From 2837094f7d9240a837a867bed253cf333d44ee13 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 31 Jul 2023 16:12:55 +0300 Subject: Update how strains are modelled Signed-off-by: Munyoki Kilyungi --- examples/dump-species-metadata.scm | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index 292c0cf..bebd329 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -51,11 +51,10 @@ (tables (Strain (left-join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples - (gnt:strainOfSpecies rdfs:domain gnt:strain) - (gnt:strainOfSpecies rdfs:range gn-term:species) - (gn-term:name rdfs:range rdfs:Literal) - (gn-term:alias rdfs:range rdfs:Literal) - (gn-term:symbol rdfs:range rdfs:Literal)) + (gnc:strain rdf:subClassOf gnc:species) + (gnt:species rdfs:domain gnc:strain) + (gnt:alias rdfs:range gnc:strain) + (gnt:symbol rdfs:range gnc:strain)) (triples (string->identifier "" (regexp-substitute/global @@ -65,13 +64,15 @@ #:separator "" #:proc string-capitalize-first) (set rdf:type 'gnc:strain) - (set gn-term:strainOfSpecies - (string->binomial-name (field Species FullName))) + (set gnt:species + (string->identifier "" (remap-species-identifiers (field Species Fullname)) + #:separator "" + #:proc string-capitalize-first)) ;; Name, and maybe a second name - (set gn-term:name (sanitize-rdf-string (field Strain Name))) - (set gn-term:name2 (sanitize-rdf-string (field Strain Name2))) - (set gn-term:alias (sanitize-rdf-string (field Strain Alias))) - (set gn-term:symbol (field Strain Symbol)))) + (set rdfs:label (sanitize-rdf-string (field Strain Name))) + (set rdfs:label (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2)))) + (set gnt:alias (sanitize-rdf-string (field Strain Alias))) + (set gnt:symbol (field Strain Symbol)))) (define-dump dump-mapping-method (tables (MappingMethod)) -- cgit v1.2.3