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| author | Munyoki Kilyungi | 2023-12-19 19:12:50 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-12-22 11:53:22 +0300 |
| commit | da5aa39b9791e697fd84cf2d4f8c881bac55d67a (patch) | |
| tree | 41a5e83978131530c56e7c6c151e32d89556e417 | |
| parent | 203442c692f205dca37a9f32494e2e71907a58e6 (diff) | |
| download | gn-transform-databases-da5aa39b9791e697fd84cf2d4f8c881bac55d67a.tar.gz | |
Use gnt:geneSymbol instead of rdfs:label/gnt:symbol.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rwxr-xr-x | examples/genelist.scm | 4 | ||||
| -rwxr-xr-x | examples/probeset.scm | 10 |
2 files changed, 5 insertions, 9 deletions
diff --git a/examples/genelist.scm b/examples/genelist.scm index 78df9d7..2d94a3b 100755 --- a/examples/genelist.scm +++ b/examples/genelist.scm @@ -84,11 +84,11 @@ "gene" (regexp-substitute/global #f "[^A-Za-z0-9:]" (string-trim-both - (field GeneList GeneSymbol)) + (field ("CONCAT_WS('_', GeneSymbol, GeneID, AlignID)" GENE_UID))) 'pre "_" 'post) #:proc (lambda (x) x)) (set rdf:type 'gnc:GeneSymbol) - (set rdfs:label (field GeneList GeneSymbol)) + (set gnt:geneSymbol (field GeneList GeneSymbol)) (set dct:description (sanitize-rdf-string (field GeneList GeneDescription))) (set gnt:hasGeneId (ontology 'gene: (field GeneList GeneId))) (set dct:references diff --git a/examples/probeset.scm b/examples/probeset.scm index 0f83a86..c7efce7 100755 --- a/examples/probeset.scm +++ b/examples/probeset.scm @@ -33,7 +33,7 @@ (gnt:hasChip rdfs:domain gnc:Probeset) (gnt:hasTargetId a owl:ObjectProperty) (gnt:hasTargetId rdfs:domain gnc:Probeset) - (gnt:symbol rdfs:domain gnc:Probeset) + (gnt:geneSymbol rdfs:domain gnc:Probeset) (gnt:location rdfs:domain gnc:ProbeSet) (gnt:location a owl:ObjectProperty) (gnt:strandPosition rdfs:domain gnc:ProbeSet) @@ -79,12 +79,8 @@ (set gnt:hasTargetId (field ("NULLIF(TRIM(ProbeSet.TargetId), '')" TargetId))) - (set gnt:symbol - (string->identifier - "gene" (regexp-substitute/global #f "[^A-Za-z0-9:]" - (field ProbeSet Symbol) - 'pre "_" 'post) - #:proc (lambda (x) x))) + (set gnt:geneSymbol + (field ProbeSet Symbol)) (set dct:description (sanitize-rdf-string (field ProbeSet description))) (set gnt:targetsRegion (sanitize-rdf-string |