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diff --git a/rdf-documentation/classification.md b/rdf-documentation/classification.md new file mode 100644 index 0000000..4c1ae45 --- /dev/null +++ b/rdf-documentation/classification.md @@ -0,0 +1,194 @@ +# Species Metadata +## 'classification-scheme-species' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT Species.Fullname FROM Species +``` + +The above query results to triples that have the form: + +```text +gnc:Species -> skos:member -> gn:Species_fullname +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> +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 * WHERE { + ?s skos:member gn:Mus_musculus . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gnc:Species skos:member gn:Mus_musculus . +``` + + +## 'classification-scheme-set' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT InbredSet.Name AS InbredSetName FROM InbredSet +``` + +The above query results to triples that have the form: + +```text +gnc:Set -> skos:member -> gn:setInbredset_inbredsetname +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> +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 * WHERE { + ?s skos:member gn:setBxd . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gnc:Set skos:member gn:setBxd . +``` + + +## 'species' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT Species.Fullname, Species.Fullname, Species.MenuName, Species.SpeciesName, Species.Name, Species.Family, Species.TaxonomyId FROM Species +``` + +The above query results to triples that have the form: + +```text +gn:Species_fullname -> skos:inScheme -> gnc:ResourceClassificationScheme +gn:Species_fullname -> rdfs:label -> Species(Fullname) +gn:Species_fullname -> skos:prefLabel -> Species(MenuName) +gn:Species_fullname -> skos:altLabel -> Species(SpeciesName) +gn:Species_fullname -> gnt:shortName -> Species(Name) +gn:Species_fullname -> gnt:family -> Species(Family) +gn:Species_fullname -> skos:notation -> taxon:Species(TaxonomyId) +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> +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 * WHERE { + ?s skos:inScheme gnc:ResourceClassificationScheme . + ?s rdfs:label "Mus musculus" . + ?s skos:prefLabel "Mouse (Mus musculus, mm10)" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:Mus_musculus skos:inScheme gnc:ResourceClassificationScheme . +gn:Mus_musculus rdfs:label "Mus musculus" . +gn:Mus_musculus skos:prefLabel "Mouse (Mus musculus, mm10)" . +gn:Mus_musculus skos:altLabel "Mouse" . +gn:Mus_musculus gnt:shortName "mouse" . +gn:Mus_musculus gnt:family "Vertebrates" . +gn:Mus_musculus skos:notation taxon:10090 . +``` + + +## 'inbred-set' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT InbredSet.Name AS InbredSetName, InbredSet.FullName, InbredSet.Name AS InbredSetName, InbredSet.GeneticType, InbredSet.Family, MappingMethod.Name, InbredSet.InbredSetCode, Species.Fullname FROM InbredSet LEFT JOIN Species ON InbredSet.SpeciesId=Species.Id LEFT JOIN MappingMethod ON InbredSet.MappingMethodId=MappingMethod.Id +``` + +The above query results to triples that have the form: + +```text +gn:setInbredset_inbredsetname -> skos:inScheme -> gnc:ResourceClassificationScheme +gn:setInbredset_inbredsetname -> rdfs:label -> InbredSet(FullName) +gn:setInbredset_inbredsetname -> skos:prefLabel -> InbredSet(InbredSetName) +gn:setInbredset_inbredsetname -> gnt:geneticType -> InbredSet(GeneticType) +gn:setInbredset_inbredsetname -> gnt:family -> InbredSet(Family) +gn:setInbredset_inbredsetname -> gnt:mappingMethod -> MappingMethod(Name) +gn:setInbredset_inbredsetname -> gnt:code -> InbredSet(InbredSetCode) +gn:setInbredset_inbredsetname -> xkos:generalizes -> gn:Species_fullname +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> +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 * WHERE { + ?s skos:inScheme gnc:ResourceClassificationScheme . + ?s rdfs:label "BXD Family" . + ?s skos:prefLabel "BXD" . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:setBxd skos:inScheme gnc:ResourceClassificationScheme . +gn:setBxd rdfs:label "BXD Family" . +gn:setBxd skos:prefLabel "BXD" . +gn:setBxd gnt:geneticType "riset" . +gn:setBxd gnt:family "Reference Populations (replicate average, SE, N)" . +gn:setBxd gnt:mappingMethod "qtlreaper" . +gn:setBxd gnt:code "BXD" . +gn:setBxd xkos:generalizes gn:Mus_musculus . +``` + |