diff options
Diffstat (limited to 'examples/phenotype.scm')
| -rwxr-xr-x | examples/phenotype.scm | 48 |
1 files changed, 25 insertions, 23 deletions
diff --git a/examples/phenotype.scm b/examples/phenotype.scm index aa1e9c5..1bec264 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -20,50 +20,52 @@ (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))) (schema-triples - (gnt:traitId a owl:ObjectProperty) - (gnt:traitId rdfs:domain gnc:Phenotype) - (gnt:traitId skos:definition "This is the unique trait id assigned from GeneNetwork") + (gnt:trait_id a owl:ObjectProperty) + (gnt:trait_id rdfs:domain gnc:phenotype) + (gnt:trait_id skos:definition "This is the unique trait id assigned from GeneNetwork") (gnt:abbreviation a owl:ObjectProperty) - (gnt:abbreviation rdfs:domain gnc:Phenotype) + (gnt:abbreviation rdfs:domain gnc:phenotype) (gnt:abbreviation skos:definition "The abbreviation used for this resource") (gnt:labCode a owl:ObjectProperty) - (gnt:labCode rdfs:domain gnc:Phenotype) + (gnt:labCode rdfs:domain gnc:phenotype) (gnt:submitter a owl:ObjectProperty) - (gnt:submitter rdfs:domain gnc:Phenotype) + (gnt:submitter rdfs:domain gnc:phenotype) (gnt:submitter skos:definition "A person who submitted this resource to GN") (gnt:mean a rdf:Property) (gnt:mean a qb:MeasureProperty) (gnt:mean rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:mean rdfs:domain gnc:Phenotype) + (gnt:mean rdfs:domain gnc:phenotype) (gnt:mean rdfs:range xsd:double) - (gnt:lodScore a rdf:Property) - (gnt:lodScore a qb:MeasureProperty) - (gnt:lodScore rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:lodScore rdfs:domain gnc:Phenotype) - (gnt:lodScore rdfs:range xsd:double) - (gnt:lodScore rdfs:label "Peak -logP") - (gnt:lodScore skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.") + (gnt:lod_score a rdf:Property) + (gnt:lod_score a qb:MeasureProperty) + (gnt:lod_score rdfs:subPropertyOf sdmx-measure:obsValue) + (gnt:lod_score rdfs:domain gnc:phenotype) + (gnt:lod_score rdfs:range xsd:double) + (gnt:lod_score rdfs:label "Peak -logP") + (gnt:lod_score skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.") (gnt:locus a rdf:Property) (gnt:locus a qb:MeasureProperty) (gnt:locus rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:locus rdfs:domain gnc:Phenotype) + (gnt:locus rdfs:domain gnc:phenotype) (gnt:locus rdfs:range rdfs:Literal) - (gnt:additive rdfs:domain gnc:Phenotype) + (gnt:additive rdfs:domain gnc:phenotype) (gnt:additive rdfs:range xsd:double) - (gnt:sequence rdfs:domain gnc:Phenotype) + (gnt:sequence rdfs:domain gnc:phenotype) (gnt:sequence rdfs:range xsd:integer)) (triples (string->identifier "trait" (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype))) - (set rdf:type 'gnc:Phenotype) - (set gnt:belongsToGroup + Phenotype)) + #:separator "_" + #:proc (lambda (x) x)) + (set rdf:type 'gnc:phenotype) + (set gnt:belongs_to_group (string->identifier "set" (field InbredSet Name InbredSetName) - #:separator "" + #:separator "_" #:proc string-capitalize-first)) ;; This is the trait's name - (set gnt:traitId + (set gnt:trait_id (let ((trait-id (field PublishXRef Id))) (if (number? trait-id) (number->string trait-id) @@ -92,7 +94,7 @@ 'pre "_" 'post) #:separator "" #:proc string-capitalize-first)) - (set gnt:lodScore (annotate-field + (set gnt:lod_score (annotate-field (field ("IFNULL((PublishXRef.LRS/4.604), '')" lrs)) '^^xsd:double)) (set gnt:additive |