diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-dataset-metadata.scm | 7 | ||||
| -rwxr-xr-x | examples/dump-genotype.scm | 6 | ||||
| -rwxr-xr-x | examples/dump-phenotype.scm | 4 | ||||
| -rwxr-xr-x | examples/dump-probesetfreeze.scm | 7 |
4 files changed, 15 insertions, 9 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index 3d2e1f9..e099bac 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -73,8 +73,9 @@ "WHERE GN_AccesionId IS NOT NULL") (schema-triples (gnc:dataset rdf:type gdmt:Dataset) - (gnc:genotype rdfs:subClassOf gnc:dataset) - (gnc:phenotype rdfs:subClassOf gnc:dataset) + (gnc:genotypeDataset rdfs:subClassOf gnc:dataset) + (gnc:phenotypeDataset rdfs:subClassOf gnc:dataset) + (gnc:probesetDataset rdfs:subClassOf gnc:dataset) (gnt:belongsToInbredSet rdfs:domain gnc:dataset) (gnt:belongsToInbredSet a owl:ObjectProperty) (gnt:belongsToInbredSet skos:definition "The InbredSet this resource belongs to") @@ -124,7 +125,7 @@ #:separator "" #:proc string-capitalize-first) (set rdf:type (string->symbol - (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotype', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotype', 'gnc:dataset'))" + (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotypeDataset', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:probesetDataset', 'gnc:dataset')))" rdfType)))) (set rdfs:label (regexp-substitute/global #f "^[Nn]one$" diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm index 4ac836d..ed23e80 100755 --- a/examples/dump-genotype.scm +++ b/examples/dump-genotype.scm @@ -37,7 +37,7 @@ 'pre "_" 'post) #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gnc:genotype) + (set rdf:type 'gnc:genotypeDataset) (set rdfs:label (field GenoFreeze Name)) (set skos:prefLabel (field GenoFreeze FullName)) (set skos:altLabel (field GenoFreeze ShortName)) @@ -54,6 +54,10 @@ (left-join InbredSet "ON InbredSet.InbredSetId = GenoFreeze.InbredSetId") (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name"))) (schema-triples + (gnc:genotype a skos:Concept) + (gnc:genotype + skos:description + "This is a set of controlled terms that are used to describe a given genotype") (gnt:chr a owl:ObjectProperty) (gnt:chr skos:description "This resource is located on a given chromosome") (gnt:chr rdfs:domain gnc:genotype) diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index f73f19f..ed10b24 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -34,7 +34,7 @@ 'pre "_" 'post) #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gnc:phenotype) + (set rdf:type 'gnc:phenotypeDataset) (set rdfs:label (field PublishFreeze Name)) (set skos:prefLabel (field PublishFreeze FullName)) (set skos:altLabel (field PublishFreeze ShortName)) @@ -59,6 +59,8 @@ ;; I.e. traits that have no associated vectors "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL") (schema-triples + (gnc:phenotype a skos:Concept) + (gnc:phenotype skos:description "This is a set of controlled terms that are used to describe a given phenotype") (gnt:abbreviation a owl:ObjectProperty) (gnt:abbreviation rdfs:domain gnc:phenotype) (gnt:abbreviation skos:definition "The abbreviation used for this resource") diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm index 86e614d..f528139 100755 --- a/examples/dump-probesetfreeze.scm +++ b/examples/dump-probesetfreeze.scm @@ -69,7 +69,6 @@ (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId")) "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id") (schema-triples - (gnc:probeset rdfs:subClassOf gnc:dataset) (gnt:usesNormalization rdfs:domain gnc:probeset) (gnt:usesDataScale rdfs:domain gnc:probeset) (gnt:usesDataScale a owl:ObjectProperty) @@ -83,16 +82,16 @@ 'pre "_" 'post) #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gnc:probeset) + (set rdf:type 'gnc:probesetDataset) (set gnt:usesNormalization (string->identifier "avgmethod" ;; If AvgMethodName is NULL, assume N/A. (if (string-blank? (field AvgMethod Name AvgMethodName)) "N/A" (field AvgMethod Name AvgMethodName)))) (set dct:title (field ProbeSetFreeze FullName)) - (set rdfs:label (field ProbeSetFreeze Name)) + (set rdfs:label (field ProbeSetFreeze ShortName)) + (set skos:prefLabel (field ProbeSetFreeze Name)) (set skos:altLabel (field ProbeSetFreeze Name2)) - (set skos:prefLabel (field ProbeSetFreeze ShortName)) (set dct:created (annotate-field (field ProbeSetFreeze CreateTime) '^^xsd:datetime)) |