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authorMunyoki Kilyungi2023-08-23 18:00:04 +0300
committerMunyoki Kilyungi2023-08-23 18:02:20 +0300
commit7998f8f2341e0acc1667b75ef899e84894e93720 (patch)
treecd1d41d4706446f8c783ebb72c96b74f60b0fc8b /examples
parent824552578284b94d37cc5bfcf7f8f0b85ac29fe5 (diff)
downloadgn-transform-databases-7998f8f2341e0acc1667b75ef899e84894e93720.tar.gz
Update how symbols from GeneRIF_BASIC are transformed
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples')
-rwxr-xr-xexamples/generif.scm16
1 files changed, 9 insertions, 7 deletions
diff --git a/examples/generif.scm b/examples/generif.scm
index d25b0f1..d6b8b25 100755
--- a/examples/generif.scm
+++ b/examples/generif.scm
@@ -46,19 +46,21 @@
(left-join Species "USING (SpeciesId)"))
"GROUP BY GeneId ORDER BY BINARY symbol")
(schema-triples
- (gnt:symbol rdfs:domain gn-term:geneWikiEntry)
- (gnt:wikiEntryOfSpecies rdfs:range gn:species)
- (gnt:taxid rdfs:domain gn-term:geneWikiEntry))
+ (gnt:belongsToSpecies rdfs:domain gnc:strain)
+ (gnt:belongsToSpecies rdfs:domain gnc:NCBIWikiEntry)
+ (gnt:symbol rdfs:domain gnc:NCBIWikiEntry))
(triples (ontology 'generif: (field GeneRIF_BASIC GeneId))
(multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol))
#\,))
- (multiset gnt:wikiEntryOfSpecies
+ (multiset gnt:belongsToSpecies
(string-split
(field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species))
#\,))
- (multiset gnt:taxId (map (cut ontology 'ncbiTaxon: <>)
- (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
- #\,)))))
+ (multiset dct:relation
+ (map
+ (cut ontology 'ncbiTaxon: <>)
+ (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId))
+ #\,)))))
(define-transformer gn-genewiki-entries
(tables (GeneRIF