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diff --git a/rdf-documentation/genelist.md b/rdf-documentation/genelist.md new file mode 100644 index 0000000..1636c49 --- /dev/null +++ b/rdf-documentation/genelist.md @@ -0,0 +1,193 @@ +# Gene Metadata +## 'genelist-rn33' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT GeneList_rn33.id AS GENE_UID, GeneList_rn33.geneSymbol, GeneList_rn33.chromosome, GeneList_rn33.txStart, GeneList_rn33.txEnd, GeneList_rn33.strand, GeneList_rn33.NM_ID, GeneList_rn33.kgID, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol FROM GeneList_rn33 +``` + +The above query results to triples that have the form: + +```text +gn:gene_rn33Genelist_rn33_gene_uid -> rdf:type -> gnc:Gene +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:belongsToSpecies -> gn:Rattus_norvegicus +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:geneSymbol -> GeneList_rn33(geneSymbol) +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:chromosome -> GeneList_rn33(chromosome) +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:TxStart -> "GeneList_rn33(txStart)"^^xsd:double +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:TxEnd -> "GeneList_rn33(txEnd)"^^xsd:double +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:Strand -> GeneList_rn33(strand) +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:transcript -> transcript:GeneList_rn33(NM_ID) +gn:gene_rn33Genelist_rn33_gene_uid -> gnt:hasKgID -> GeneList_rn33(kgID) +gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList_rn33(geneSymbol)> . +<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList_rn33(geneSymbol)> a gnc:PantherLink +gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <https://www.ebi.ac.uk/gwas/search?query=GeneList_rn33(geneSymbol)> . +<https://www.ebi.ac.uk/gwas/search?query=GeneList_rn33(geneSymbol)> a gnc:ebiGwasLink +gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList_rn33%28geneSymbol%29> . +<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList_rn33%28geneSymbol%29> a gnc:stringLink +gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <https://www.gtexportal.org/home/gene/GeneList_rn33%28geneSymbol%29> . +<https://www.gtexportal.org/home/gene/GeneList_rn33%28geneSymbol%29> a gnc:gtexLink +gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://www.proteinatlas.org/search/GeneList_rn33%28geneSymbol%29> . +<http://www.proteinatlas.org/search/GeneList_rn33%28geneSymbol%29> a gnc:proteinAtlasLink +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX probeset: <http://genenetwork.org/probeset/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX dct: <http://purl.org/dc/terms/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> +PREFIX qb: <http://purl.org/linked-data/cube#> +PREFIX gene: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> +PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> +PREFIX transcript: <https://portals.broadinstitute.org/gpp/public/trans/details?transName=> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> + +SELECT * WHERE { + ?s rdf:type gnc:Gene . + ?s gnt:belongsToSpecies gn:Rattus_norvegicus . + ?s gnt:geneSymbol "0610031j06rik" . + ?s gnt:chromosome "2" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:gene_rn331 rdf:type gnc:Gene . +gn:gene_rn331 gnt:belongsToSpecies gn:Rattus_norvegicus . +gn:gene_rn331 gnt:geneSymbol "0610031j06rik" . +gn:gene_rn331 gnt:chromosome "2" . +gn:gene_rn331 gnt:TxStart "180.388175"^^xsd:double . +gn:gene_rn331 gnt:TxEnd "180.391765"^^xsd:double . +gn:gene_rn331 gnt:Strand "+" . +gn:gene_rn331 gnt:transcript transcript:NM_001004226 . +gn:gene_rn331 dct:references <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=0610031j06rik> . +<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=0610031j06rik> a gnc:PantherLink . +gn:gene_rn331 dct:references <https://www.ebi.ac.uk/gwas/search?query=0610031j06rik> . +<https://www.ebi.ac.uk/gwas/search?query=0610031j06rik> a gnc:ebiGwasLink . +gn:gene_rn331 dct:references <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=0610031j06rik> . +<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=0610031j06rik> a gnc:stringLink . +gn:gene_rn331 dct:references <https://www.gtexportal.org/home/gene/0610031j06rik> . +<https://www.gtexportal.org/home/gene/0610031j06rik> a gnc:gtexLink . +gn:gene_rn331 dct:references <http://www.proteinatlas.org/search/0610031j06rik> . +<http://www.proteinatlas.org/search/0610031j06rik> a gnc:proteinAtlasLink . +``` + + +## 'genelist' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT CONCAT_WS('_', GeneSymbol, GeneID, AlignID) AS GENE_UID, GeneList.GeneSymbol, GeneList.GeneDescription, GeneList.GeneId, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneID, Species.Name, GeneList.GeneSymbol, Species.Name, GeneList.GeneID, Species.Name, GeneList.GeneID, GeneList.GeneSymbol, Species.FullName, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.Chromosome, GeneList.TxStart, GeneList.TxEnd, GeneList.Strand, Species.Name, GeneList.NM_ID, GeneList.kgID, GeneList.UnigenID, GeneList.ProteinID, GeneList.AlignID, IFNULL(RGD_ID, '') AS RGD_ID FROM GeneList LEFT JOIN Species USING (SpeciesId) +``` + +The above query results to triples that have the form: + +```text +gn:geneGENE_UID -> rdf:type -> gnc:Gene +gn:geneGENE_UID -> gnt:geneSymbol -> GeneList(GeneSymbol) +gn:geneGENE_UID -> dct:description -> GeneListGeneDescription +gn:geneGENE_UID -> gnt:hasGeneId -> gene:GeneList(GeneId) +gn:geneGENE_UID -> dct:references -> <https://www.ebi.ac.uk/gwas/search?query=GeneList%28GeneSymbol%29> . +<https://www.ebi.ac.uk/gwas/search?query=GeneList%28GeneSymbol%29> a gnc:ebiGwasLink +gn:geneGENE_UID -> dct:references -> +gn:geneGENE_UID -> dct:references -> +gn:geneGENE_UID -> dct:references -> +gn:geneGENE_UID -> dct:references -> <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=GeneList(GeneID)> . +<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=GeneList(GeneID)> a gnc:gemmaLink +gn:geneGENE_UID -> dct:references -> +gn:geneGENE_UID -> dct:references -> <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList%28GeneSymbol%29> . +<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList%28GeneSymbol%29> a gnc:pantherLink +gn:geneGENE_UID -> dct:references -> <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList%28GeneSymbol%29> . +<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList%28GeneSymbol%29> a gnc:stringLink +gn:geneGENE_UID -> dct:references -> <https://www.gtexportal.org/home/gene/GeneList%28GeneSymbol%29> . +<https://www.gtexportal.org/home/gene/GeneList%28GeneSymbol%29> a gnc:gtexLink +gn:geneGENE_UID -> dct:references -> <http://www.proteinatlas.org/search/GeneList%28GeneSymbol%29> . +<http://www.proteinatlas.org/search/GeneList%28GeneSymbol%29> a gnc:proteinAtlasLink +gn:geneGENE_UID -> gnt:chromosome -> GeneList(Chromosome) +gn:geneGENE_UID -> gnt:TxStart -> "GeneList(TxStart)"^^xsd:double +gn:geneGENE_UID -> gnt:TxEnd -> "GeneList(TxEnd)"^^xsd:double +gn:geneGENE_UID -> gnt:Strand -> GeneList(Strand) +gn:geneGENE_UID -> gnt:belongsToSpecies -> gn:Species_name +gn:geneGENE_UID -> gnt:transcript -> transcript:GeneList(NM_ID) +gn:geneGENE_UID -> gnt:hasKgID -> GeneList(kgID) +gn:geneGENE_UID -> gnt:hasUnigenID -> GeneList(UnigenID) +gn:geneGENE_UID -> gnt:hasProteinID -> GeneList(ProteinID) +gn:geneGENE_UID -> gnt:hasAlignID -> GeneList(AlignID) +gn:geneGENE_UID -> gnt:hasRgdID -> RGD_ID +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX probeset: <http://genenetwork.org/probeset/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX dct: <http://purl.org/dc/terms/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> +PREFIX qb: <http://purl.org/linked-data/cube#> +PREFIX gene: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> +PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> +PREFIX transcript: <https://portals.broadinstitute.org/gpp/public/trans/details?transName=> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> + +SELECT * WHERE { + ?s rdf:type gnc:Gene . + ?s gnt:geneSymbol "OTTMUSG00000007" . + ?s dct:description "predicted gene, OTTMUSG00000007987" . + ?s gnt:hasGeneId gene:100137011 . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:geneOTTMUSG00000007_100137011_G211062 rdf:type gnc:Gene . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:geneSymbol "OTTMUSG00000007" . +gn:geneOTTMUSG00000007_100137011_G211062 dct:description "predicted gene, OTTMUSG00000007987" . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasGeneId gene:100137011 . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://www.ebi.ac.uk/gwas/search?query=OTTMUSG00000007> . +<https://www.ebi.ac.uk/gwas/search?query=OTTMUSG00000007> a gnc:ebiGwasLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://mouse.brain-map.org/search/show?search_type=gene&search_term=> . +<http://mouse.brain-map.org/search/show?search_type=gene&search_term=> a gnc:abaLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://rgd.mcw.edu/rgdweb/elasticResults.html?term=OTTMUSG00000007&category=Gene&species=Mouse> . +<https://rgd.mcw.edu/rgdweb/elasticResults.html?term=OTTMUSG00000007&category=Gene&species=Mouse> a gnc:rgdLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://biogps.org/?org=mouse#goto=genereport&id=100137011> . +<http://biogps.org/?org=mouse#goto=genereport&id=100137011> a gnc:biogpsLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=100137011> . +<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=100137011> a gnc:gemmaLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://genemania.org/search/mus-musculus/OTTMUSG00000007> . +<https://genemania.org/search/mus-musculus/OTTMUSG00000007> a gnc:genemaniaLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=OTTMUSG00000007> . +<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=OTTMUSG00000007> a gnc:pantherLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=OTTMUSG00000007> . +<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=OTTMUSG00000007> a gnc:stringLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://www.gtexportal.org/home/gene/OTTMUSG00000007> . +<https://www.gtexportal.org/home/gene/OTTMUSG00000007> a gnc:gtexLink . +gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.proteinatlas.org/search/OTTMUSG00000007> . +<http://www.proteinatlas.org/search/OTTMUSG00000007> a gnc:proteinAtlasLink . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:chromosome "11" . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:TxStart "60.630829"^^xsd:double . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:TxEnd "60.632734"^^xsd:double . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:belongsToSpecies gn:Mouse . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:transcript transcript:AK046412 . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasProteinID "Q8BQU9" . +gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasAlignID "G211062" . +``` + |