| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-02-08 | Remove "string->identifier" for the dataset directory name. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Use correct format string literal when printing out sql results. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Update local git-repo directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Add a basic guile script to transform stored rtf data to files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-08 | Add InfoFiles.Experiment_Type metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-05 | Correct formatting for the gnt:location predicate for ProbeSets. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Fix typo with pantherLink ResourceLink. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use correct property for classifying pantherLink as a resource. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Delete duplicate entries for gnc:biogpsLink/gnc:gtexLink. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Update handling of RGD_ID field in genelist metadata transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Replace gnt:symbol with gnt:geneSymbol. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Refactor 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> | |||
| 2023-12-22 | Replace gnc:GeneSymbol with gnc:Gene. | Munyoki Kilyungi | |
| A GeneSymbol != Gene. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use gnt:geneSymbol instead of rdfs:label/gnt:symbol. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use gnt:hasGeneId instead of gnt:gene/dct:references. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Move gnt:hasGeneId definitions to genelist.scm | Munyoki Kilyungi | |
| * examples/generif.scm: Move definitions for gnt:hasGeneId from here to... * examples/genelist.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-20 | Set up as Guix channel for CI. | Arun Isaac | |
| * .guix-channel, .guix/gn-transform-databases-package.scm, guix.scm: New files. | |||
| 2023-12-20 | Use guile to run tests. | Arun Isaac | |
| Disuse run64. * Makefile (RUN64): Delete variable. (GUILE): New variable. (check): Use GUILE to run tests. | |||
| 2023-12-20 | Set correct top level module directory. | Arun Isaac | |
| 2023-12-20 | Fix srfi-26 import typo. | Arun Isaac | |
| 2023-12-15 | Preserve 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> | |||
| 2023-12-15 | 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 | Add 'lower-case-and-replace-spaces' function | Munyoki Kilyungi | |
| * transform/strings.scm (lower-case-and-replace-spaces): New function. 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> | |||
 |
index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
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