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diff --git a/rdf-documentation/dump-probeset-metadata.md b/rdf-documentation/dump-probeset-metadata.md new file mode 100644 index 0000000..b47ce20 --- /dev/null +++ b/rdf-documentation/dump-probeset-metadata.md @@ -0,0 +1,58 @@ +# Probeset Metadata +## 'dump-probeset-metadata' + + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id)) AS ProbeSetName, IFNULL(ProbeSet.Name, ProbeSet.Id) AS name, ProbeSetFreeze.Name, IFNULL(ProbeSetXRef.mean, '') AS mean, IFNULL(ProbeSetXRef.se, '') AS se, ProbeSetXRef.Locus, IFNULL(ProbeSetXRef.LRS, '') AS LRS, IFNULL(ProbeSetXRef.pValue, '') AS pValue, IFNULL(ProbeSetXRef.additive, '') AS additive, IFNULL(ProbeSetXRef.h2, '') AS h2 FROM ProbeSetXRef LEFT JOIN ProbeSet ON ProbeSetXRef.ProbeSetId = ProbeSet.Id LEFT JOIN ProbeSetFreeze ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1 +``` + +The above query results to triples that have the form: + +```text +gn:probesetData_probesetname -> rdf:type -> gn:probesetData +gn:probesetData_probesetname -> gn-term:hasProbeset -> probeset:name +gn:probesetData_probesetname -> gn-term:probesetOfDataset -> probeset:ProbeSetFreeze_Name_ +gn:probesetData_probesetname -> gn-term:mean -> "mean"^^xsd:double +gn:probesetData_probesetname -> gn-term:se -> "se"^^xsd:double +gn:probesetData_probesetname -> gn-term:locus -> ProbeSetXRef(Locus) +gn:probesetData_probesetname -> gn:LRS -> "LRS"^^xsd:double +gn:probesetData_probesetname -> gn-term:pValue -> "pValue"^^xsd:double +gn:probesetData_probesetname -> gn-term:additive -> "additive"^^xsd:double +gn:probesetData_probesetname -> gn-term:h2 -> "h2"^^xsd:float +``` +Here's an example query: + +```sparql +@prefix gn: <http://genenetwork.org/id/> . +@prefix gn-term: <http://genenetwork.org/id/> . +@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:probesetData . + ?s gn-term:hasProbeset probeset:100001_at . + ?s gn-term:probesetOfDataset probeset:HC_U_0304_R . + ?s gn-term:mean #{"8.14033666666667"^^xsd:double}# . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:probesetData_hc_u_0304_r:100001_at rdf:type gn:probesetData . +gn:probesetData_hc_u_0304_r:100001_at gn-term:hasProbeset probeset:100001_at . +gn:probesetData_hc_u_0304_r:100001_at gn-term:probesetOfDataset probeset:HC_U_0304_R . +gn:probesetData_hc_u_0304_r:100001_at gn-term:mean "8.14033666666667"^^xsd:double . +gn:probesetData_hc_u_0304_r:100001_at gn-term:se "0.023595817125580502"^^xsd:double . +gn:probesetData_hc_u_0304_r:100001_at gn-term:locus "rsm10000021399" . +gn:probesetData_hc_u_0304_r:100001_at gn:LRS "12.2805314427567"^^xsd:double . +gn:probesetData_hc_u_0304_r:100001_at gn-term:pValue "0.118"^^xsd:double . +gn:probesetData_hc_u_0304_r:100001_at gn-term:additive "0.0803547619047631"^^xsd:double . +``` + |