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-rw-r--r--rdf-documentation/dump-species-metadata.md120
1 files changed, 63 insertions, 57 deletions
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md
index a35e1b1..4c0e123 100644
--- a/rdf-documentation/dump-species-metadata.md
+++ b/rdf-documentation/dump-species-metadata.md
@@ -1,5 +1,4 @@
-# Species Metadata
-## 'dump-species'
+# Species Metadata## 'dump-species'
## Generated Triples:
@@ -7,32 +6,34 @@
The following SQL query was executed:
```sql
-SELECT Species.FullName, Species.SpeciesName, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
+SELECT Species.Fullname, Species.SpeciesName, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
```
The above query results to triples that have the form:
```text
-gn:Species_fullname -> rdf:type -> gn:species
-gn:Species_fullname -> gn-term:name -> Species(SpeciesName)
-gn:Species_fullname -> gn-term:displayName -> Species(MenuName)
-gn:Species_fullname -> gn-term:binomialName -> Species(FullName)
-gn:Species_fullname -> gn-term:family -> Species(Family)
-gn:Species_fullname -> gn-term:organism -> taxon:Species(TaxonomyId)
+gn:Species_fullname -> rdf:type -> gnc:species
+gn:Species_fullname -> gnt:name -> Species(SpeciesName)
+gn:Species_fullname -> rdfs:label -> Species(MenuName)
+gn:Species_fullname -> gnt:binomialName -> Species(FullName)
+gn:Species_fullname -> gnt:family -> Species(Family)
+gn:Species_fullname -> gnt:organism -> taxon:Species(TaxonomyId)
```
Here's an example query:
```sparql
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 gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:species .
- ?s gn-term:name "Mouse" .
- ?s gn-term:displayName "Mouse (Mus musculus, mm10)" .
+SELECT * WHERE {
+ ?s rdf:type gnc:species .
+ ?s gnt:name "Mouse" .
+ ?s rdfs:label "Mouse (Mus musculus, mm10)" .
?s ?p ?o .
}
```
@@ -40,15 +41,14 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:Mus_musculus rdf:type gn:species .
-gn:Mus_musculus gn-term:name "Mouse" .
-gn:Mus_musculus gn-term:displayName "Mouse (Mus musculus, mm10)" .
-gn:Mus_musculus gn-term:binomialName "Mus musculus" .
-gn:Mus_musculus gn-term:family "Vertebrates" .
-gn:Mus_musculus gn-term:organism taxon:10090 .
+gn:Mus_musculus rdf:type gnc:species .
+gn:Mus_musculus gnt:name "Mouse" .
+gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
+gn:Mus_musculus gnt:binomialName "Mus musculus" .
+gn:Mus_musculus gnt:family "Vertebrates" .
+gn:Mus_musculus gnt:organism taxon:10090 .
```
-
## 'dump-strain'
@@ -57,32 +57,34 @@ gn:Mus_musculus gn-term:organism taxon:10090 .
The following SQL query was executed:
```sql
-SELECT CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000)) AS StrainName, Species.FullName, Strain.Name, Strain.Name2, Strain.Alias, Strain.Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
+SELECT CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000)) AS StrainName, Species.Fullname, Strain.Name, IF ((Strain.Name2 != Strain.Name), Strain.Name2, '') AS Name2, IF ((Strain.Alias != Strain.Name), Strain.Alias, '') AS Alias, IF ((Strain.Symbol != Strain.Name), Strain.Alias, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
```
The above query results to triples that have the form:
```text
-gn:Strainname -> rdf:type -> gn:strain
-gn:Strainname -> gn-term:strainOfSpecies -> gn:Species_fullname
-gn:Strainname -> gn-term:name -> StrainName
-gn:Strainname -> gn-term:name2 -> StrainName2
-gn:Strainname -> gn-term:alias -> StrainAlias
-gn:Strainname -> gn-term:symbol -> Strain(Symbol)
+gn:Strainname -> rdf:type -> gnc:strain
+gn:Strainname -> gnt:species -> gn:Species_fullname
+gn:Strainname -> rdfs:label -> StrainName
+gn:Strainname -> rdfs:label -> Name2
+gn:Strainname -> gnt:alias -> Alias
+gn:Strainname -> gnt:symbol -> Symbol
```
Here's an example query:
```sparql
PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gn-term: <http://genenetwork.org/term/>
-PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:strain .
- ?s gn-term:strainOfSpecies gn:Mus_musculus .
- ?s gn-term:name "B6D2F1" .
+SELECT * WHERE {
+ ?s rdf:type gnc:strain .
+ ?s gnt:species gn:Mus_musculus .
+ ?s rdfs:label "B6D2F1" .
?s ?p ?o .
}
```
@@ -90,13 +92,11 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:B6d2f1 rdf:type gn:strain .
-gn:B6d2f1 gn-term:strainOfSpecies gn:Mus_musculus .
-gn:B6d2f1 gn-term:name "B6D2F1" .
-gn:B6d2f1 gn-term:name2 "B6D2F1" .
+gn:B6d2f1 rdf:type gnc:strain .
+gn:B6d2f1 gnt:species gn:Mus_musculus .
+gn:B6d2f1 rdfs:label "B6D2F1" .
```
-
## 'dump-mapping-method'
@@ -105,25 +105,29 @@ gn:B6d2f1 gn-term:name2 "B6D2F1" .
The following SQL query was executed:
```sql
-SELECT MappingMethod.Name FROM MappingMethod
+SELECT MappingMethod.Name, MappingMethod.Name FROM MappingMethod
```
The above query results to triples that have the form:
```text
-gn:mappingMethod_mappingmethod_name -> rdf:type -> gn:mappingMethod
+gn:mappingMethod_mappingmethod_name -> rdf:type -> gnc:mappingMethod
+gn:mappingMethod_mappingmethod_name -> rdfs:label -> MappingMethod(Name)
```
Here's an example query:
```sparql
PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gn-term: <http://genenetwork.org/term/>
-PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:mappingMethod .
+SELECT * WHERE {
+ ?s rdf:type gnc:mappingMethod .
+ ?s rdfs:label "qtlreaper" .
?s ?p ?o .
}
```
@@ -131,10 +135,10 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:mappingMethod_qtlreaper rdf:type gn:mappingMethod .
+gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod .
+gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" .
```
-
## 'dump-avg-method'
@@ -149,21 +153,23 @@ SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod
The above query results to triples that have the form:
```text
-gn:avgmethod_avgmethod_name -> rdf:type -> gn:avgMethod
-gn:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization)
+gn:avgmethod_avgmethod_name -> rdf:type -> gnc:avgMethod
+gn:avgmethod_avgmethod_name -> rdfs:label -> AvgMethod(Normalization)
```
Here's an example query:
```sparql
PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gn-term: <http://genenetwork.org/term/>
-PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:avgMethod .
- ?s gn-term:normalization "MAS5" .
+SELECT * WHERE {
+ ?s rdf:type gnc:avgMethod .
+ ?s rdfs:label "MAS5" .
?s ?p ?o .
}
```
@@ -171,7 +177,7 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:avgmethod_mas5 rdf:type gn:avgMethod .
-gn:avgmethod_mas5 gn-term:normalization "MAS5" .
+gn:avgmethod_mas5 rdf:type gnc:avgMethod .
+gn:avgmethod_mas5 rdfs:label "MAS5" .
```
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-19 22:11:11 +0000