BH14.14/genomeRDF/RefEx

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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


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
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