| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-12-15 | Use URI encoding for OMIM and homologene resource link handling. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Refactor Uniprot and GeneId handling in ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Add missing "gene:" prefix in ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Trim gene symbol rdfs:label for the GeneList_rn33 table. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Use URI encoding for symbol-based resource link URLs. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Remove "remap-species-identifiers" from generif transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Link extra resources to genes and trim gene symbols. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Refactor symbol identifier in strains.scm. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Add GeneList metadata RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Remove some resource links from ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Use correct identifier for the AvgMethod table. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiedUnder -> gnt:belongsToGroup. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiedUnder -> gnt:belongsToSpecies for species. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiendUnder with gnt:belongsToGroup for groups. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Fix typo in publishfreeze transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-30 | Trim the contributor's name when transforming phenotype metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-30 | Add a label to the "gnt:lodScore" term. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-30 | Set a phenotype's gnt:locus to a genotype. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-30 | Replace LRS with LOD Score. | Munyoki Kilyungi | |
| * examples/phenotype.scm (phenotypes): Replace gnt:LRS with gnt:lodScore. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-24 | Move remap-species-identifier to strings.scm. | 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> | |||
| 2023-11-22 | Construct URIs for external data in RDF ProbeSet transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-22 | Add 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> | |||
| 2023-11-22 | Delete 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> | |||
| 2023-11-22 | Remove 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> | |||
| 2023-11-22 | Add 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> | |||
| 2023-11-21 | Add extra gnt:location term when transforming ProbeSet metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-21 | Add strand position when transforming ProbeSet metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-21 | Delete un-necessary predicates from ProbeSet transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-20 | Add "gnt:belongsToSpecies" and "gnt:belongsToGroup" gn terms. | Munyoki Kilyungi | |
| These terms are useful when constructing a graph for framing purposes in json-ld. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-17 | Remove "FamilyOrder" join when transforming Species table. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-17 | Capitalize InbredSetName id's consistently. | Munyoki Kilyungi | |
| 2023-11-17 | Make species identifiers consistent. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-11-17 | Revert "Make Phenotypy InbredSet classification consistent." | Munyoki Kilyungi | |
| This reverts commit 092b9b4967133fc5a04d9fbf2255f4ce07dedb8b. | |||
| 2023-11-17 | Make Phenotypy InbredSet classification consistent. | Munyoki Kilyungi | |
| * examples/phenotype.scm (phenotypes): Remove "separator" and "proc" args. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-20 | Use the correct URL for "gnt:" prefix. | Munyoki Kilyungi | |
| * examples/phenotype.scm (option-spec): Replace http://genenetwork.org/terms/ with http://genenetwork.org/term/. * examples/publication.scm (option-spec): Ditto. * examples/tissue.scm (option-spec): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-20 | Alias Publication.Id to PublicationId | Munyoki Kilyungi | |
| Using "(field Publication Id)" will somehow default to PublishXRef.Id. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-19 | Use InbredSetCode instead of Name when creating a trait name. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-19 | Check (Publish/Geno)Freeze for InbredSet if NULL in InfoFiles. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-19 | Remove un-necessary WHERE clause when dumping phenotypes. | Munyoki Kilyungi | |
| * examples/phenotype.scm (phenotypes): Delete "WHERE" clause. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-19 | Add missing xkos prefix in phenotype dump. | Munyoki Kilyungi | |
| * examples/phenotype.scm (with-documentation): Add "xkos:" to prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-17 | Replace skos:prefLabel with rdfs:label for genotypes. | Munyoki Kilyungi | |
| * examples/genotype.scm (genotypes)[triples]: Replace skos:prefLabel with rdfs:label. | |||
| 2023-10-16 | Group genotype labels together. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-16 | Add a prefLabel for gnc:Probeset. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-16 | Fix typo. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-03 | Classify pheno/genotype and probeset datasets using dcat:Dataset. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-11 | Add genbank dump. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-11 | Update generif metadata dump. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-11 | Filter out empty symbols when dumping generif metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-08-30 | Delete this probeset-data tranform | Munyoki Kilyungi | |
| * examples/probeset-data.scm: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
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index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
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