	0
2504	52	CAAX_box	A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E. []	2772	0	0
2505	52	self_cleaving_ribozyme	An RNA that catalyzes its own cleavage. []	2773	0	0
2506	52	selection_marker	A genetic feature that encodes a trait used for artificial selection of a subpopulation. []	2774	0	0
2507	52	homologous_chromosome_recognition_and_pairing_locus	A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I. [PMID:22582262, PMID:31811152]	2775	0	0
2508	52	pumilio_response_element	A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA). [PMID:30601114]	2776	0	0
2509	52	SUMO_interaction_motif	A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3. [PMID:15388847\\,PMID\\:16524884]	2777	0	0
2510	52	cytosolic_SSU_rRNA_gene	A gene that codes for cytosolic SSU rRNA. []	2778	0	0
2511	52	cytosolic_LSU_rRNA_gene	A gene that codes for cytosolic LSU rRNA. []	2779	0	0
2512	52	rRNA_21S_gene	A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria. []	2780	1	0
2513	52	partially_duplicated_transcript	A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional. []	2781	0	0
2514	52	five_prime_duplicated_transcript	A partially_duplicated_transcript where the 5' end of the transcript is duplicated. []	2782	0	0
2515	52	three_prime_duplicated_transcript	A partially_duplicated_transcript where the 3' end of the transcript is duplicated. []	2783	0	0
2516	52	spurious_protein	A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature. [PMID:21771858]	2784	0	0
2517	52	stem_loop_region	A portion of a stem loop secondary structure in RNA. []	2785	0	0
2518	52	loop	The loop portion of a stem loop, which is not folded back upon itself.  []	2786	0	0
2519	52	stem	The portion of a stem loop where the RNA is folded back upon itself.  []	2787	0	0
2520	52	non_complimentary_stem	A region of a stem in a stem loop structure where the sequences are non-complimentary. []	2788	0	0
2521	52	knob	Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons. [PMID:6439888]	2789	0	0
2522	52	teb1_recognition_motif	A binding motif with the consensus sequence TTAGGG to which Teb1 binds. [PMID:23314747, PMID:27901072]	2790	0	0
2523	52	polyA_site_cluster	A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal. [PMID:17202160, PMID:24072873, PMID:25906188]	2791	0	0
2524	52	LARD	Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins. [PMID:15082561]	2792	0	0
2525	52	TRIM	TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100300 bp. TRIMs lack coding domains and thus do not encode proteins. [PMID:11717436]	2793	0	0
2526	52	Watson_strand	An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym. [PMID:21303550]	2794	0	0
2527	52	Crick_strand	An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym. [PMID:21303550]	2795	0	0
2528	52	Copia_LTR_retrotransposon	LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. [PMID:17984973]	2796	0	0
2529	52	Gypsy_LTR_retrotransposon	LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. [PMID:17984973]	2797	0	0
2530	52	Bel_Pao_LTR_retrotransposon	LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. [PMID:17984973]	2798	0	0
2624	52	C_D_box_scaRNA	A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs. [PMID:17099227, PMID:24659245]	2895	0	0
2531	52	Retrovirus_LTR_retrotransposon	LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein. [PMID:17984973]	2799	0	0
2532	52	R2_LINE_retrotransposon	R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes. [PMID:21734471]	2800	0	0
2533	52	RTE_LINE_retrotransposon	RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain. [PMID:9729877]	2801	0	0
2534	52	Jockey_LINE_retrotransposon	Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~5kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT). [PMID:31709017]	2802	0	0
2535	52	I_LINE_retrotransposon	Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes Apurinic endonuclease (APE) and reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain. []	2803	0	0
2536	52	tRNA_SINE_retrotransposon	Short interspersed elements that originated from tRNAs. [PMID:21673742]	2805	0	0
2537	52	7SL_SINE_retrotransposon	Short interspersed elements that originated from 7SL RNAs. [PMID:21673742]	2806	0	0
2538	52	5S_SINE_retrotransposon	Short interspersed elements that originated from 5S rRNAs. [PMID:21673742]	2807	0	0
2539	52	Crypton_YR_transposon	Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules. [PMID:22011512]	2808	0	0
2540	52	Tc1_Mariner_TIR_transposon	Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp. [PMID:17984973, PMID:8556864]	2809	0	0
2541	52	hAT_TIR_transposon	The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 527 bp and overall lengths of less than 4 kb. [PMID:11454746]	2810	0	0
2542	52	Mutator_TIR_transposon	Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal GC nucleotides, or with the GC nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification. [PMID:17984973]	2811	0	0
2543	52	Merlin_TIR_transposon	Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD). [PMID:17984973]	2812	0	0
2544	52	Transib_TIR_transposon	Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination. [PMID:17984973]	2813	0	0
2545	52	piggyBac_TIR_transposon	Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA. [PMID:17984973]	2814	0	0
2546	52	PIF_Harbinger_TIR_transposon	Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCCGGC/GCC' or 'GA/GGCATGCC/TC'. [PMID:26709091]	2815	0	0
2547	52	CACTA_TIR_transposon	This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/GC/TAGTG'. [PMID:26709091]	2816	0	0
2548	52	YR_retrotransposon	Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs). [PMID:24086727]	2817	0	0
2549	52	DIRS_YR_retrotransposon	Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase. [PMID:24086727]	2818	0	0
2550	52	Ngaro_YR_retrotransposon	Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs. [PMID:24086727]	2819	0	0
2551	52	Viper_YR_retrotransposon	VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes. [PMID:16297462]	2820	0	0
2552	52	Penelope_retrotransposon	Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease. [PMID:23914310]	2821	0	0
2685	52	G_to_T_transversion	A transversion from guanine to thymine. [SO:ke]	2957	0	0
2553	52	circular_ncRNA	A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5 cap or 3 polyA tail. [PMID:29086764, PMID:29182528, PMID:29230098, PMID:29576969, PMID:29626935]	2822	0	0
2554	52	circular_mRNA	An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5 cap or 3 polyA tail. [PMID:29086764, PMID:29182528, PMID:29576969]	2823	0	0
2555	52	mitochondrial_control_region	The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis. [PMID: 19407924, PMID:10968878]	2824	0	0
2556	52	mitochondrial_D_loop	Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. [http://www.insdc.org/files/feature_table.html]	2826	0	0
2557	52	transcription_factor_regulatory_site	A TF_binding_site that is involved in regulation of expression. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2827	0	0
2558	52	TFRS_module	The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter.  [Bacterial_regulation_working_group:CMA, PMID:32665585]	2828	0	0
2559	52	TFRS_collection	The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2829	0	0
2560	52	simple_operon	An operon whose transcription is coordinated on a single transcription unit. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2830	0	0
2561	52	complex_operon	An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2831	0	0
2562	52	transcription_unit	DNA regions delimited by different nonspurious TSS-TTS pairs. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2832	0	0
2563	52	simple_regulon	A regulon defined by considering one regulatory gene product. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2833	0	0
2564	52	regulon	A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products. [ISBN:0198506732, PMID:32665585]	2834	0	0
2565	52	complex_regulon	A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products. [Bacterial_regulation_working_group:CMA, PMID:32665585]	2835	0	0
2566	52	topologically_associated_domain	An instance of a self-interacting DNA region flanked by left and right TAD boundaries. [GREEKC:cl, PMID:32782014]	2836	0	0
2567	52	topologically_associated_domain_boundary	A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance. [GREEKC:cl, PMID:32782014]	2837	0	0
2568	52	chromatin_regulatory_region	A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications. [GREEKC:cl, PMID:32782014]	2838	0	0
2569	52	DNA_loop	A region of DNA between two loop anchor positions that are held in close physical proximity. [GREEKC:cl, PMID:32782014]	2839	0	0
2570	52	DNA_loop_anchor	The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites. [GREEKC:cl, PMID:32782014]	2840	0	0
2571	52	cryptic_promoter	The promoter of a cryptic gene. [GREEKC:cl]	2841	0	0
2572	52	core_prokaryotic_promoter_element	An element that always exists within the promoter region of a prokaryotic gene. [GREEKC:rl]	2842	0	0
2573	52	core_viral_promoter_element	An element that always exists within the promoter region of a viral gene. [GREEKC:rl]	2843	0	0
2574	52	altered_gene_product_level	A sequence variant that alters the level or amount of gene product produced. This high level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed. [GenCC:AR]	2844	0	0
2575	52	increased_gene_product_level	A variant that increases the level or amount of gene product produced. [GenCC:AR]	2845	0	0
2576	52	decreased_gene_product_level	A sequence variant that decreases the level or amount of gene product produced. [GenCC:AR]	2846	0	0
2577	52	absent_gene_product	A sequence variant that results in no gene product. [GenCC:AR]	2847	0	0
2578	52	altered_gene_product_structure	A sequence variant that alters the structure of a gene product. [GenCC:AR]	2848	0	0
2579	52	NMD_triggering_variant	A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants. [GenCC:AR]	2849	0	0
2580	52	NMD_escaping_variant	A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants. [GenCC:AR]	2850	0	0
2581	52	stop_gained_NMD_triggering	A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD). [GenCC:AR]	2851	0	0
2582	52	stop_gained_NMD_escaping	A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). [GenCC:AR]	2852	0	0
2583	52	frameshift_variant_NMD_triggering	A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD). [GenCC:AR]	2853	0	0
2584	52	frameshift_variant_NMD_escaping	A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD). [GenCC:AR]	2854	0	0
2585	52	splice_donor_variant_NMD_triggering	A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD). [GenCC:AR]	2855	0	0
2978	31	Journal Code		3287	0	0
2586	52	splice_donor_variant_NMD_escaping	A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD). [GenCC:AR]	2856	0	0
2587	52	splice_acceptor_variant_NMD_triggering	A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD). [GenCC:AR]	2857	0	0
2588	52	splice_acceptor_variant_NMD_escaping	A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD). [GenCC:AR]	2858	0	0
2589	52	minus_1_translational_frameshift	The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. [SO:ds]	2859	0	0
2590	52	minus_2_translational_frameshift	The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. [SO:ds]	2860	0	0
2591	52	epigenomically_modified_region	A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. [http://en.wikipedia.org/wiki/Epigenetics, SO:ds]	2861	0	0
2592	52	amber_stop_codon	A stop codon with the DNA sequence TAG. [https://en.wikipedia.org/wiki/Stop_codon]	2863	0	0
2593	52	ochre_stop_codon	A stop codon with the DNA sequence TAA. [https://en.wikipedia.org/wiki/Stop_codon]	2864	0	0
2594	52	opal_stop_codon	A stop codon with the DNA sequence TGA. [https://en.wikipedia.org/wiki/Stop_codon]	2865	0	0
2595	52	cytosolic_rRNA_2S_gene	A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera. [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]	2866	0	0
2596	52	cytosolic_2S_rRNA	Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules. [PMID: 118436, PMID: 29474379, PMID: 3136294, PMID:10788608, PMID:407103, PMID:4847940, PMID:768488]	2867	0	0
2597	52	U7_snRNA	A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing. [PMID:15526162]	2868	0	0
2598	52	scaRNA_gene	A gene that encodes for a scaRNA (small Cajal body-specific RNA). [PMID:27775477, PMID:28869095]	2869	0	0
2599	52	RNA_7SK	An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length. [PMID:19246988, PMID:21853533, PMID:27369380]	2870	0	0
2600	52	RNA_7SK_gene	A gene encoding a 7SK RNA (SO:0002340). [PMID:19246988, PMID:21853533, PMID:27369380]	2871	0	0
2601	52	mt_SSU_rRNA	Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes. [PMID: 24572720, PMID:3044395]	2872	0	0
2602	52	mt_LSU_rRNA	Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes. [PMID: 24572720, PMID:3044395]	2873	0	0
2603	52	plastid_rRNA	Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes. [PMID: 24572720, PMID:3044395]	2874	0	0
2604	52	plastid_SSU_rRNA	Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes. [PMID: 24572720, PMID:3044395]	2875	0	0
2605	52	plastid_LSU_rRNA	Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes. [PMID: 24572720, PMID:3044395]	2876	0	0
2606	52	fragile_site	A heritable locus on a chromosome that is prone to DNA breakage. []	2877	0	0
2607	52	common_fragile_site	A fragile site considered part of the normal chromosomal structure. [PMID: 16236432, PMID: 17608616]	2878	0	0
2608	52	rare_fragile_site	A fragile site found in the chromosomes of less than five percent of the human population. [PMID:16236432, PMID:17608616]	2879	0	0
2609	52	sisRNA	A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5 caps, and/or polyA tails. [PMID:27147469, PMID:29397203, PMID:30391089]	2880	0	0
2610	52	sbRNA_gene	A gene encoding a stem-bulge RNA. [PMID:25908866, PMID:30666901]	2881	0	0
2611	52	sbRNA	A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA. [PMID:25908866, PMID:30666901]	2882	0	0
2612	52	hpRNA_gene	A gene encoding a hpRNA. [PMID:18463630, PMID:18719707, PMID:25544562]	2883	0	0
2613	52	hpRNA	An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs). [PMID:18463630, PMID:18719707, PMID:25544562]	2884	0	0
2614	52	biosynthetic_gene_cluster	A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants). [PMID:26284661]	2885	0	0
2615	52	vault_RNA_gene	A gene that encodes a vault RNA. [PMID:19298825, PMID:19491402, PMID:22058117, PMID:22926522, PMID:30773316, PMID:9535882]	2886	0	0
2616	52	Y_RNA_gene	A gene that encodes a Y RNA. [PMID:1698620, PMID:6187471, PMID:6816230, PMID:7520568, PMID:7539809, PMID:8836182]	2887	0	0
2617	52	cytosolic_rRNA_gene	A gene that codes for cytosolic rRNA. []	2888	0	0
2618	52	mt_rRNA_gene	A gene that codes for mitochondrial rRNA. []	2889	0	0
2619	52	mt_LSU_rRNA_gene	A gene that codes for mitochondrial LSU rRNA. []	2890	0	0
2620	52	mt_SSU_rRNA_gene	A gene that codes for mitochondrial SSU rRNA. []	2891	0	0
2621	52	plastid_rRNA_gene	A gene that codes for plastid rRNA. []	2892	0	0
3151	18	longest		3460	0	0
2625	52	H_ACA_box_scaRNA	A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs. [PMID:17099227, PMID:24659245]	2896	0	0
2626	52	C-D_H_ACA_box_scaRNA	A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs. [PMID:17099227, PMID:24659245]	2897	0	0
2627	52	C_D_box_scaRNA_gene	A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs. [PMID:17099227, PMID:24659245]	2898	0	0
2628	52	H_ACA_box_scaRNA_gene	A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs. [PMID:17099227, PMID:24659245]	2899	0	0
2629	52	C-D_H_ACA_box_scaRNA_gene	A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs. [PMID:17099227, PMID:24659245]	2900	0	0
2630	52	C_D_box_snoRNA_gene	A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. [PMID:12457565, PMID:22065625]	2901	0	0
2631	52	H_ACA_box_snoRNA_gene	A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. [PMID:12457565, PMID:22065625]	2902	0	0
2632	52	U14_snoRNA_gene	A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. []	2903	0	0
2633	52	U3_snoRNA_gene	A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. []	2904	0	0
2634	52	methylation_guide_snoRNA_gene	A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. [PMID:12457565]	2905	0	0
2635	52	pseudouridylation_guide_snoRNA_gene	A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. [PMID:12457565]	2906	0	0
2636	52	bidirectional_promoter_lncRNA	A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction." [PMID:30175284, PMID:34956340] {comment="PMID:26578749}	2907	0	0
2637	52	methylation_guide_snoRNA	A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. [GOC:mah, PMID:12457565]	2908	0	0
2638	52	rRNA_cleavage_RNA	An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. [GOC:kgc]	2909	0	0
2639	52	exon_of_single_exon_gene	An exon that is the only exon in a gene. [RSC:cb]	2910	0	0
2640	52	cassette_array_member	A gene that is a member of a gene cassette, which is a mobile genetic element. []	2911	0	0
2641	52	gene_cassette_member	A gene that is a member of a gene cassette, which is a mobile genetic element. []	2912	0	0
2642	52	gene_subarray_member	A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together. []	2913	0	0
2643	52	primer_binding_site	Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. [http://www.insdc.org/files/feature_table.html]	2914	0	0
2644	52	gene_array	An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. [SO:ma]	2915	0	0
2645	52	gene_subarray	A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. [SO:ma]	2916	0	0
2646	52	gene_cassette	A gene that can be substituted for a related gene at a different site in the genome. [SGD:se]	2917	0	0
2647	52	selenocysteine_tRNA_primary_transcript	A primary transcript encoding seryl tRNA (SO:000269). [SO:ke]	2918	0	0
2648	52	selenocysteinyl_tRNA	A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. [SO:ke]	2919	0	0
2649	52	syntenic_region	A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species. [http://www.informatics.jax.org/silverbook/glossary.shtml]	2920	0	0
2650	52	intrinsically_unstructured_polypeptide_region	A region of polypeptide chain with high conformational flexibility. [EBIBS:GAR]	2921	0	0
2762	52	polypeptide_post_translational_processing_affected		3043	1	0
2651	52	catmat_left_handed_three	A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	2922	0	0
2652	52	catmat_left_handed_four	A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	2923	0	0
2653	52	catmat_right_handed_three	A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	2924	0	0
2654	52	catmat_right_handed_four	A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	2925	0	0
2655	52	alpha_beta_motif	A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]	2926	0	0
2656	52	lipoprotein_signal_peptide	A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes. [EBIBS:GA