diff options
Diffstat (limited to 'examples/dump-species-metadata.scm')
| -rwxr-xr-x | examples/dump-species-metadata.scm | 39 |
1 files changed, 19 insertions, 20 deletions
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index a6be89a..5c9ef49 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -31,27 +31,25 @@ (define-dump dump-species (tables (Species)) (schema-triples - (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)) + (gnt:name rdfs:range rdfs:Literal) + (gnt:displayName rdfs:range rdfs:Literal) + (gnt:binomialName rdfs:range rdfs:Literal) + (gnt:family rdfs:range rdfs:Literal)) (triples - (string->identifier "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gn:species) - (set gn-term:name (field Species SpeciesName)) - (set gn-term:displayName (field Species MenuName)) - (set gn-term:binomialName (remap-species-identifiers (field Species FullName))) - (set gn-term:family (field Species Family)) - (set gn-term:organism (ontology 'taxon: (field Species TaxonomyId))))) + (string->binomial-name (field Species FullName)) + (set rdf:type 'gnc:species) + (set gnt:name (field Species SpeciesName)) + (set gnt:displayName (field Species MenuName)) + (set gnt:binomialName (field Species FullName)) + (set gnt:family (field Species Family)) + (set gnt:organism (ontology 'taxon: (field Species TaxonomyId))))) (define-dump dump-strain (tables (Strain (left-join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples - (gn-term:strainOfSpecies rdfs:domain gn-term:strain) - (gn-term:strainOfSpecies rdfs:range gn-term:species) + (gnt:strainOfSpecies rdfs:domain gnt:strain) + (gnt: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)) @@ -63,7 +61,7 @@ 'pre "_" 'post) #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gn:strain) + (set rdf:type 'gnc:strain) (set gn-term:strainOfSpecies (string->identifier "" (remap-species-identifiers (field Species FullName)) #:separator "" @@ -78,7 +76,7 @@ (tables (MappingMethod)) (triples (string->identifier "mappingMethod" (field MappingMethod Name)) - (set rdf:type 'gn:mappingMethod))) + (set rdf:type 'gnc:mappingMethod))) (define-dump dump-inbred-set (tables (InbredSet @@ -99,7 +97,7 @@ "" (field InbredSet Name) #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gn:inbredSet) + (set rdf:type 'gnc:inbredSet) (set gn-term:binomialName (field InbredSet FullName)) (set gn-term:geneticType (field InbredSet GeneticType)) (set gn-term:inbredFamily (field InbredSet Family)) @@ -120,7 +118,7 @@ (schema-triples (gn-term:normalization rdfs:range rdfs:Literal)) (triples (string->identifier "avgmethod" (field AvgMethod Name)) - (set rdf:type 'gn:avgMethod) + (set rdf:type 'gnc:avgMethod) (set gn-term:normalization (field AvgMethod Normalization)))) @@ -131,7 +129,8 @@ (table-metadata? #f) (prefixes '(("gn:" "<http://genenetwork.org/id/>") - ("gn-term:" "<http://genenetwork.org/term/>") + ("gnc:" "<http://genenetwork.org/category/>") + ("gnt:" "<http://genenetwork.org/term/>") ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") ("taxon:" "<http://purl.uniprot.org/taxonomy/>"))) |