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October 1, 2012 09:19
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Example of refseq2rdf_urn.rb (PfCRT gene in NC_004328.2)
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| @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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