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NCBI-PubMed DEFINITIONS with all dependencies
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pubmed.asn
--$Revision: 32084 $
--**********************************************************************
--
-- PUBMED data definitions
--
--**********************************************************************
NCBI-PubMed DEFINITIONS ::=
BEGIN
EXPORTS Pubmed-entry, Pubmed-url;
IMPORTS PubMedId FROM NCBI-Biblio
Medline-entry FROM NCBI-Medline;
Pubmed-entry ::= SEQUENCE { -- a PubMed entry
-- PUBMED records must include the PubMedId
pmid PubMedId,
-- Medline entry information
medent Medline-entry OPTIONAL,
-- Publisher name
publisher VisibleString OPTIONAL,
-- List of URL to publisher cite
urls SET OF Pubmed-url OPTIONAL,
-- Publisher's article identifier
pubid VisibleString OPTIONAL
}
Pubmed-url ::= SEQUENCE {
location VisibleString OPTIONAL, -- Location code
url VisibleString -- Selected URL for location
}
END
--$Revision: 32084 $
--**********************************************************************
--
-- MEDLINE data definitions
-- James Ostell, 1990
--
-- enhanced in 1996 to support PubMed records as well by simply adding
-- the PubMedId and making MedlineId optional
--
--**********************************************************************
NCBI-Medline DEFINITIONS ::=
BEGIN
EXPORTS Medline-entry, Medline-si;
IMPORTS Cit-art, PubMedId FROM NCBI-Biblio
Date FROM NCBI-General;
-- a MEDLINE or PubMed entry
Medline-entry ::= SEQUENCE {
uid INTEGER OPTIONAL , -- MEDLINE UID, sometimes not yet available if from PubMed
em Date , -- Entry Month
cit Cit-art , -- article citation
abstract VisibleString OPTIONAL ,
mesh SET OF Medline-mesh OPTIONAL ,
substance SET OF Medline-rn OPTIONAL ,
xref SET OF Medline-si OPTIONAL ,
idnum SET OF VisibleString OPTIONAL , -- ID Number (grants, contracts)
gene SET OF VisibleString OPTIONAL ,
pmid PubMedId OPTIONAL , -- MEDLINE records may include the PubMedId
pub-type SET OF VisibleString OPTIONAL, -- may show publication types (review, etc)
mlfield SET OF Medline-field OPTIONAL , -- additional Medline field types
status INTEGER {
publisher (1) , -- record as supplied by publisher
premedline (2) , -- premedline record
medline (3) } DEFAULT medline } -- regular medline record
Medline-mesh ::= SEQUENCE {
mp BOOLEAN DEFAULT FALSE , -- TRUE if main point (*)
term VisibleString , -- the MeSH term
qual SET OF Medline-qual OPTIONAL } -- qualifiers
Medline-qual ::= SEQUENCE {
mp BOOLEAN DEFAULT FALSE , -- TRUE if main point
subh VisibleString } -- the subheading
Medline-rn ::= SEQUENCE { -- medline substance records
type ENUMERATED { -- type of record
nameonly (0) ,
cas (1) , -- CAS number
ec (2) } , -- EC number
cit VisibleString OPTIONAL , -- CAS or EC number if present
name VisibleString } -- name (always present)
Medline-si ::= SEQUENCE { -- medline cross reference records
type ENUMERATED { -- type of xref
ddbj (1) , -- DNA Data Bank of Japan
carbbank (2) , -- Carbohydrate Structure Database
embl (3) , -- EMBL Data Library
hdb (4) , -- Hybridoma Data Bank
genbank (5) , -- GenBank
hgml (6) , -- Human Gene Map Library
mim (7) , -- Mendelian Inheritance in Man
msd (8) , -- Microbial Strains Database
pdb (9) , -- Protein Data Bank (Brookhaven)
pir (10) , -- Protein Identification Resource
prfseqdb (11) , -- Protein Research Foundation (Japan)
psd (12) , -- Protein Sequence Database (Japan)
swissprot (13) , -- SwissProt
gdb (14) } , -- Genome Data Base
cit VisibleString OPTIONAL } -- the citation/accession number
Medline-field ::= SEQUENCE {
type INTEGER { -- Keyed type
other (0) , -- look in line code
comment (1) , -- comment line
erratum (2) } , -- retracted, corrected, etc
str VisibleString , -- the text
ids SEQUENCE OF DocRef OPTIONAL } -- pointers relevant to this text
DocRef ::= SEQUENCE { -- reference to a document
type INTEGER {
medline (1) ,
pubmed (2) ,
ncbigi (3) } ,
uid INTEGER }
END
--$Revision: 48194 $
--****************************************************************
--
-- NCBI Bibliographic data elements
-- by James Ostell, 1990
--
-- Taken from the American National Standard for
-- Bibliographic References
-- ANSI Z39.29-1977
-- Version 3.0 - June 1994
-- PubMedId added in 1996
-- ArticleIds and eprint elements added in 1999
--
--****************************************************************
NCBI-Biblio DEFINITIONS ::=
BEGIN
EXPORTS Cit-art, Cit-jour, Cit-book, Cit-pat, Cit-let, Id-pat, Cit-gen,
Cit-proc, Cit-sub, Title, Author, PubMedId, DOI;
IMPORTS Person-id, Date, Dbtag FROM NCBI-General;
-- Article Ids
ArticleId ::= CHOICE { -- can be many ids for an article
pubmed PubMedId , -- see types below
medline MedlineUID ,
doi DOI ,
pii PII ,
pmcid PmcID ,
pmcpid PmcPid ,
pmpid PmPid ,
other Dbtag } -- generic catch all
PubMedId ::= INTEGER -- Id from the PubMed database at NCBI
MedlineUID ::= INTEGER -- Id from MEDLINE
DOI ::= VisibleString -- Document Object Identifier
PII ::= VisibleString -- Controlled Publisher Identifier
PmcID ::= INTEGER -- PubMed Central Id
PmcPid ::= VisibleString -- Publisher Id supplied to PubMed Central
PmPid ::= VisibleString -- Publisher Id supplied to PubMed
ArticleIdSet ::= SET OF ArticleId
-- Status Dates
PubStatus ::= INTEGER { -- points of publication
received (1) , -- date manuscript received for review
accepted (2) , -- accepted for publication
epublish (3) , -- published electronically by publisher
ppublish (4) , -- published in print by publisher
revised (5) , -- article revised by publisher/author
pmc (6) , -- article first appeared in PubMed Central
pmcr (7) , -- article revision in PubMed Central
pubmed (8) , -- article citation first appeared in PubMed
pubmedr (9) , -- article citation revision in PubMed
aheadofprint (10), -- epublish, but will be followed by print
premedline (11), -- date into PreMedline status
medline (12), -- date made a MEDLINE record
other (255) }
PubStatusDate ::= SEQUENCE { -- done as a structure so fields can be added
pubstatus PubStatus ,
date Date } -- time may be added later
PubStatusDateSet ::= SET OF PubStatusDate
-- Citation Types
Cit-art ::= SEQUENCE { -- article in journal or book
title Title OPTIONAL , -- title of paper (ANSI requires)
authors Auth-list OPTIONAL , -- authors (ANSI requires)
from CHOICE { -- journal or book
journal Cit-jour ,
book Cit-book ,
proc Cit-proc } ,
ids ArticleIdSet OPTIONAL } -- lots of ids
Cit-jour ::= SEQUENCE { -- Journal citation
title Title , -- title of journal
imp Imprint }
Cit-book ::= SEQUENCE { -- Book citation
title Title , -- Title of book
coll Title OPTIONAL , -- part of a collection
authors Auth-list, -- authors
imp Imprint }
Cit-proc ::= SEQUENCE { -- Meeting proceedings
book Cit-book , -- citation to meeting
meet Meeting } -- time and location of meeting
-- Patent number and date-issue were made optional in 1997 to
-- support patent applications being issued from the USPTO
-- Semantically a Cit-pat must have either a patent number or
-- an application number (or both) to be valid
Cit-pat ::= SEQUENCE { -- patent citation
title VisibleString ,
authors Auth-list, -- author/inventor
country VisibleString , -- Patent Document Country
doc-type VisibleString , -- Patent Document Type
number VisibleString OPTIONAL, -- Patent Document Number
date-issue Date OPTIONAL, -- Patent Issue/Pub Date
class SEQUENCE OF VisibleString OPTIONAL , -- Patent Doc Class Code
app-number VisibleString OPTIONAL , -- Patent Doc Appl Number
app-date Date OPTIONAL , -- Patent Appl File Date
applicants Auth-list OPTIONAL , -- Applicants
assignees Auth-list OPTIONAL , -- Assignees
priority SEQUENCE OF Patent-priority OPTIONAL , -- Priorities
abstract VisibleString OPTIONAL } -- abstract of patent
Patent-priority ::= SEQUENCE {
country VisibleString , -- Patent country code
number VisibleString , -- number assigned in that country
date Date } -- date of application
Id-pat ::= SEQUENCE { -- just to identify a patent
country VisibleString , -- Patent Document Country
id CHOICE {
number VisibleString , -- Patent Document Number
app-number VisibleString } , -- Patent Doc Appl Number
doc-type VisibleString OPTIONAL } -- Patent Doc Type
Cit-let ::= SEQUENCE { -- letter, thesis, or manuscript
cit Cit-book , -- same fields as a book
man-id VisibleString OPTIONAL , -- Manuscript identifier
type ENUMERATED {
manuscript (1) ,
letter (2) ,
thesis (3) } OPTIONAL }
-- NOTE: this is just to cite a
-- direct data submission, see NCBI-Submit
-- for the form of a sequence submission
Cit-sub ::= SEQUENCE { -- citation for a direct submission
authors Auth-list , -- not necessarily authors of the paper
imp Imprint OPTIONAL , -- this only used to get date.. will go
medium ENUMERATED { -- medium of submission
paper (1) ,
tape (2) ,
floppy (3) ,
email (4) ,
other (255) } OPTIONAL ,
date Date OPTIONAL , -- replaces imp, will become required
descr VisibleString OPTIONAL } -- description of changes for public view
Cit-gen ::= SEQUENCE { -- NOT from ANSI, this is a catchall
cit VisibleString OPTIONAL , -- anything, not parsable
authors Auth-list OPTIONAL ,
muid INTEGER OPTIONAL , -- medline uid
journal Title OPTIONAL ,
volume VisibleString OPTIONAL ,
issue VisibleString OPTIONAL ,
pages VisibleString OPTIONAL ,
date Date OPTIONAL ,
serial-number INTEGER OPTIONAL , -- for GenBank style references
title VisibleString OPTIONAL , -- eg. cit="unpublished",title="title"
pmid PubMedId OPTIONAL } -- PubMed Id
-- Authorship Group
Auth-list ::= SEQUENCE {
names CHOICE {
std SEQUENCE OF Author , -- full citations
ml SEQUENCE OF VisibleString , -- MEDLINE, semi-structured
str SEQUENCE OF VisibleString } , -- free for all
affil Affil OPTIONAL } -- author affiliation
Author ::= SEQUENCE {
name Person-id , -- Author, Primary or Secondary
level ENUMERATED {
primary (1),
secondary (2) } OPTIONAL ,
role ENUMERATED { -- Author Role Indicator
compiler (1),
editor (2),
patent-assignee (3),
translator (4) } OPTIONAL ,
affil Affil OPTIONAL ,
is-corr BOOLEAN OPTIONAL } -- TRUE if corresponding author
Affil ::= CHOICE {
str VisibleString , -- unparsed string
std SEQUENCE { -- std representation
affil VisibleString OPTIONAL , -- Author Affiliation, Name
div VisibleString OPTIONAL , -- Author Affiliation, Division
city VisibleString OPTIONAL , -- Author Affiliation, City
sub VisibleString OPTIONAL , -- Author Affiliation, County Sub
country VisibleString OPTIONAL , -- Author Affiliation, Country
street VisibleString OPTIONAL , -- street address, not ANSI
email VisibleString OPTIONAL ,
fax VisibleString OPTIONAL ,
phone VisibleString OPTIONAL ,
postal-code VisibleString OPTIONAL }}
-- Title Group
-- Valid for = A = Analytic (Cit-art)
-- J = Journals (Cit-jour)
-- B = Book (Cit-book)
-- Valid for:
Title ::= SET OF CHOICE {
name VisibleString , -- Title, Anal,Coll,Mono AJB
tsub VisibleString , -- Title, Subordinate A B
trans VisibleString , -- Title, Translated AJB
jta VisibleString , -- Title, Abbreviated J
iso-jta VisibleString , -- specifically ISO jta J
ml-jta VisibleString , -- specifically MEDLINE jta J
coden VisibleString , -- a coden J
issn VisibleString , -- ISSN J
abr VisibleString , -- Title, Abbreviated B
isbn VisibleString } -- ISBN B
Imprint ::= SEQUENCE { -- Imprint group
date Date , -- date of publication
volume VisibleString OPTIONAL ,
issue VisibleString OPTIONAL ,
pages VisibleString OPTIONAL ,
section VisibleString OPTIONAL ,
pub Affil OPTIONAL, -- publisher, required for book
cprt Date OPTIONAL, -- copyright date, " " "
part-sup VisibleString OPTIONAL , -- part/sup of volume
language VisibleString DEFAULT "ENG" , -- put here for simplicity
prepub ENUMERATED { -- for prepublication citations
submitted (1) , -- submitted, not accepted
in-press (2) , -- accepted, not published
other (255) } OPTIONAL ,
part-supi VisibleString OPTIONAL , -- part/sup on issue
retract CitRetract OPTIONAL , -- retraction info
pubstatus PubStatus OPTIONAL , -- current status of this publication
history PubStatusDateSet OPTIONAL } -- dates for this record
CitRetract ::= SEQUENCE {
type ENUMERATED { -- retraction of an entry
retracted (1) , -- this citation retracted
notice (2) , -- this citation is a retraction notice
in-error (3) , -- an erratum was published about this
erratum (4) } , -- this is a published erratum
exp VisibleString OPTIONAL } -- citation and/or explanation
Meeting ::= SEQUENCE {
number VisibleString ,
date Date ,
place Affil OPTIONAL }
END
--$Revision: 57316 $
--**********************************************************************
--
-- NCBI General Data elements
-- by James Ostell, 1990
-- Version 3.0 - June 1994
--
--**********************************************************************
NCBI-General DEFINITIONS ::=
BEGIN
EXPORTS Date, Person-id, Object-id, Dbtag, Int-fuzz, User-object, User-field;
-- StringStore is really a VisibleString. It is used to define very
-- long strings which may need to be stored by the receiving program
-- in special structures, such as a ByteStore, but it's just a hint.
-- AsnTool stores StringStores in ByteStore structures.
-- OCTET STRINGs are also stored in ByteStores by AsnTool
--
-- typedef struct bsunit { /* for building multiline strings */
-- Nlm_Handle str; /* the string piece */
-- Nlm_Int2 len_avail,
-- len;
-- struct bsunit PNTR next; } /* the next one */
-- Nlm_BSUnit, PNTR Nlm_BSUnitPtr;
--
-- typedef struct bytestore {
-- Nlm_Int4 seekptr, /* current position */
-- totlen, /* total stored data length in bytes */
-- chain_offset; /* offset in ByteStore of first byte in curchain */
-- Nlm_BSUnitPtr chain, /* chain of elements */
-- curchain; /* the BSUnit containing seekptr */
-- } Nlm_ByteStore, PNTR Nlm_ByteStorePtr;
--
-- AsnTool incorporates this as a primitive type, so the definition
-- is here just for completeness
--
-- StringStore ::= [APPLICATION 1] IMPLICIT OCTET STRING
--
-- BigInt is really an INTEGER. It is used to warn the receiving code to expect
-- a value bigger than Int4 (actually Int8). It will be stored in DataVal.bigintvalue
--
-- Like StringStore, AsnTool incorporates it as a primitive. The definition would be:
-- BigInt ::= [APPLICATION 2] IMPLICIT INTEGER
--
-- Date is used to replace the (overly complex) UTCTtime, GeneralizedTime
-- of ASN.1
-- It stores only a date
--
Date ::= CHOICE {
str VisibleString , -- for those unparsed dates
std Date-std } -- use this if you can
Date-std ::= SEQUENCE { -- NOTE: this is NOT a unix tm struct
year INTEGER , -- full year (including 1900)
month INTEGER OPTIONAL , -- month (1-12)
day INTEGER OPTIONAL , -- day of month (1-31)
season VisibleString OPTIONAL , -- for "spring", "may-june", etc
hour INTEGER OPTIONAL , -- hour of day (0-23)
minute INTEGER OPTIONAL , -- minute of hour (0-59)
second INTEGER OPTIONAL } -- second of minute (0-59)
-- Dbtag is generalized for tagging
-- eg. { "Social Security", str "023-79-8841" }
-- or { "member", id 8882224 }
Dbtag ::= SEQUENCE {
db VisibleString , -- name of database or system
tag Object-id } -- appropriate tag
-- Object-id can tag or name anything
--
Object-id ::= CHOICE {
id INTEGER ,
str VisibleString }
-- Person-id is to define a std element for people
--
Person-id ::= CHOICE {
dbtag Dbtag , -- any defined database tag
name Name-std , -- structured name
ml VisibleString , -- MEDLINE name (semi-structured)
-- eg. "Jones RM"
str VisibleString, -- unstructured name
consortium VisibleString } -- consortium name
Name-std ::= SEQUENCE { -- Structured names
last VisibleString ,
first VisibleString OPTIONAL ,
middle VisibleString OPTIONAL ,
full VisibleString OPTIONAL , -- full name eg. "J. John Smith, Esq"
initials VisibleString OPTIONAL, -- first + middle initials
suffix VisibleString OPTIONAL , -- Jr, Sr, III
title VisibleString OPTIONAL } -- Dr., Sister, etc
--**** Int-fuzz **********************************************
--*
--* uncertainties in integer values
Int-fuzz ::= CHOICE {
p-m INTEGER , -- plus or minus fixed amount
range SEQUENCE { -- max to min
max INTEGER ,
min INTEGER } ,
pct INTEGER , -- % plus or minus (x10) 0-1000
lim ENUMERATED { -- some limit value
unk (0) , -- unknown
gt (1) , -- greater than
lt (2) , -- less than
tr (3) , -- space to right of position
tl (4) , -- space to left of position
circle (5) , -- artificial break at origin of circle
other (255) } , -- something else
alt SET OF INTEGER } -- set of alternatives for the integer
--**** User-object **********************************************
--*
--* a general object for a user defined structured data item
--* used by Seq-feat and Seq-descr
User-object ::= SEQUENCE {
class VisibleString OPTIONAL , -- endeavor which designed this object
type Object-id , -- type of object within class
data SEQUENCE OF User-field } -- the object itself
User-field ::= SEQUENCE {
label Object-id , -- field label
num INTEGER OPTIONAL , -- required for strs, ints, reals, oss
data CHOICE { -- field contents
str UTF8String ,
int INTEGER ,
real REAL ,
bool BOOLEAN ,
os OCTET STRING ,
object User-object , -- for using other definitions
strs SEQUENCE OF UTF8String ,
ints SEQUENCE OF INTEGER ,
reals SEQUENCE OF REAL ,
oss SEQUENCE OF OCTET STRING ,
fields SEQUENCE OF User-field ,
objects SEQUENCE OF User-object } }
END
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