From 1ca7e679b834ccaf53a3243d0e1c2f3f9e8d56d8 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 23 Dec 2025 12:06:06 +0300 Subject: Snake case gn/gnt/gnc identifiers. Signed-off-by: Munyoki Kilyungi --- examples/genbank.scm | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) (limited to 'examples/genbank.scm') diff --git a/examples/genbank.scm b/examples/genbank.scm index c83643c..7aae5ba 100755 --- a/examples/genbank.scm +++ b/examples/genbank.scm @@ -14,30 +14,20 @@ -(define (remap-species-identifiers str) - "This procedure remaps identifiers to standard binominal. Obviously this should - be sorted by correcting the database!" - (match str - ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"] - ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"] - ["Macaca mulatta" "Macaca nemestrina"] - ["Bat (Glossophaga soricina)" "Glossophaga soricina"] - [str str])) - (define-transformer genbank (tables (Genbank (left-join Species "USING (SpeciesId)"))) (schema-triples (gnc:nucleotide a skos:Concept) - (gnt:hasSequence rdfs:domain gnc:nucleotide)) + (gnt:has_sequence rdfs:domain gnc:nucleotide)) (triples (ontology 'genbank: (field Genbank Id)) - (set gnt:hasSequence (field Genbank Sequence)) - (set gnt:belongsToSpecies + (set gnt:has_sequence (field Genbank Sequence)) + (set gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first)))) + #:separator "_" + #:proc string-downcase)))) -- cgit 1.4.1