Update docs for species matadata dump

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" .
 ```