diff options
Diffstat (limited to 'rdf-documentation/dump-species-metadata.md')
| -rw-r--r-- | rdf-documentation/dump-species-metadata.md | 130 |
1 files changed, 68 insertions, 62 deletions
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md index 7c0f8be..ca09458 100644 --- a/rdf-documentation/dump-species-metadata.md +++ b/rdf-documentation/dump-species-metadata.md @@ -4,10 +4,10 @@ ## Schema Triples: ```text -gn:name -> rdfs:range -> rdfs:Literal -gn:displayName -> rdfs:range -> rdfs:Literal -gn:binomialName -> rdfs:range -> rdfs:Literal -gn:family -> rdfs:range -> rdfs:Literal +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: @@ -20,25 +20,26 @@ SELECT Species.FullName, Species.SpeciesName, Species.MenuName, Species.FullName The above query results to triples that have the form: ```text -gn:species_species_fullname_ -> rdf:type -> gn:species -gn:species_species_fullname_ -> gn:name -> Species(SpeciesName) -gn:species_species_fullname_ -> gn:displayName -> Species(MenuName) -gn:species_species_fullname_ -> gn:binomialName -> Species(FullName) -gn:species_species_fullname_ -> gn:family -> Species(Family) -gn:species_species_fullname_ -> gn:organism -> #{taxon:Species\x28;TaxonomyId\x29;}# +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) ``` Here's an example query: ```sparql -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX gn: <http://genenetwork.org/terms/> -PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +@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 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:name "Mouse" . - ?s gn:displayName "Mouse (Mus musculus, mm10)" . + ?s rdf:type gn-id:species . + ?s gn-term:name "Mouse" . + ?s gn-term:displayName "Mouse (Mus musculus, mm10)" . ?s ?p ?o . } ``` @@ -46,12 +47,12 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:species_mus_musculus rdf:type gn:species . -gn:species_mus_musculus gn:name "Mouse" . -gn:species_mus_musculus gn:displayName "Mouse (Mus musculus, mm10)" . -gn:species_mus_musculus gn:binomialName "Mus musculus" . -gn:species_mus_musculus gn:family "Vertebrates" . -gn:species_mus_musculus gn:organism taxon:10090 . +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 . ``` @@ -60,11 +61,11 @@ gn:species_mus_musculus gn:organism taxon:10090 . ## Schema Triples: ```text -gn:strainOfSpecies -> rdfs:domain -> gn:strain -gn:strainOfSpecies -> rdfs:range -> gn:species -gn:name -> rdfs:range -> rdfs:Literal -gn:alias -> rdfs:range -> rdfs:Literal -gn:symbol -> rdfs:range -> rdfs:Literal +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: @@ -77,25 +78,26 @@ 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:strain_strainname -> rdf:type -> gn:strain -gn:strain_strainname -> gn:strainOfSpecies -> gn:species_species_fullname_ -gn:strain_strainname -> gn:name -> StrainName -gn:strain_strainname -> gn:name -> StrainName2 -gn:strain_strainname -> gn:alias -> StrainAlias -gn:strain_strainname -> gn:symbol -> Strain(Symbol) +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) ``` Here's an example query: ```sparql -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX gn: <http://genenetwork.org/terms/> -PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +@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 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:strainOfSpecies gn:species_mus_musculus . - ?s gn:name "B6D2F1" . + ?s rdf:type gn-id:strain . + ?s gn-term:strainOfSpecies gn-id:Mus_musculus . + ?s gn-term:name "B6D2F1" . ?s ?p ?o . } ``` @@ -103,10 +105,10 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:strain_b6d2f1 rdf:type gn:strain . -gn:strain_b6d2f1 gn:strainOfSpecies gn:species_mus_musculus . -gn:strain_b6d2f1 gn:name "B6D2F1" . -gn:strain_b6d2f1 gn:name "B6D2F1" . +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" . ``` @@ -127,17 +129,19 @@ SELECT MappingMethod.Name FROM MappingMethod The above query results to triples that have the form: ```text -gn:mappingMethod_mappingmethod_name_ -> rdf:type -> gn:mappingMethod +gn-id:mappingMethod_mappingmethod_name -> rdf:type -> gn-id:mappingMethod ``` Here's an example query: ```sparql -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX gn: <http://genenetwork.org/terms/> -PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +@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 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 ?p ?o . } ``` @@ -145,7 +149,7 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:mappingMethod_qtlreaper rdf:type gn:mappingMethod . +gn-id:mappingMethod_qtlreaper rdf:type gn-id:mappingMethod . ``` @@ -154,32 +158,34 @@ gn:mappingMethod_qtlreaper rdf:type gn:mappingMethod . ## Schema Triples: ```text -gn:name -> rdfs:range -> rdfs:Literal +gn-term:normalization -> rdfs:range -> rdfs:Literal ``` ## Generated Triples: The following SQL query was executed: ```sql -SELECT AvgMethod.Name, AvgMethod.Name FROM AvgMethod +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:name -> AvgMethod(Name) +gn-id:avgmethod_avgmethod_name -> rdf:type -> gn-id:avgMethod +gn-id:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization) ``` Here's an example query: ```sparql -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX gn: <http://genenetwork.org/terms/> -PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +@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 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 rdf:type gn-id:avgMethod . + ?s gn-term:normalization "MAS5" . ?s ?p ?o . } ``` @@ -187,7 +193,7 @@ SELECT ?s ?p ?o WHERE { Expected Result: ```rdf -gn:avgmethod_mas5 rdf:type gn:avgMethod . -gn:avgmethod_mas5 gn:name "MAS5" . +gn-id:avgmethod_mas5 rdf:type gn-id:avgMethod . +gn-id:avgmethod_mas5 gn-term:normalization "MAS5" . ``` |