BH14.14/genomeRDF/RefEx
提供：TogoWiki
RefEx RDF化
- BioHackathon 2014 で取り掛かった RefEx RDF化 の継続作業 Ref
- Funtom5 の CAGE データ Human, Mouse に関するRefEx のデータをRDF化完了
- RDFファイル
- SPARQLエンドポイント
- Fantom5 データ 76983950トリプル
- サンプルデータ 20701トリプル
SPARQL sample 1
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix dc: <http://purl.org/dc/elements/1.1/> prefix refexs: <http://refex.dbcls.jp/sample/> prefix refexo: <http://purl.jp/bio/01/refexo#> prefix ff: <http://fantom.gsc.riken.jp/5/sstar/FF:> prefix bs: <http://identifiers.org/biosample/> prefix obo: <http://purl.obolibrary.org/obo/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?refexid ?gene ?v ?sample ?age WHERE { ?sample ?p ?bn . ?bn refexo:belongsToAnatomy obo:UBERON_0000468 . ?sample refexo:sex obo:PATO_0000384 . ?sample refexo:age ?o . ?refex a refexo:RefExEntry . ?refex dc:identifier ?refexid . ?refex refexo:refexSample ?sample . ?refex refexo:expValue ?val . ?refex rdfs:seeAlso ?gene . BIND(xsd:decimal(?o) as ?age) BIND(xsd:float(?val) as ?v) FILTER(?age > 20) FILTER(?v > 2) } LIMIT 200
SPARQL sample 2
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix dc: <http://purl.org/dc/elements/1.1/> prefix refexs: <http://refex.dbcls.jp/sample/> prefix refexo: <http://purl.jp/bio/01/refexo#> prefix ff: <http://fantom.gsc.riken.jp/5/sstar/FF:> prefix bs: <http://identifiers.org/biosample/> prefix obo: <http://purl.obolibrary.org/obo/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?refexid ?gene ?v ?age ?dlabel as ?disease ?alabel as ?anatomy ?slabel as ?gender WHERE { ?sample ?p ?bn . ?bn refexo:belongsToAnatomy ?anatomy . ?anatomy rdfs:label ?anatomy_label . ?bn refexo:belongsToDisease ?disease . ?disease rdfs:label ?disease_label . ?sample refexo:sex ?sex . ?sex rdfs:label ?sex_label . ?sample refexo:age ?o . ?refex a refexo:RefExEntry . ?refex dc:identifier ?refexid . ?refex refexo:refexSample ?sample . ?refex refexo:expValue ?val . ?refex rdfs:seeAlso ?gene . BIND(xsd:decimal(?o) as ?age) BIND(xsd:float(?val) as ?v) BIND(xsd:string(?anatomy_label) as ?alabel) BIND(xsd:string(?sex_label) as ?slabel) BIND(xsd:string(?disease_label) as ?dlabel) FILTER(?age > 20) FILTER(?v > 7) } LIMIT 100
refexid gene v age disease anatomy gender "RFX0000025051" http://www.ncbi.nlm.nih.gov/gene/60 7.95728 44 respiratory system cancer lung female "RFX0000026163" http://www.ncbi.nlm.nih.gov/gene/71 7.81811 44 respiratory system cancer lung female "RFX0000260239" http://www.ncbi.nlm.nih.gov/gene/689 7.11791 44 respiratory system cancer lung female "RFX0000720051" http://www.ncbi.nlm.nih.gov/gene/1938 7.22957 44 respiratory system cancer lung female "RFX0000738399" http://www.ncbi.nlm.nih.gov/gene/1982 7.00645 44 respiratory system cancer lung female "RFX0002225699" http://www.ncbi.nlm.nih.gov/gene/6206 7.38385 44 respiratory system cancer lung female "RFX0002230703" http://www.ncbi.nlm.nih.gov/gene/6227 7.10329 44 respiratory system cancer lung female "RFX0002231259" http://www.ncbi.nlm.nih.gov/gene/6228 7.30949 44 respiratory system cancer lung female "RFX0002231815" http://www.ncbi.nlm.nih.gov/gene/6229 8.03302 44 respiratory system cancer lung female "RFX0000025051" http://www.ncbi.nlm.nih.gov/gene/60 7.95728 44 organ system cancer lung female "RFX0000026163" http://www.ncbi.nlm.nih.gov/gene/71 7.81811 44 organ system cancer lung female "RFX0000260239" http://www.ncbi.nlm.nih.gov/gene/689 7.11791 44 organ system cancer lung female "RFX0000720051" http://www.ncbi.nlm.nih.gov/gene/1938 7.22957 44 organ system cancer lung female "RFX0000738399" http://www.ncbi.nlm.nih.gov/gene/1982 7.00645 44 organ system cancer lung female "RFX0001091459" http://www.ncbi.nlm.nih.gov/gene/3006 7.22503 44 organ system cancer lung female "RFX0001880979" http://www.ncbi.nlm.nih.gov/gene/5315 7.73395 44 organ system cancer lung female "RFX0002211243" http://www.ncbi.nlm.nih.gov/gene/6169 7.4575 44 organ system cancer lung female "RFX0002214023" http://www.ncbi.nlm.nih.gov/gene/6181 7.83049 44 organ system cancer lung female "RFX0002225699" http://www.ncbi.nlm.nih.gov/gene/6206 7.38385 44 organ system cancer lung female "RFX0002230703" http://www.ncbi.nlm.nih.gov/gene/6227 7.10329 44 organ system cancer lung female "RFX0002231259" http://www.ncbi.nlm.nih.gov/gene/6228 7.30949 44 organ system cancer lung female "RFX0002231815" http://www.ncbi.nlm.nih.gov/gene/6229 8.03302 44 organ system cancer lung female "RFX0000025051" http://www.ncbi.nlm.nih.gov/gene/60 7.95728 44 cell type cancer lung female "RFX0000026163" http://www.ncbi.nlm.nih.gov/gene/71 7.81811 44 cell type cancer lung female "RFX0000260239" http://www.ncbi.nlm.nih.gov/gene/689 7.11791 44 cell type cancer lung female "RFX0000720051" http://www.ncbi.nlm.nih.gov/gene/1938 7.22957 44 cell type cancer lung female "RFX0000738399" http://www.ncbi.nlm.nih.gov/gene/1982 7.00645 44 cell type cancer lung female "RFX0001091459" http://www.ncbi.nlm.nih.gov/gene/3006 7.22503 44 cell type cancer lung female "RFX0001880979" http://www.ncbi.nlm.nih.gov/gene/5315 7.73395 44 cell type cancer lung female "RFX0002193451" http://www.ncbi.nlm.nih.gov/gene/6125 7.03563 44 cell type cancer lung female "RFX0002195675" http://www.ncbi.nlm.nih.gov/gene/6132 7.18212 44 cell type cancer lung female "RFX0002205127" http://www.ncbi.nlm.nih.gov/gene/6156 7.2347 44 cell type cancer lung female "RFX0002206239" http://www.ncbi.nlm.nih.gov/gene/6158 7.50536 44 cell type cancer lung female "RFX0002232371" http://www.ncbi.nlm.nih.gov/gene/6230 7.46208 44 cell type cancer lung female "RFX0002195675" http://www.ncbi.nlm.nih.gov/gene/6132 7.18212 44 lung cancer lung female "RFX0002205127" http://www.ncbi.nlm.nih.gov/gene/6156 7.2347 44 lung cancer lung female "RFX0002206239" http://www.ncbi.nlm.nih.gov/gene/6158 7.50536 44 lung cancer lung female "RFX0002232371" http://www.ncbi.nlm.nih.gov/gene/6230 7.46208 44 lung cancer lung female "RFX0002252387" http://www.ncbi.nlm.nih.gov/gene/6282 7.1047 44 lung cancer lung female "RFX0002630467" http://www.ncbi.nlm.nih.gov/gene/7178 7.6537 44 lung cancer lung female "RFX0001842615" http://www.ncbi.nlm.nih.gov/gene/5216 7.07845 44 lung cancer lung female "RFX0002573755" http://www.ncbi.nlm.nih.gov/gene/7052 7.20095 44 lung cancer lung female
