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diff --git a/rdf-documentation/dump-gene-chip.md b/rdf-documentation/dump-gene-chip.md new file mode 100644 index 0000000..e25573a --- /dev/null +++ b/rdf-documentation/dump-gene-chip.md @@ -0,0 +1,100 @@ +# Probeset freeze metadata +## 'dump-gene-chip' + + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.GeoPlatform FROM GeneChip +``` + +The above query results to triples that have the form: + +```text +gn:platform_genechip_name -> rdf:type -> gn:platform +gn:platform_genechip_name -> gn-term:name -> GeneChip(GeneChipName) +gn:platform_genechip_name -> gn-term:geoPlatform -> geoSeries:GeneChip(GeoPlatform) +``` +Here's an example query: + +```sparql +@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . +@prefix gn: <http://genenetwork.org/id/> . +@prefix gn-term: <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 xsd: <http://www.w3.org/2001/XMLSchema#> . + +SELECT ?s ?p ?o WHERE { + ?s rdf:type gn:platform . + ?s gn-term:name "Affy Mouse Genome U74Av2 (GPL81)" . + ?s gn-term:geoPlatform geoSeries:GPL81 . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:platform_mg_u74av2 rdf:type gn:platform . +gn:platform_mg_u74av2 gn-term:name "Affy Mouse Genome U74Av2 (GPL81)" . +gn:platform_mg_u74av2 gn-term:geoPlatform geoSeries:GPL81 . +``` + + +## 'dump-probesetfreeze' + + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT ProbeSetFreeze.Name, AvgMethod.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.CreateTime, ProbeSetFreeze.DataScale, Tissue.Short_Name, InbredSet.Name AS InbredSetName FROM ProbeSetFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = ProbeSetFreeze.Name LEFT JOIN ProbeFreeze USING (ProbeFreezeId) LEFT JOIN AvgMethod ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID LEFT JOIN InbredSet ON ProbeFreeze.InbredSetId = InbredSet.Id LEFT JOIN Tissue ON ProbeFreeze.TissueId = Tissue.TissueId WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id +``` + +The above query results to triples that have the form: + +```text +gn:Probesetfreeze_name_ -> rdf:type -> gn:probesetDataset +gn:Probesetfreeze_name_ -> gn-term:avgMethod -> gn:avgmethod_avgmethod_name +gn:Probesetfreeze_name_ -> gn-term:fullName -> ProbeSetFreeze(FullName) +gn:Probesetfreeze_name_ -> gn-term:shortName -> ProbeSetFreeze(ShortName) +gn:Probesetfreeze_name_ -> dct:created -> "ProbeSetFreeze(CreateTime)"^^xsd:datetime +gn:Probesetfreeze_name_ -> gn-term:dataScale -> ProbeSetFreeze(DataScale) +gn:Probesetfreeze_name_ -> gn-term:tissueName -> gn:tissue_tissue_short_name +gn:Probesetfreeze_name_ -> gn-term:datasetOfInbredSet -> gn:inbredSet_inbredset_inbredsetname +``` +Here's an example query: + +```sparql +@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . +@prefix gn: <http://genenetwork.org/id/> . +@prefix gn-term: <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 xsd: <http://www.w3.org/2001/XMLSchema#> . + +SELECT ?s ?p ?o WHERE { + ?s rdf:type gn:probesetDataset . + ?s gn-term:avgMethod gn:avgmethod_cmmtubcbxdp00cerilm0513 . + ?s gn-term:fullName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:Cmmtubcbxdp00cerilm0513 rdf:type gn:probesetDataset . +gn:Cmmtubcbxdp00cerilm0513 gn-term:avgMethod gn:avgmethod_cmmtubcbxdp00cerilm0513 . +gn:Cmmtubcbxdp00cerilm0513 gn-term:fullName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +gn:Cmmtubcbxdp00cerilm0513 gn-term:shortName "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" . +gn:Cmmtubcbxdp00cerilm0513 dct:created "2013-04-22"^^xsd:datetime . +gn:Cmmtubcbxdp00cerilm0513 gn-term:dataScale "log2" . +gn:Cmmtubcbxdp00cerilm0513 gn-term:tissueName gn:tissue_cb . +gn:Cmmtubcbxdp00cerilm0513 gn-term:datasetOfInbredSet gn:inbredSet_bxd . +``` + |