BH12.12/SPARQLthon5/INSDCオントロジー
提供：TogoWiki
目次 |
INSDC
- insdc.owlアップデート
bioproject
INSDC公開データの確認を行なった。
公開データ
2013-02-20時点のFTPサイトのデータを確認した。ENAについては不明。
Organism Name TaxID Project Accession Project ID Project Type Project Data Type Date Borrelia burgdorferi B31 224326 PRJNA3 3 Primary submission Genome sequencing 2003/02/23 Treponema denticola ATCC 35405 243275 PRJNA4 4 Primary submission Genome sequencing 2004/04/06 Treponema pallidum subsp. pallidum str. Nichols 243276 PRJNA5 5 Primary submission Genome sequencing 2003/02/25 Magnetospirillum magnetotacticum MS-1 272627 PRJNA6 6 Primary submission Genome sequencing 2003/02/25 Campylobacter fetus subsp. venerealis str. Azul-94 593452 PRJNA7 7 Primary submission Genome sequencing 2009/04/22 . . . 68749件
Refseq accn,Genbank accn,Organism name,TaxID PRJNA116,PRJNA10719,Arabidopsis thaliana,3702 PRJNA122,PRJNA12269,Oryza sativa Japonica Group,39947 PRJNA122,PRJNA13141,Oryza sativa Japonica Group,39947 PRJNA127,PRJNA13836,Schizosaccharomyces pombe 972h-,284812 PRJNA127,PRJNA20755,Schizosaccharomyces pombe,4896 PRJNA128,PRJNA13838,Saccharomyces cerevisiae S288c,559292 PRJNA128,PRJNA43747,Saccharomyces cerevisiae S288c,559292 PRJNA132,PRJNA13841,Neurospora crassa OR74A,367110 PRJNA148,PRJNA13173,Plasmodium falciparum 3D7,36329 PRJNA155,PRJNA13833,Encephalitozoon cuniculi GB-M1,284813 . . . 7606件
Organism Name Project Accession Project ID Project Type Project Data Type Released Updated Gluconobacter frateurii NBRC 101659 PRJDB2 Primary submission Genome sequencing 2012/05/14 2012/05/14 Gordonia otitidis NBRC 100426 PRJDB3 Primary submission Genome sequencing 2011/11/01 2012/02/16 Gordonia rhizosphera NBRC 16068 PRJDB4 Primary submission Genome sequencing 2011/11/01 2012/08/29 Escherichia coli str. K-12 substr. MDS42 PRJDB5 Primary submission Genome sequencing 2011/12/02 2012/02/08 . . . 448件
RDF
- prokaryotes.txt.bioproject_refseq.nt
<http://www.ncbi.nlm.nih.gov/bioproject/43389> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000855.1> . <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000855.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/43389> . <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000855.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/43389> <http://www.w3.org/2000/01/rdf-schema#label> "Campylobacter jejuni subsp. jejuni 414" . <http://www.ncbi.nlm.nih.gov/bioproject/43389> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CM000855.1> . <http://www.ncbi.nlm.nih.gov/nuccore/CM000855.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/43389> . <http://www.ncbi.nlm.nih.gov/nuccore/CM000855.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/43391> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000854.1> . <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000854.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/43391> . <http://www.ncbi.nlm.nih.gov/nuccore/NZ_CM000854.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/43391> <http://www.w3.org/2000/01/rdf-schema#label> "Campylobacter jejuni subsp. jejuni 1336" . <http://www.ncbi.nlm.nih.gov/bioproject/43391> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CM000854.1> . <http://www.ncbi.nlm.nih.gov/nuccore/CM000854.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/43391> . <http://www.ncbi.nlm.nih.gov/nuccore/CM000854.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/57587> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NC_002163.1> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_002163.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/57587> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_002163.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/57587> <http://www.w3.org/2000/01/rdf-schema#label> "Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819" . <http://www.ncbi.nlm.nih.gov/bioproject/57587> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/AL111168.1> . <http://www.ncbi.nlm.nih.gov/nuccore/AL111168.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/57587> . <http://www.ncbi.nlm.nih.gov/nuccore/AL111168.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/57899> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NC_003912.7> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_003912.7> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/57899> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_003912.7> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/57899> <http://www.w3.org/2000/01/rdf-schema#label> "Campylobacter jejuni RM1221" . <http://www.ncbi.nlm.nih.gov/bioproject/57899> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CP000025.1> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000025.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/57899> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000025.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/58503> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#label> "Campylobacter jejuni subsp. jejuni 81-176" . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CP000538.1> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000538.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/58503> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000538.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000340> . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/58503> . <http://www.ncbi.nlm.nih.gov/nuccore/NC_008787.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000155> . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CP000549.1> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000549.1> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/58503> . <http://www.ncbi.nlm.nih.gov/nuccore/CP000549.1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000155> . <http://www.ncbi.nlm.nih.gov/bioproject/58503> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/nuccore/CP000550.1> .
- summary.txt.bioproject_taxid_gold.nt
<http://www.ncbi.nlm.nih.gov/bioproject/116> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/taxonomy/3702> . <http://www.ncbi.nlm.nih.gov/taxonomy/3702> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/116> . <http://www.ncbi.nlm.nih.gov/bioproject/116> <http://www.w3.org/2000/01/rdf-schema#label> "RefSeq Genome" . <http://www.ncbi.nlm.nih.gov/bioproject/116> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/10719> . <http://www.ncbi.nlm.nih.gov/bioproject/10719> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/116> . <http://www.ncbi.nlm.nih.gov/bioproject/10719> <http://www.w3.org/2000/01/rdf-schema#label> "Genome sequencing" . <http://www.ncbi.nlm.nih.gov/bioproject/10719> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/taxonomy/3702> . <http://www.ncbi.nlm.nih.gov/taxonomy/3702> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/10719> . <http://www.ncbi.nlm.nih.gov/bioproject/122> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/taxonomy/39947> . <http://www.ncbi.nlm.nih.gov/taxonomy/39947> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/122> . <http://www.ncbi.nlm.nih.gov/bioproject/122> <http://www.w3.org/2000/01/rdf-schema#label> "RefSeq Genome" . <http://www.ncbi.nlm.nih.gov/bioproject/122> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/13141> . <http://www.ncbi.nlm.nih.gov/bioproject/13141> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/122> . <http://www.ncbi.nlm.nih.gov/bioproject/13141> <http://www.w3.org/2000/01/rdf-schema#label> "Genome sequencing" . <http://www.ncbi.nlm.nih.gov/bioproject/13141> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/taxonomy/39947> . <http://www.ncbi.nlm.nih.gov/taxonomy/39947> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/13141> . <http://www.ncbi.nlm.nih.gov/bioproject/13141> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=Gc00603> . <http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=Gc00603> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/13141> . <http://www.ncbi.nlm.nih.gov/bioproject/127> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/taxonomy/284812> . <http://www.ncbi.nlm.nih.gov/taxonomy/284812> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/127> . <http://www.ncbi.nlm.nih.gov/bioproject/127> <http://www.w3.org/2000/01/rdf-schema#label> "RefSeq Genome" . <http://www.ncbi.nlm.nih.gov/bioproject/127> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/20755> . <http://www.ncbi.nlm.nih.gov/bioproject/20755> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://www.ncbi.nlm.nih.gov/bioproject/127> . <http://www.ncbi.nlm.nih.gov/bioproject/20755> <http://www.w3.org/2000/01/rdf-schema#label> "Genome sequencing" .
XML2RDFコンバーター開発
フラットファイルではなくXMLからのコンバーターを作成する
- BioProjectID -- INSDC Entry Accession のデータがXMLにない
- xmlファイルが大きいため、Nokogiri:XML::SAX::Document を使ってパースする
- project id はプレフィックスPRJDBが付く http://identifiers.org/bioproject/PRJDB116 をSubjectにする？
