| Age | Commit message (Expand) | Author |
|---|---|---|
| 2023-11-30 | Replace LRS with LOD Score.•••* examples/phenotype.scm (phenotypes): Replace gnt:LRS with gnt:lodScore. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-24 | Move remap-species-identifier to strings.scm.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | "Add special-case for blank Chr field".•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Construct URIs for external data in RDF ProbeSet transform.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Add extra joins for GeneList and GeneList_rn33.•••These tables are referenced when constructing URIs for mouse and rat data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Delete some RDF prefixes when transforming ProbeSet metadata.•••External resources are explicitly defined so we don't need these prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Add 'lower-case-and-replace-spaces' function•••* transform/strings.scm (lower-case-and-replace-spaces): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Remove unused properties during ProbeSet RDF transform.•••The removed terms are actually used when constructing terms. Most of this values are NULL anyways. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-22 | Add Species join when during RDF ProbeSet transform.•••We add the species join since when constructing resource links, this table is required. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-21 | Add extra gnt:location term when transforming ProbeSet metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-21 | Add strand position when transforming ProbeSet metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-21 | Delete un-necessary predicates from ProbeSet transform.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-20 | Add "gnt:belongsToSpecies" and "gnt:belongsToGroup" gn terms.•••These terms are useful when constructing a graph for framing purposes in json-ld. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-17 | Remove "FamilyOrder" join when transforming Species table.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-17 | Capitalize InbredSetName id's consistently. | Munyoki Kilyungi |
| 2023-11-17 | Make species identifiers consistent.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-17 | Revert "Make Phenotypy InbredSet classification consistent."•••This reverts commit 092b9b4967133fc5a04d9fbf2255f4ce07dedb8b. | Munyoki Kilyungi |
| 2023-11-17 | Make Phenotypy InbredSet classification consistent.•••* examples/phenotype.scm (phenotypes): Remove "separator" and "proc" args. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-20 | Use the correct URL for "gnt:" prefix.•••* 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> | Munyoki Kilyungi |
| 2023-10-20 | Alias Publication.Id to PublicationId•••Using "(field Publication Id)" will somehow default to PublishXRef.Id. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-19 | Use InbredSetCode instead of Name when creating a trait name.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-19 | Check (Publish/Geno)Freeze for InbredSet if NULL in InfoFiles.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-19 | Remove un-necessary WHERE clause when dumping phenotypes.•••* examples/phenotype.scm (phenotypes): Delete "WHERE" clause. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-19 | Add missing xkos prefix in phenotype dump.•••* examples/phenotype.scm (with-documentation): Add "xkos:" to prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-17 | Index text when loading data.•••* load-rdf.scm (bulk-load-data): Remove "quit;". This will be done after indexing. (index-data): New function (main): Add index-data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-17 | Replace skos:prefLabel with rdfs:label for genotypes.•••* examples/genotype.scm (genotypes)[triples]: Replace skos:prefLabel with rdfs:label. | Munyoki Kilyungi |
| 2023-10-16 | Group genotype labels together.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-16 | Add a prefLabel for gnc:Probeset.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-16 | Fix typo.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-03 | Classify pheno/genotype and probeset datasets using dcat:Dataset.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-09-28 | quit after bulk-loading triples.•••* load-rdf.scm (bulk-load-data): Add "quit;" to bulk-load-data command. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-09-11 | Add genbank dump.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-09-11 | Update generif metadata dump.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-09-11 | Filter out empty symbols when dumping generif metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-30 | Delete this probeset-data tranform•••* examples/probeset-data.scm: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-30 | Add extra mappings for broken utf-8 characters to be replaced•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-30 | Add an extra alias to InbredSet.InbredSetName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-30 | Remodel how GeneRIF metadata is transformed•••* examples/generif.scm: Import (ice-9 format). (genewiki-symbols): Transform symbols and their names only. This way there's no need to transform the symbol names in the other names thereby preventing duplication. (gn-genewiki-entries): Use format strings to create the comment blank-node. (ncbi-genewiki-entries): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Set string->identifier to defaut to "" sep and string-capitalize•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Update how generif metadata is dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Update how strains are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Update how genotypes are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Add qb: and sdmx-measure: prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Update phenotype dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Replace gnc:probeset with gnc:Probeset•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Update how datasets are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Fix typo•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Replace gnt:belongsToSpecies/Set with xkos:classifiedUnder•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Replace gnc:Type with gnc:DatasetType•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-08-28 | Use the correct name for the Species•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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| Data transformers for GeneNetwork (particularly to RDF) |
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