diff options
| author | Munyoki Kilyungi | 2023-07-18 16:18:54 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-07-21 14:36:40 +0300 |
| commit | fe4355cc0ea5c0adb4eca5a8094b6793ede9f699 (patch) | |
| tree | 9c550c6ff080f075405484810e79fbbd86acf358 /examples | |
| parent | fb281f2c835907ee061b12cc58f4d2a96133dbc7 (diff) | |
| download | gn-transform-databases-fe4355cc0ea5c0adb4eca5a8094b6793ede9f699.tar.gz | |
Capitalize species identifier
Replace gn:species_mus_musculus with gn:species:Mus_musculus.
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-species-metadata.scm | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index 4ea9ce7..898aa5a 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -25,7 +25,11 @@ (gn:displayName rdfs:range rdfs:Literal) (gn:binomialName rdfs:range rdfs:Literal) (gn:family rdfs:range rdfs:Literal)) - (triples (string->identifier "species" (field Species FullName)) + (triples + (string->identifier "" (field Species FullName) + #:ontology "gn:species:" + #:separator "" + #:proc string-capitalize-first) (set rdf:type 'gn:species) (set gn:name (field Species SpeciesName)) (set gn:displayName (field Species MenuName)) @@ -50,7 +54,10 @@ 'pre "_" 'post)) (set rdf:type 'gn:strain) (set gn:strainOfSpecies - (string->identifier "species" (field Species FullName))) + (string->identifier "" (field Species FullName) + #:ontology "gn:species:" + #:separator "" + #:proc string-capitalize-first)) ;; Name, and maybe a second name (set gn:name (sanitize-rdf-string (field Strain Name))) (set gn:name (sanitize-rdf-string (field Strain Name2))) @@ -85,7 +92,10 @@ (set gn:inbredSetOfMappingMethod (field MappingMethod Name)) (set gn:inbredSetCode (field InbredSet InbredSetCode)) (set gn:inbredSetOfSpecies - (string->identifier "species" (field Species FullName BinomialName))) + (string->identifier "" (field Species FullName BinomialName) + #:ontology "gn:species:" + #:separator "" + #:proc string-capitalize-first)) (set gn:genotype (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP))) (set gn:phenotype |