diff options
| author | Munyoki Kilyungi | 2023-12-15 21:31:43 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-12-15 21:32:19 +0300 |
| commit | 56d09222742cbff7767ff5ff9e794b81101ef7a7 (patch) | |
| tree | ebd4aae64c79ed250566dc16e7ef97a03d9121e3 | |
| parent | 8ef04f4a3a1696fa976945f4977aee749a8cfdbc (diff) | |
| download | gn-transform-databases-56d09222742cbff7767ff5ff9e794b81101ef7a7.tar.gz | |
Refactor Uniprot and GeneId handling in ProbeSet RDF transform.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rwxr-xr-x | examples/probeset.scm | 23 |
1 files changed, 9 insertions, 14 deletions
diff --git a/examples/probeset.scm b/examples/probeset.scm index 7775aa6..7a304ab 100755 --- a/examples/probeset.scm +++ b/examples/probeset.scm @@ -3,6 +3,7 @@ (use-modules (srfi srfi-1) (srfi srfi-26) + (ice-9 format) (ice-9 getopt-long) (ice-9 match) (ice-9 regex) @@ -23,9 +24,9 @@ (gnc:homologeneLink rdfs:Class gnc:ResourceLink) (gnc:homologeneLink rdfs:label "HomoloGene") (gnc:homologeneLink rdfs:comments "Find similar genes in other species") - (gnc:uniprotLink rdfs:Class gnc:ResourceLink) - (gnc:uniprotLink rdfs:label "UniProt") - (gnc:uniprotLink rdfs:comments "UniProt") + (gnc:uniprot a owl:ObjectProperty) + (gnc:uniprot rdfs:label "UniProt") + (gnc:uniprot rdfs:comments "UniProt resource") (gnt:hasChip a owl:ObjectProperty) (gnt:hasChip rdfs:domain gnc:Probeset) (gnt:hasTargetId a owl:ObjectProperty) @@ -114,6 +115,9 @@ ((string=? "-" strand-probe) " on the minus strand") (else ""))))))) + (set dct:references + (ontology 'gene: + (string-trim-both (field ProbeSet GeneId)))) ;; OMIM Link (set dct:references (let ((omim (field ProbeSet OMIM))) @@ -136,17 +140,8 @@ homologene "a gnc:homologeneLink")) ""))) - ;; UniProt Link - (set dct:references - (let ((uniprot (field ProbeSet UniProtID))) - (if (not (string-blank? uniprot)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "https://www.uniprot.org/uniprot/" - uniprot - "a gnc:uniprotLink")) - ""))) + (set gnt:uniprot + (ontology 'uniprot: (field ProbeSet UniProtID))) (set gnt:strandProbe (field ProbeSet Strand_Probe)) (set gnt:hasSpecificity |