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October 1, 2012 08:58
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Convert RefSeq genome entry into RDF/Turtle using FALDO (BH12) and URN
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| #!/usr/bin/env ruby-1.9 | |
| require 'rubygems' | |
| require 'uri' | |
| require 'bio' | |
| require 'json' | |
| require 'securerandom' | |
| # [TODO] integrate this into BioRuby | |
| module Bio | |
| class GenBank | |
| def dblink | |
| fetch('DBLINK') | |
| end | |
| def bioproject | |
| dblink[/\d+/] | |
| end | |
| end | |
| end | |
| ### | |
| ### Utilities for RDF generation | |
| ### | |
| module RDFSupport | |
| def new_uuid(prefix = "http://purl.jp/bio/10/genome/uuid/") | |
| #return "<#{prefix}#{SecureRandom.uuid}>" | |
| #return "genome:uuid-#{SecureRandom.uuid}" | |
| return "<urn:uuid:#{SecureRandom.uuid}>" | |
| end | |
| def quote(str) | |
| return str.gsub('\\', '\\\\').gsub("\t", '\\t').gsub("\n", '\\n').gsub("\r", '\\r').gsub('"', '\\"').inspect | |
| end | |
| def triple(s, p, o) | |
| return [s, p, o].join("\t") + " ." | |
| end | |
| def default_prefix | |
| return [ | |
| triple("@prefix", "rdf:", "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>"), | |
| triple("@prefix", "rdfs:", "<http://www.w3.org/2000/01/rdf-schema#>"), | |
| #triple("@prefix", "dcterms:", "<http://purl.org/dc/terms/>"), | |
| triple("@prefix", "xsd:", "<http://www.w3.org/2001/XMLSchema#>"), | |
| #triple("@prefix", "sio:", "<http://semanticscience.org/resource#>"), | |
| #triple("@prefix", "so:", "<http://purl.org/obo/owl/SO#>"), | |
| triple("@prefix", "obo:", "<http://purl.obolibrary.org/obo/>"), | |
| triple("@prefix", "faldo:", "<http://biohackathon.org/resource/faldo#>"), | |
| ] | |
| end | |
| def usdate2date(str) | |
| return Date.parse(str).strftime("%Y-%m-%d") | |
| end | |
| end | |
| ### | |
| ### Mapping RefSeq db_xref to Identifiers.org | |
| ### | |
| # https://gist.github.com/3985701 | |
| # https://gist.github.com/4146256 | |
| class RS_ID | |
| include RDFSupport | |
| def initialize | |
| @rs_id = JSON.parse(File.read("rs_id.json")) | |
| end | |
| def fetch(db) | |
| @rs_id[db] | |
| end | |
| def labels | |
| @rs_id.sort.each do |db, hash| | |
| puts triple("insdc:#{hash['class']}", "rdfs:label", quote(hash['label'])) | |
| end | |
| end | |
| end | |
| ### | |
| ### Mapping RefSeq feature table to Sequence Ontology | |
| ### | |
| # https://gist.github.com/3650401 | |
| class FT_SO | |
| def initialize | |
| @data = JSON.parse(File.read("ft_so.json")) | |
| end | |
| # ftso = FT_SO.new | |
| # puts ftso.so_id("-10_signal") # => "SO:0000175" | |
| def so_id(feature) | |
| if hash = @data[feature] | |
| return hash["so_id"] | |
| end | |
| end | |
| def so_term(feature) | |
| if hash = @data[feature] | |
| return hash["so_term"] | |
| end | |
| end | |
| def so_desc(feature) | |
| if hash = @data[feature] | |
| return hash["so_desc"] | |
| end | |
| end | |
| def ft_desc(feature) | |
| if hash = @data[feature] | |
| return hash["ft_desc"] | |
| end | |
| end | |
| end | |
| ### | |
| ### Convert RefSeq (prokaryote) entries to RDF | |
| ### | |
| class RefSeq2RDF | |
| include RDFSupport | |
| def initialize(io = ARGF, seqtype = nil) | |
| set_prefixes | |
| @seqtype = seqtype | |
| @rs_id = RS_ID.new | |
| @ft_so = FT_SO.new | |
| @locus = {} | |
| @xref_warn = {} | |
| puts prefix | |
| puts | |
| parse_refseq(io) | |
| end | |
| attr_accessor :prefix | |
| def set_prefixes | |
| @prefix = default_prefix + [ | |
| #triple("@prefix", "genome:", "<http://purl.jp/bio/10/genome/>"), | |
| #triple("@prefix", "idorg:", "<http://ns.identifiers.org/>"), | |
| triple("@prefix", "insdc:", "<http://rdf.insdc.org/>"), | |
| ] | |
| end | |
| def xref(subject, db, id) | |
| case db | |
| when "HOMD" | |
| id.sub!(/^tax_/, '') | |
| when "ECOCYC" | |
| #id = "ECOCYC:#{id}" | |
| when "GI", "ERIC", "HMP", "PSEUDO", "Pathema" | |
| unless @xref_warn[db] | |
| $stderr.puts "Warning: Need to register '#{db}' in Identifiers.org" | |
| @xref_warn[db] = true | |
| end | |
| end | |
| if hash = @rs_id.fetch(db) | |
| uri = "<#{hash['prefix']}#{id}>" | |
| puts triple(subject, "rdfs:seeAlso", uri) | |
| puts triple(uri, "rdfs:label", quote("#{db}:#{id}")) | |
| puts triple(uri, "rdf:type", "insdc:#{hash['class']}") | |
| else | |
| unless @xref_warn[db] | |
| $stderr.puts "Error: New database '#{db}' found. Add it to the rs_id.json file and/or Identifiers.org." | |
| @xref_warn[db] = true | |
| end | |
| end | |
| end | |
| ### | |
| ### FALDO http://biohackathon.org/faldo | |
| ### | |
| def new_location(pos, elem_type = false) | |
| loc_id = new_uuid | |
| puts triple(loc_id, "insdc:location_string", quote(pos)) | |
| @locations = Bio::Locations.new(pos) | |
| pos_start = new_uuid | |
| pos_end = new_uuid | |
| puts triple(loc_id, "rdf:type", "faldo:Region") | |
| puts triple(loc_id, "faldo:begin", pos_start) | |
| puts triple(loc_id, "faldo:end", pos_end) | |
| new_position(pos_start, @locations.range.min, @locations.first.strand) | |
| new_position(pos_end, @locations.range.max, @locations.last.strand) | |
| list = [] | |
| if elem_type | |
| @locations.each do |loc| | |
| elem_id = new_uuid | |
| elem_start = new_uuid | |
| elem_end = new_uuid | |
| puts triple(elem_id, "obo:so_part_of", loc_id) | |
| puts triple(elem_id, "rdf:type", elem_type[:id]) + " # #{elem_type[:term]}" | |
| puts triple(elem_id, "rdf:type", "faldo:Region") | |
| puts triple(elem_id, "faldo:begin", elem_start) | |
| puts triple(elem_id, "faldo:end", elem_end) | |
| new_position(elem_start, loc.from, loc.strand) | |
| new_position(elem_end, loc.to, loc.strand) | |
| list << elem_id | |
| end | |
| end | |
| return loc_id, list | |
| end | |
| def new_position(pos_id, pos, strand) | |
| puts triple(pos_id, "faldo:position", pos) | |
| puts triple(pos_id, "faldo:reference", @sequence_id) | |
| puts triple(pos_id, "rdf:type", "faldo:ExactPosition") | |
| if strand > 0 | |
| puts triple(pos_id, "rdf:type", "faldo:ForwardStrandPosition") | |
| else | |
| puts triple(pos_id, "rdf:type", "faldo:ReverseStrandPosition") | |
| end | |
| end | |
| ### | |
| ### Main | |
| ### | |
| def parse_refseq(io) | |
| # Read RefSeq entry | |
| Bio::FlatFile.auto(io).each do |entry| | |
| @entry = entry | |
| @features = entry.features | |
| @source = @features.shift | |
| parse_sequence | |
| parse_source | |
| parse_genes | |
| parse_cds | |
| parse_features | |
| end | |
| end | |
| ### | |
| ### Sequence | |
| ### | |
| # [TODO] | |
| # * bind sequences by BioProject ID | |
| # * complete/draft? | |
| def parse_sequence | |
| @sequence_id = new_uuid | |
| # [TODO] How to identify the input is chromosome/plasmid/contig/...? | |
| sequence_type(@seqtype) | |
| # [TODO] Obtain rdfs:label from source /chromosome (eukaryotes) /plasmid (prokaryotes) -> see insdc:source_chromosome, insdc:source_plasmid | |
| sequence_label(@entry.definition) | |
| sequence_version(@entry.acc_version) | |
| sequence_length(@entry.nalen) | |
| # [TODO] provide REST API to retreive genomic DNA sequence by <@sequence_id.fasta> | |
| sequence_seq(@entry.acc_version) | |
| sequence_form(@entry.circular) | |
| # [TODO] sequenced date, modified in the source db or in our RDF data? | |
| sequence_date(@entry.date) | |
| # [TODO] rdfs:seeAlso (like UniProt) or dc:relation, owl:sameAs | |
| sequence_link_gi(@entry.gi.sub('GI:','')) | |
| sequence_link_accver(@entry.acc_version) | |
| sequence_link_bioproject(@entry.bioproject) | |
| # [TODO] how to deal with direct submissions (references without PMID)? | |
| sequence_ref(@entry.references) | |
| end | |
| def sequence_type(so = "SO:chromosome") | |
| case so | |
| when /0000340/, "SO:chromosome" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000340") + " # SO:chromosome" | |
| when /0000155/, "SO:plasmid" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000155") + " # SO:plasmid" | |
| when /0000736/, "SO:organelle_sequence" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000736") + " # SO:organelle_sequence" | |
| when /0000819/, "SO:mitochondrial_chromosome" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000819") + " # SO:mitochondrial_chromosome" | |
| when /0000740/, "SO:plastid_sequence" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000740") + " # SO:plastid_sequence" | |
| when /0000719/, "SO:ultracontig" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000719") + " # SO:ultracontig" | |
| when /0000148/, "SO:supercontig", "SO:scaffold" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000148") + " # SO:supercontig/scaffold" | |
| when /0000149/, "SO:contig" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000149") + " # SO:contig" | |
| else | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000353") + " # SO:sequence_assembly" | |
| end | |
| end | |
| def sequence_label(str) | |
| # Use "name:" key in the JSON representation | |
| puts triple(@sequence_id, "rdfs:label", quote(str)) | |
| end | |
| def sequence_version(str) | |
| puts triple(@sequence_id, "insdc:sequence_version", quote(str)) | |
| end | |
| def sequence_length(int) | |
| puts triple(@sequence_id, "insdc:sequence_length", int) | |
| end | |
| def sequence_seq(str) | |
| # [TODO] Where to privide the actual DNA sequence? | |
| fasta_uri = "<http://togows.dbcls.jp/entry/nucleotide/#{str}.fasta>" | |
| #fasta_uri = "<http://www.ncbi.nlm.nih.gov/nuccore/#{str}?report=fasta>" | |
| puts triple(@sequence_id, "insdc:sequence_fasta", fasta_uri) | |
| end | |
| def sequence_form(form) | |
| case form | |
| when "linear" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000987") + " # SO:linear" | |
| when "circular" | |
| puts triple(@sequence_id, "rdf:type", "obo:SO_0000988") + " # SO:circular" | |
| end | |
| end | |
| def sequence_date(date) | |
| puts triple(@sequence_id, "insdc:sequence_date", quote(usdate2date(date))+"^^xsd:date") | |
| end | |
| def sequence_link_gi(str) | |
| xref(@sequence_id, 'GI', str) | |
| end | |
| def sequence_link_accver(str) | |
| xref(@sequence_id, 'RefSeq', str) | |
| end | |
| def sequence_link_bioproject(str) | |
| xref(@sequence_id, 'BioProject', str) | |
| end | |
| def sequence_ref(refs) | |
| refs.each do |ref| | |
| pmid = ref.pubmed | |
| if pmid.length > 0 | |
| xref(@sequence_id, 'PubMed', pmid) | |
| end | |
| end | |
| end | |
| ### | |
| ### Source | |
| ### | |
| def parse_source | |
| # Use @sequence_id for @source_id | |
| @source_id = @sequence_id | |
| hash = @source.to_hash | |
| source_location(@source.position) | |
| source_link(hash["db_xref"]) | |
| hash.delete("db_xref") | |
| source_qualifiers(hash) | |
| end | |
| def source_location(pos) | |
| loc_id, = new_location(pos) | |
| puts triple(@source_id, "faldo:location", loc_id) | |
| end | |
| def source_link(links) | |
| links.each do |link| | |
| db, entry_id = link.split(':', 2) | |
| xref(@source_id, db, entry_id) | |
| end | |
| end | |
| def source_qualifiers(hash) | |
| hash.each do |qual, vals| | |
| vals.each do |val| | |
| if val == true | |
| puts triple(@source_id, "insdc:source_#{qual}", true) | |
| else | |
| data = val.to_s.gsub(/\s+/, ' ').strip | |
| if data[/^\d+$/] | |
| puts triple(@source_id, "insdc:source_#{qual}", data) | |
| else | |
| puts triple(@source_id, "insdc:source_#{qual}", quote(data)) | |
| end | |
| end | |
| end | |
| end | |
| end | |
| ### | |
| ### genes | |
| ### | |
| def parse_genes | |
| genes = @features.select {|x| x.feature == "gene"} | |
| count = 1 | |
| genes.each do |gene| | |
| gene_id = new_uuid | |
| hash = gene.to_hash | |
| puts triple(gene_id, "rdf:type", "obo:SO_0000704") + " # SO:gene" | |
| puts triple(gene_id, "obo:so_part_of", @sequence_id) | |
| loc_id, _ = new_location(gene.position) | |
| puts triple(gene_id, "faldo:location", loc_id) | |
| if hash["locus_tag"] | |
| locus_tag = hash["locus_tag"].first | |
| @locus[locus_tag] = gene_id | |
| puts triple(gene_id, "rdfs:label", quote(locus_tag)) | |
| elsif hash["gene"] | |
| puts triple(gene_id, "rdfs:label", quote(hash["gene"].first)) | |
| else | |
| # [TODO] Where else to find gene name? | |
| puts triple(gene_id, "rdfs:label", quote("gene#{count}")) | |
| end | |
| count += 1 | |
| parse_qualifiers(gene_id, hash) | |
| end | |
| end | |
| ### | |
| ### CDS | |
| ### | |
| def parse_cds | |
| cdss = @features.select {|x| x.feature == "CDS"} | |
| count = 1 | |
| cdss.each do |cds| | |
| cds_id = new_uuid | |
| hash = cds.to_hash | |
| puts triple(cds_id, "rdf:type", "obo:SO_0000316") + " # SO:CDS" | |
| if hash["locus_tag"] | |
| if locus_tag = hash["locus_tag"].first | |
| gene_id = @locus[locus_tag] | |
| end | |
| end | |
| if gene_id | |
| puts triple(cds_id, "obo:so_part_of", gene_id) | |
| else | |
| # [TODO] sure to do this? | |
| puts triple(cds_id, "obo:so_part_of", @sequence_id) | |
| end | |
| if locus_tag | |
| puts triple(cds_id, "rdfs:label", quote(locus_tag)) | |
| elsif hash["gene"] | |
| puts triple(cds_id, "rdfs:label", quote(hash["gene"].first)) | |
| else | |
| puts triple(cds_id, "rdfs:label", quote("CDS#{count}")) | |
| end | |
| count += 1 | |
| elem_type = { :id => "obo:SO_0000147", :term => "SO:exon" } | |
| loc_id, exons = new_location(cds.position, elem_type) | |
| puts triple(cds_id, "faldo:location", loc_id) | |
| puts triple(cds_id, "obo:so_has_part", "(#{exons.join(' ')})") # rdf:List | |
| parse_qualifiers(cds_id, hash) | |
| end | |
| end | |
| ### | |
| ### Features | |
| ### | |
| def parse_features | |
| features = @features.select {|x| ! x.feature[/^(gene|CDS)$/]} | |
| features.each do |feat| | |
| feature = feat.feature | |
| feature_id = new_uuid | |
| hash = feat.to_hash | |
| puts triple(feature_id, "obo:so_part_of", @sequence_id) | |
| puts triple(feature_id, "rdfs:label", quote(feature)) | |
| if so_id = @ft_so.so_id(feature) | |
| if so_id != "undefined" | |
| so = so_id.sub(':', '_') | |
| puts triple(feature_id, "rdf:type", "obo:#{so}") + " # SO:#{@ft_so.so_term(feature)}" | |
| else | |
| puts triple(feature_id, "rdf:type", "obo:SO_0000110") + " # SO:sequence_feature" | |
| end | |
| end | |
| loc_id, _ = new_location(feat.position) | |
| puts triple(feature_id, "faldo:location", loc_id) | |
| parse_qualifiers(feature_id, hash) | |
| end | |
| end | |
| def parse_qualifiers(feature_id, hash) | |
| hash.each do |qual, vals| | |
| vals.each do |val| | |
| if val == true | |
| puts triple(feature_id, "insdc:feature_#{qual}", true) | |
| else | |
| data = val.to_s.gsub(/\s+/, ' ').strip | |
| case qual | |
| when "protein_id" | |
| xref(feature_id, 'Protein', val) | |
| when "db_xref" | |
| db, id = val.split(':', 2) | |
| # ad hoc | |
| if db == 'InterPro' and @entry.acc_version[/(NC_010994.1|NC_014958.1|NC_015385.1|NC_015386.1|NC_015387.1|NC_015388.1|NC_015389.1)/] | |
| # PRJNA59115/NC_010994.1 | |
| # PRJNA62225/NC_014958.1 | |
| # PRJNA65781/NC_015385.1 | |
| # PRJNA65781/plasmids/NC_015386.1 | |
| # PRJNA65783/NC_015387.1 | |
| # PRJNA65785/NC_015388.1 | |
| # PRJNA65787/NC_015389.1 | |
| # /db_xref="InterPro:Chromosomal replication control, | |
| # initiator (DnaA)/regulator (Hda" | |
| xref(feature_id, db, id) if id[/IPR\d+/] | |
| elsif db == "ASAP" and @entry.acc_version[/(NC_017263.1|NC_017264.1|NC_017265.1|NC_017266.1)/] | |
| # PRJNA158537/plasmids/NC_017263.1 | |
| # PRJNA158537/plasmids/NC_017264.1 | |
| # PRJNA158537/NC_017265.1 | |
| # PRJNA158537/plasmids/NC_017266.1 | |
| # /db_xref="ASAP:BBE-0004740" | |
| # /db_xref="ASAP:BBE-0004740 ERIC" | |
| xref(feature_id, db, id) unless id[/\s/] | |
| elsif db == 'TIGRFAM' and @entry.acc_version[/NC_013418.2/] | |
| # PRJNA41287/NC_013418.2 | |
| # /db_xref="TIGRFAM:TIGR00197; TF" | |
| xref(feature_id, db, id.sub(/;.*/, '')) | |
| else | |
| xref(feature_id, db, id) | |
| end | |
| else | |
| if data[/^\d+$/] | |
| puts triple(feature_id, "insdc:feature_#{qual}", data) | |
| else | |
| puts triple(feature_id, "insdc:feature_#{qual}", quote(data)) | |
| end | |
| end | |
| end | |
| end | |
| end | |
| end | |
| end | |
| if __FILE__ == $0 | |
| require 'getoptlong' | |
| args = GetoptLong.new( | |
| [ '--seqtype', '-t', GetoptLong::REQUIRED_ARGUMENT ], | |
| ) | |
| opts = { | |
| :seqtype => "SO:chromosome", | |
| } | |
| args.each_option do |name, value| | |
| case name | |
| when /--seqtype/ | |
| opts[:seqtype] = value | |
| end | |
| end | |
| RefSeq2RDF.new(ARGF, opts[:seqtype]) | |
| end |
Author
ktym
commented
Oct 1, 2012
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
# SO:chromosome, SO:linear
<urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6>
<http://genome.db/sw/feature_chromosome> 7 ;
<http://genome.db/sw/feature_isolate> "3D7" ;
<http://genome.db/sw/length> 1501717 ;
<http://genome.db/sw/location> "1..1501717" ;
<http://genome.db/sw/molecularType> "genomic DNA" ;
<http://genome.db/sw/organism> "Plasmodium falciparum 3D7" ;
<http://genome.db/sw/sequence> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6.fasta> ;
<http://genome.db/sw/start> 1 ;
<http://genome.db/sw/stop> 1501717 ;
<http://genome.db/sw/version> "NC_004328.2" ;
<http://genome.db/sw/xref> <urn:xref:bioproject:148>, <urn:xref:gi:296004920>, <urn:xref:refseq:NC_004328.2>, <urn:xref:taxon:36329> ;
<http://purl.org/dc/terms/modified> "2010-07-29"^^<http://www.w3.org/2001/XMLSchema#date> ;
a <http://purl.obolibrary.org/obo/SO_0000340>, <http://purl.obolibrary.org/obo/SO_0000987> ;
<http://www.w3.org/2000/01/rdf-schema#comment> "Plasmodium falciparum 3D7 chromosome 7." ;
<http://www.w3.org/2000/01/rdf-schema#label> "Chromosome 7" .
# SO:gene
<urn:uuid:5c3a336b-8d9c-4c88-a514-b390859d53e9>
<http://genome.db/sw/feature_gene> "PfCRT" ;
<http://genome.db/sw/feature_gene_synonym> "CRT; digestive vacuole transmembrane protein" ;
<http://genome.db/sw/feature_locus_tag> "MAL7P1.27" ;
<http://genome.db/sw/location> <urn:uuid:88af6bf4-1696-4c16-bd88-54ed8f32a77b> ;
<http://genome.db/sw/xref> <urn:xref:geneid:2655199> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://purl.obolibrary.org/obo/SO_0000704> ;
<http://www.w3.org/2000/01/rdf-schema#label> "MAL7P1.27" .
# SO:STS
<urn:uuid:e3841e58-1a11-4bd2-b67a-5736604fa065>
<http://genome.db/sw/feature_gene> "PfCRT" ;
<http://genome.db/sw/feature_gene_synonym> "CRT; digestive vacuole transmembrane protein" ;
<http://genome.db/sw/feature_locus_tag> "MAL7P1.27" ;
<http://genome.db/sw/feature_standard_name> "B5M47" ;
<http://genome.db/sw/location> <urn:uuid:a2de1405-719c-4c17-98a9-262b323bff1a> ;
<http://genome.db/sw/xref> <urn:xref:UniSTS:105285> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://purl.obolibrary.org/obo/SO_0000331> ;
<http://www.w3.org/2000/01/rdf-schema#label> "STS" .
# location of STS
<urn:uuid:a2de1405-719c-4c17-98a9-262b323bff1a>
<http://biohackathon.org/faldo/end> <urn:uuid:d1fb8f71-f7cc-47cf-a3a4-e2fca59f9968> ;
<http://biohackathon.org/faldo/start> <urn:uuid:fa2ce3b5-8114-4888-8169-61063312efcd> ;
<http://genome.db/sw/position> "458646..458807" .
<urn:uuid:fa2ce3b5-8114-4888-8169-61063312efcd>
<http://biohackathon.org/faldo/position> 458646 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
<urn:uuid:d1fb8f71-f7cc-47cf-a3a4-e2fca59f9968>
<http://biohackathon.org/faldo/position> 458807 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
# SO:mRNA
<urn:uuid:e4c305db-611c-478f-b3e7-9f0397a603f9>
<http://genome.db/sw/feature_gene> "PfCRT" ;
<http://genome.db/sw/feature_gene_synonym> "CRT; digestive vacuole transmembrane protein" ;
<http://genome.db/sw/feature_locus_tag> "MAL7P1.27" ;
<http://genome.db/sw/feature_transcript_id> "XM_001348968.1" ;
<http://genome.db/sw/location> <urn:uuid:6b155c2f-69a7-4405-8648-aceed0e4fb7e> ;
<http://genome.db/sw/xref> <urn:xref:geneid:2655199>, <urn:xref:gi:124511741> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://purl.obolibrary.org/obo/SO_0000234> ;
<http://www.w3.org/2000/01/rdf-schema#label> "mRNA" .
# SO:CDS (parent -> "gene"; should be changed to "mRNA"?; how to make it consistent with Prokaryote RefSeq records?)
<urn:uuid:e5d162dd-b4c0-4b82-94be-c252e49aa091>
<http://genome.db/sw/exons> (<urn:uuid:b404b2d3-3642-4803-8523-76570cf846be>
<urn:uuid:d925c5bf-ec45-4542-82c8-c59f6ea6ddf4>
<urn:uuid:57202a72-4b79-4901-9a15-21daeb467274>
<urn:uuid:7eb80305-e087-40cb-bf3f-afea6eedb127>
<urn:uuid:e3bfa90d-26fb-44cd-8989-b11aff549b1d>
<urn:uuid:78027e45-4223-4e14-a0d7-b8db2002bf30>
<urn:uuid:a64773a4-a26c-4a44-be58-3977dbeade0d>
<urn:uuid:4e683dc2-60b8-4647-8fbc-99c0755a8eb2>
<urn:uuid:155d3345-511d-41fa-b477-d67bcb8471c0>
<urn:uuid:0bb4fcf5-cbfc-404a-bb1c-b9dc94444665>
<urn:uuid:65be2ca5-e962-4a43-ad9e-66c783c6c382>
<urn:uuid:27eff893-726e-4bde-b9f6-56b37929610c>
<urn:uuid:03b70581-d98b-4c76-8cb3-e6cd32ef7700>
) ;
<http://genome.db/sw/feature_codon_start> 1 ;
<http://genome.db/sw/feature_gene> "PfCRT" ;
<http://genome.db/sw/feature_gene_synonym> "CRT; digestive vacuole transmembrane protein" ;
<http://genome.db/sw/feature_locus_tag> "MAL7P1.27" ;
<http://genome.db/sw/location> <urn:uuid:99d11132-6cab-44cd-b651-56549491325a> ;
<http://genome.db/sw/xref> <urn:xref:InterPro:IPR017258>, <urn:xref:UniProtKB%2FTrEMBL:Q8IBZ9>, <urn:xref:geneid:2655199>, <urn:xref:gi:124511742>, <urn:xref:protein:XP_001349004.1> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:5c3a336b-8d9c-4c88-a514-b390859d53e9> ;
a <http://purl.obolibrary.org/obo/SO_0000316> ;
<http://www.w3.org/2000/01/rdf-schema#label> "MAL7P1.27" .
# location of CDS
<urn:uuid:99d11132-6cab-44cd-b651-56549491325a>
<http://biohackathon.org/faldo/start> <urn:uuid:88bd57e0-960b-409d-a211-54f179a93884> ;
<http://biohackathon.org/faldo/end> <urn:uuid:dc966d60-5e01-421b-913a-8378f48a0b8b> ;
<http://genome.db/sw/position> "join(458600..458690,458868..459136,459316..459488,459661..459793,459947..460018,460142..460217,460314..460396,460524..460574,460712..460768,460917..461009,461203..461247,461395..461449,461619..461695)" .
# location start
<urn:uuid:88bd57e0-960b-409d-a211-54f179a93884>
<http://biohackathon.org/faldo/position> 458600 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
# location end
<urn:uuid:dc966d60-5e01-421b-913a-8378f48a0b8b>
<http://biohackathon.org/faldo/position> 461695 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
# exon1
<urn:uuid:b404b2d3-3642-4803-8523-76570cf846be>
<http://biohackathon.org/faldo/start> <urn:uuid:6e1fe409-7879-4a68-bf21-33398c79e50d> ;
<http://biohackathon.org/faldo/end> <urn:uuid:90256c52-22aa-4852-90eb-32809c3bbc68> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:99d11132-6cab-44cd-b651-56549491325a> ;
<http://www.w3.org/2000/01/rdf-schema#type> <http://purl.obolibrary.org/obo/SO_0000147> .
# exon1 start
<urn:uuid:6e1fe409-7879-4a68-bf21-33398c79e50d>
<http://biohackathon.org/faldo/position> 458600 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
# exon1 end
<urn:uuid:90256c52-22aa-4852-90eb-32809c3bbc68>
<http://biohackathon.org/faldo/position> 458690 ;
<http://biohackathon.org/faldo/reference> <urn:uuid:63a091c1-1409-4a91-9f46-db9b04bce8f6> ;
a <http://biohackathon.org/faldo/ExactlyKnownPosition>, <http://biohackathon.org/faldo/ForwardStrandPosition> .
# exon2
<urn:uuid:d925c5bf-ec45-4542-82c8-c59f6ea6ddf4>
<http://biohackathon.org/faldo/start> <urn:uuid:2f3b1a61-0a1e-4c4b-b2e9-5604780de5ed> ;
<http://biohackathon.org/faldo/end> <urn:uuid:fdb47c15-f585-4393-a94d-1dcd42d5d60b> ;
<http://purl.org/dc/terms/isPartOf> <urn:uuid:99d11132-6cab-44cd-b651-56549491325a> ;
<http://www.w3.org/2000/01/rdf-schema#type> <http://purl.obolibrary.org/obo/SO_0000147> .
:
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