diff options
| -rwxr-xr-x | examples/dump-species-metadata.scm | 48 |
1 files changed, 26 insertions, 22 deletions
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index bebd329..c68d205 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -76,9 +76,12 @@ (define-dump dump-mapping-method (tables (MappingMethod)) + (schema-triples + (gnc:mappingMethod rdf:type owl:Class)) (triples (string->identifier "mappingMethod" (field MappingMethod Name)) - (set rdf:type 'gnc:mappingMethod))) + (set rdf:type 'gnc:mappingMethod) + (set rdfs:label (field MappingMethod Name)))) (define-dump dump-inbred-set (tables (InbredSet @@ -86,31 +89,31 @@ (left-join MappingMethod "ON InbredSet.MappingMethodId=MappingMethod.Id"))) (schema-triples - (gn-term:fullName rdfs:range rdfs:Literal) - (gn-term:geneticType rdfs:range rdfs:Literal) - (gn-term:inbredSetCode rdfs:range rdfs:Literal) - (gn-term:inbredFamily rdfs:range rdfs:Literal) - (gn-term:inbredSetOfSpecies rdfs:range gn:species) - (gn-term:inbredSetType rdfs:range rdfs:Literal) - (gn-term:phenotype rdfs:range gn-term:inbredSetType) - (gn-term:genotype rdfs:range gn-term:inbredSetType) - (gn-term:inbredSetOfMappingMethod rdfs:range gn-term:mappingMethod)) + (gnc:inbredSet rdf:subClassOf gnc:species) + (gnt:geneticType rdfs:domain gnc:inbredSet) + (gnt:code rdfs:domain gnc:inbredSet) + (gnt:family rdfs:domain gnc:inbredSet) + (gnt:type rdfs:domain gnc:inbredSet) + (gnt:phenotype rdfs:domain gnc:inbredSet) + (gnt:genotype rdfs:domain gnt:inbredSet) + (gnt:mappingMethod rdfs:domain gnc:inbredSet)) (triples (string->identifier "" (field InbredSet Name) #:separator "" #:proc string-capitalize-first) (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)) - (set gn-term:inbredSetOfMappingMethod (field MappingMethod Name)) - (set gn-term:inbredSetCode (field InbredSet InbredSetCode)) - (set gn-term:inbredSetOfSpecies - (string->binomial-name - (field Species FullName BinomialName))) - (set gn-term:genotype + (set rdfs:label (field InbredSet FullName)) + (set gnt:geneticType (field InbredSet GeneticType)) + (set gnt:inbredFamily (field InbredSet Family)) + (set gnt:inbredSetOfMappingMethod (field MappingMethod Name)) + (set gnt:inbredSetCode (field InbredSet InbredSetCode)) + (set gnt:species + (string->identifier "" (remap-species-identifiers (field Species Fullname)) + #:separator "" + #:proc string-capitalize-first)) + (set gnt:genotype (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP))) - (set gn-term:phenotype + (set gnt:phenotype (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP))))) (define-dump dump-avg-method @@ -118,10 +121,10 @@ ;; the Name field. (tables (AvgMethod)) (schema-triples - (gn-term:normalization rdfs:range rdfs:Literal)) + (gnc:avgMethod rdf:type owl:Class)) (triples (string->identifier "avgmethod" (field AvgMethod Name)) (set rdf:type 'gnc:avgMethod) - (set gn-term:normalization (field AvgMethod Normalization)))) + (set rdfs:label (field AvgMethod Normalization)))) @@ -132,6 +135,7 @@ (prefixes '(("gn:" "<http://genenetwork.org/id/>") ("gnc:" "<http://genenetwork.org/category/>") + ("owl:" "<http://www.w3.org/2002/07/owl#>") ("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#>") |