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2023-12-22Update handling of RGD_ID field in genelist metadata transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Refactor gene metadata RDF transform.Munyoki Kilyungi
In the case of the GeneList_rn33 table, the table id is used, since there is no other way to uniquely identify a gene using the other fields. See the following for more details: https://issues.genenetwork.org/issues/transform-genelist-to-rdf Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Replace gnc:GeneSymbol with gnc:Gene.Munyoki Kilyungi
A GeneSymbol != Gene. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Use gnt:geneSymbol instead of rdfs:label/gnt:symbol.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Use gnt:hasGeneId instead of gnt:gene/dct:references.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Move gnt:hasGeneId definitions to genelist.scmMunyoki Kilyungi
* examples/generif.scm: Move definitions for gnt:hasGeneId from here to... * examples/genelist.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Preserve gene symbol case when used as an identifer.Munyoki Kilyungi
Genes with varying casing (e.g., Shh, SHH) result in `string->identifier` capitalizing the first letter by default. This creates inconsistencies in gene symbols, leading to different predicates and objects for the same entity, introducing errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Trim gene symbol rdfs:label for the GeneList_rn33 table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Use URI encoding for symbol-based resource link URLs.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Link extra resources to genes and trim gene symbols.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Add GeneList metadata RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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