diff options
Diffstat (limited to 'examples/genotype.scm')
| -rwxr-xr-x | examples/genotype.scm | 61 |
1 files changed, 30 insertions, 31 deletions
diff --git a/examples/genotype.scm b/examples/genotype.scm index 7e72cf8..257a3fa 100755 --- a/examples/genotype.scm +++ b/examples/genotype.scm @@ -21,30 +21,30 @@ (schema-triples (gnt:chr a owl:ObjectProperty) (gnt:chr skos:description "This resource is located on a given chromosome") - (gnt:chr rdfs:domain gnc:Genotype) + (gnt:chr rdfs:domain gnc:genotype) (gnt:mb a owl:ObjectProperty) (gnt:mb skos:definition "The size of this resource in Mb") - (gnt:mb rdfs:domain gnc:Genotype) - (gnt:mbMm8 a owl:ObjectProperty) - (gnt:mbMm8 skos:definition "TODO") - (gnt:mbMm8 rdfs:domain gnc:Genotype) + (gnt:mb rdfs:domain gnc:genotype) + (gnt:mb_mm8 a owl:ObjectProperty) + (gnt:mb_mm8 skos:definition "TODO") + (gnt:mb_mm8 rdfs:domain gnc:genotype) (gnt:mb2016 a owl:ObjectProperty) (gnt:mb2016 skos:definition "TODO") - (gnt:mb2016 rdfs:domain gnc:Genotype) - (gnt:hasSequence a owl:ObjectProperty) - (gnt:hasSequence skos:definition "This resource has a given sequence") - (gnt:hasSequence rdfs:domain gnc:Genotype) - (gnt:hasSource a owl:ObjectProperty) - (gnt:hasSource rdfs:domain gnc:Genotype) - (gnt:hasSource skos:definition "This resource was obtained from this given source") - (gnt:hasAltSourceName a owl:ObjectProperty) - (gnt:hasAltSourceName rdfs:domain gnc:Genotype) - (gnt:hasAltSourceName + (gnt:mb2016 rdfs:domain gnc:genotype) + (gnt:has_sequence a owl:ObjectProperty) + (gnt:has_sequence skos:definition "This resource has a given sequence") + (gnt:has_sequence rdfs:domain gnc:genotype) + (gnt:has_source a owl:ObjectProperty) + (gnt:has_source rdfs:domain gnc:genotype) + (gnt:has_source skos:definition "This resource was obtained from this given source") + (gnt:has_alt_source_name a owl:ObjectProperty) + (gnt:has_alt_source_name rdfs:domain gnc:genotype) + (gnt:has_alt_source_name skos:definition "The alternative name this resource was obtained from") - (gnt:chrNum a owl:ObjectProperty) - (gnt:chrNum rdfs:domain gnc:Genotype) - (gnt:chrNum skos:definition "The chromosome number for this resource")) + (gnt:chr_num a owl:ObjectProperty) + (gnt:chr_num rdfs:domain gnc:genotype) + (gnt:chr_num skos:definition "The chromosome number for this resource")) (triples (string->identifier "" @@ -52,30 +52,29 @@ #f "[^A-Za-z0-9:]" (field Geno Name) 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:Genotype) + #:separator "_" + #:proc (lambda (x) x)) + (set rdf:type 'gnc:genotype) (set rdfs:label (sanitize-rdf-string (field Geno Name))) (set gnt:chr (field Geno Chr)) (set gnt:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double)) - (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8)) + (set gnt:mb_mm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8)) '^^xsd:double)) (set gnt:mb2016 (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016)) '^^xsd:double)) - (set gnt:hasSequence (field Geno Sequence)) - (set gnt:hasSource (field Geno Source)) + (set gnt:has_sequence (field Geno Sequence)) + (set gnt:has_source (field Geno Source)) ;; Only transform Source2 if it differs from Source - (set gnt:hasAltSourceName + (set gnt:has_alt_source_name (field ("IF((Source2 = Source), NULL, Source2)" Source2))) - (set gnt:belongsToSpecies - (string->identifier - "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first)) - (set gnt:chrNum + (set gnt:belongs_to_species + (string->identifier "" (remap-species-identifiers (field Species Fullname)) + #:separator "_" + #:proc string-downcase)) + (set gnt:chr_num (annotate-field (field Geno chr_num) '^^xsd:int)) |