diff options
Diffstat (limited to 'rdf-documentation/dump-species-metadata.md')
| -rw-r--r-- | rdf-documentation/dump-species-metadata.md | 112 |
1 files changed, 45 insertions, 67 deletions
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md index ca09458..f64232f 100644 --- a/rdf-documentation/dump-species-metadata.md +++ b/rdf-documentation/dump-species-metadata.md @@ -1,14 +1,7 @@ # Species Metadata ## 'dump-species' -## Schema Triples: -```text -gn-term:name -> rdfs:range -> rdfs:Literal -gn-term:displayName -> rdfs:range -> rdfs:Literal -gn-term:binomialName -> rdfs:range -> rdfs:Literal -gn-term:family -> rdfs:range -> rdfs:Literal -``` ## Generated Triples: The following SQL query was executed: @@ -20,24 +13,24 @@ SELECT Species.FullName, Species.SpeciesName, Species.MenuName, Species.FullName The above query results to triples that have the form: ```text -gn-id:Species_fullname -> rdf:type -> gn-id:species -gn-id:Species_fullname -> gn-term:name -> Species(SpeciesName) -gn-id:Species_fullname -> gn-term:displayName -> Species(MenuName) -gn-id:Species_fullname -> gn-term:binomialName -> Species(FullName) -gn-id:Species_fullname -> gn-term:family -> Species(Family) -gn-id:Species_fullname -> gn-term:organism -> taxon:Species(TaxonomyId) +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) ``` Here's an example query: ```sparql -@prefix gn-id: <http://genenetwork.org/terms/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +@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 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-id:species . + ?s rdf:type gn:species . ?s gn-term:name "Mouse" . ?s gn-term:displayName "Mouse (Mus musculus, mm10)" . ?s ?p ?o . @@ -47,26 +40,18 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn-id:Mus_musculus rdf:type gn-id:species . -gn-id:Mus_musculus gn-term:name "Mouse" . -gn-id:Mus_musculus gn-term:displayName "Mouse (Mus musculus, mm10)" . -gn-id:Mus_musculus gn-term:binomialName "Mus musculus" . -gn-id:Mus_musculus gn-term:family "Vertebrates" . -gn-id:Mus_musculus gn-term:organism taxon:10090 . +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 . ``` ## 'dump-strain' -## Schema Triples: -```text -gn-term:strainOfSpecies -> rdfs:domain -> gn-term:strain -gn-term:strainOfSpecies -> rdfs:range -> gn-term:species -gn-term:name -> rdfs:range -> rdfs:Literal -gn-term:alias -> rdfs:range -> rdfs:Literal -gn-term:symbol -> rdfs:range -> rdfs:Literal -``` ## Generated Triples: The following SQL query was executed: @@ -78,25 +63,25 @@ SELECT CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARC The above query results to triples that have the form: ```text -gn-id:Strainname -> rdf:type -> gn-id:strain -gn-id:Strainname -> gn-term:strainOfSpecies -> gn-id:Species_fullname -gn-id:Strainname -> gn-term:name -> StrainName -gn-id:Strainname -> gn-term:name2 -> StrainName2 -gn-id:Strainname -> gn-term:alias -> StrainAlias -gn-id:Strainname -> gn-term:symbol -> Strain(Symbol) +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) ``` Here's an example query: ```sparql -@prefix gn-id: <http://genenetwork.org/terms/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +@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 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-id:strain . - ?s gn-term:strainOfSpecies gn-id:Mus_musculus . + ?s rdf:type gn:strain . + ?s gn-term:strainOfSpecies gn:Mus_musculus . ?s gn-term:name "B6D2F1" . ?s ?p ?o . } @@ -105,19 +90,16 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn-id:B6d2f1 rdf:type gn-id:strain . -gn-id:B6d2f1 gn-term:strainOfSpecies gn-id:Mus_musculus . -gn-id:B6d2f1 gn-term:name "B6D2F1" . -gn-id:B6d2f1 gn-term:name2 "B6D2F1" . +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" . ``` ## 'dump-mapping-method' -## Schema Triples: -```text -``` ## Generated Triples: The following SQL query was executed: @@ -129,19 +111,19 @@ SELECT MappingMethod.Name FROM MappingMethod The above query results to triples that have the form: ```text -gn-id:mappingMethod_mappingmethod_name -> rdf:type -> gn-id:mappingMethod +gn:mappingMethod_mappingmethod_name -> rdf:type -> gn:mappingMethod ``` Here's an example query: ```sparql -@prefix gn-id: <http://genenetwork.org/terms/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +@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 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-id:mappingMethod . + ?s rdf:type gn:mappingMethod . ?s ?p ?o . } ``` @@ -149,17 +131,13 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn-id:mappingMethod_qtlreaper rdf:type gn-id:mappingMethod . +gn:mappingMethod_qtlreaper rdf:type gn:mappingMethod . ``` ## 'dump-avg-method' -## Schema Triples: -```text -gn-term:normalization -> rdfs:range -> rdfs:Literal -``` ## Generated Triples: The following SQL query was executed: @@ -171,20 +149,20 @@ SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod The above query results to triples that have the form: ```text -gn-id:avgmethod_avgmethod_name -> rdf:type -> gn-id:avgMethod -gn-id:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization) +gn:avgmethod_avgmethod_name -> rdf:type -> gn:avgMethod +gn:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization) ``` Here's an example query: ```sparql -@prefix gn-id: <http://genenetwork.org/terms/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +@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 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-id:avgMethod . + ?s rdf:type gn:avgMethod . ?s gn-term:normalization "MAS5" . ?s ?p ?o . } @@ -193,7 +171,7 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn-id:avgmethod_mas5 rdf:type gn-id:avgMethod . -gn-id:avgmethod_mas5 gn-term:normalization "MAS5" . +gn:avgmethod_mas5 rdf:type gn:avgMethod . +gn:avgmethod_mas5 gn-term:normalization "MAS5" . ``` |