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2024-01-05Correct formatting for the gnt:location predicate for ProbeSets.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>
2023-12-15Preserve 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>
2023-12-15Use URI encoding for OMIM and homologene resource link handling.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Refactor Uniprot and GeneId handling in ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Add missing "gene:" prefix in ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Remove some resource links from ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22"Add special-case for blank Chr field".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Construct URIs for external data in RDF ProbeSet transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add extra joins for GeneList and GeneList_rn33.Munyoki Kilyungi
These tables are referenced when constructing URIs for mouse and rat data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Delete some RDF prefixes when transforming ProbeSet metadata.Munyoki Kilyungi
External resources are explicitly defined so we don't need these prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Remove unused properties during ProbeSet RDF transform.Munyoki Kilyungi
The removed terms are actually used when constructing terms. Most of this values are NULL anyways. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add Species join when during RDF ProbeSet transform.Munyoki Kilyungi
We add the species join since when constructing resource links, this table is required. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Add extra gnt:location term when transforming ProbeSet metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Add strand position when transforming ProbeSet metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Delete un-necessary predicates from ProbeSet transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Add qb: and sdmx-measure: prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Replace gnc:probeset with gnc:ProbesetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Remove hard-coded pathsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Rename dump -> transformMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Remove "dump-" prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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