diff options
Diffstat (limited to 'examples/phenotype.scm')
| -rwxr-xr-x | examples/phenotype.scm | 64 |
1 files changed, 28 insertions, 36 deletions
diff --git a/examples/phenotype.scm b/examples/phenotype.scm index aa1e9c5..ae24d66 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -20,50 +20,50 @@ (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 "_") + (set rdf:type 'gnc:phenotype) + (set gnt:belongs_to_group (string->identifier "set" (field InbredSet Name InbredSetName) - #:separator "" - #:proc string-capitalize-first)) + #:separator "_")) ;; 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) @@ -83,16 +83,8 @@ (set dct:contributor (sanitize-rdf-string (field Phenotype Owner))) (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean)) '^^xsd:double)) - (set gnt:locus - (string->identifier - "" - (regexp-substitute/global - #f "[^A-Za-z0-9:]" - (sanitize-rdf-string (field PublishXRef Locus)) - 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first)) - (set gnt:lodScore (annotate-field + (set gnt:locus (sanitize-rdf-string (field PublishXRef Locus))) + (set gnt:lod_score (annotate-field (field ("IFNULL((PublishXRef.LRS/4.604), '')" lrs)) '^^xsd:double)) (set gnt:additive @@ -128,10 +120,10 @@ (table-metadata? #f) (prefixes '(("dct:" "<http://purl.org/dc/terms/>") - ("gn:" "<http://genenetwork.org/id/>") + ("gn:" "<http://rdf.genenetwork.org/v1/id/>") ("owl:" "<http://www.w3.org/2002/07/owl#>") - ("gnc:" "<http://genenetwork.org/category/>") - ("gnt:" "<http://genenetwork.org/term/>") + ("gnc:" "<http://rdf.genenetwork.org/v1/category/>") + ("gnt:" "<http://rdf.genenetwork.org/v1/term/>") ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>") ("skos:" "<http://www.w3.org/2004/02/skos/core#>") ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") |