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-rw-r--r--rdf-documentation/dump-gene-chip.md88
1 files changed, 52 insertions, 36 deletions
diff --git a/rdf-documentation/dump-gene-chip.md b/rdf-documentation/dump-gene-chip.md
index 80217d8..abd68d8 100644
--- a/rdf-documentation/dump-gene-chip.md
+++ b/rdf-documentation/dump-gene-chip.md
@@ -1,37 +1,43 @@
# Probeset freeze metadata
## 'dump-gene-chip'
-
## Generated Triples:
The following SQL query was executed:
```sql
-SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.GeoPlatform FROM GeneChip
+SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.Name, IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL) AS Title, GeneChip.Go_tree_value, Species.Fullname, GeneChip.GeoPlatform FROM GeneChip LEFT JOIN Species USING (SpeciesId)
```
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)
+gn:platform_genechip_name -> rdf:type -> gnc:geneChip
+gn:platform_genechip_name -> rdfs:label -> GeneChip(GeneChipName)
+gn:platform_genechip_name -> skos:prefLabel -> GeneChip(Name)
+gn:platform_genechip_name -> skos:altLabel -> Title
+gn:platform_genechip_name -> gnt:hasGOTreeValue -> GeneChip(Go_tree_value)
+gn:platform_genechip_name -> gnt:belongsToSpecies -> gn:Species_fullname
+gn:platform_genechip_name -> gnt:hasGeoSeriesId -> 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 dct: <>
-PREFIX gn-term: <http://genenetwork.org/term/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+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 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 .
+SELECT * WHERE {
+ ?s rdf:type gnc:geneChip .
+ ?s rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
+ ?s skos:prefLabel "MG_U74AV2" .
?s ?p ?o .
}
```
@@ -39,50 +45,58 @@ SELECT ?s ?p ?o WHERE {
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 .
+gn:platform_mg_u74av2 rdf:type gnc:geneChip .
+gn:platform_mg_u74av2 rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
+gn:platform_mg_u74av2 skos:prefLabel "MG_U74AV2" .
+gn:platform_mg_u74av2 gnt:hasGOTreeValue "affy_mg_u74av2" .
+gn:platform_mg_u74av2 gnt:belongsToSpecies gn:Mus_musculus .
+gn:platform_mg_u74av2 gnt:hasGeoSeriesId 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
+SELECT ProbeSetFreeze.Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.Name, ProbeSetFreeze.Name2, 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_ -> rdf:type -> gnc:probesetDataset
+gn:Probesetfreeze_name_ -> gnt:usesNormalization -> gn:avgmethod_avgmethod_avgmethodname
+gn:Probesetfreeze_name_ -> dct:title -> ProbeSetFreeze(FullName)
+gn:Probesetfreeze_name_ -> rdfs:label -> ProbeSetFreeze(ShortName)
+gn:Probesetfreeze_name_ -> skos:prefLabel -> ProbeSetFreeze(Name)
+gn:Probesetfreeze_name_ -> skos:altLabel -> ProbeSetFreeze(Name2)
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
+gn:Probesetfreeze_name_ -> gnt:usesDataScale -> ProbeSetFreeze(DataScale)
+gn:Probesetfreeze_name_ -> gnt:hasTissue -> gn:tissue_tissue_short_name
+gn:Probesetfreeze_name_ -> gnt:belongsToInbredSet -> 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 dct: <>
-PREFIX gn-term: <http://genenetwork.org/term/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+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 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" .
+SELECT * WHERE {
+ ?s rdf:type gnc:probesetDataset .
+ ?s gnt:usesNormalization gn:avgmethod_rankinv .
+ ?s dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+ ?s rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
?s ?p ?o .
}
```
@@ -90,13 +104,15 @@ SELECT ?s ?p ?o WHERE {
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 rdf:type gnc:probesetDataset .
+gn:Cmmtubcbxdp00cerilm0513 gnt:usesNormalization gn:avgmethod_rankinv .
+gn:Cmmtubcbxdp00cerilm0513 dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+gn:Cmmtubcbxdp00cerilm0513 rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+gn:Cmmtubcbxdp00cerilm0513 skos:prefLabel "CMMTUBCBXDP00CerILM0513" .
+gn:Cmmtubcbxdp00cerilm0513 skos:altLabel "CMMTUBCBXDP00CerILMMay13" .
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 .
+gn:Cmmtubcbxdp00cerilm0513 gnt:usesDataScale "log2" .
+gn:Cmmtubcbxdp00cerilm0513 gnt:hasTissue gn:tissue_cb .
+gn:Cmmtubcbxdp00cerilm0513 gnt:belongsToInbredSet gn:inbredSet_bxd .
```
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 00:13:40 +0000