Age | Commit message (Expand) | Author |
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 |
2023-08-28 | Replace gnt:belongsToSpecies with xkos:classifiedUnder•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-28 | Re-introduce gnt:shortName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-28 | Treat strings wrapped in "()" as symbols•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-28 | Rename file•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-28 | Add new file with classification hierarchy ontology•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-25 | Replace gdmt: with dcat:•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-24 | Remove match-case for RDF-FILE•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-24 | Add new methods for bulk-loading data•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-24 | Delete http methods for adding data•••* load-rdf.scm (random-cnonce, md5-digest-authorization,
http-upload-file, put-graph, delete-graph): Delete
(main): Remove call to put-graph.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Add all transformers as inputs to transform-with-documentation•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Update how NCBI genewiki entries are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Update how symbols from GeneRIF_BASIC are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Delete blank-node construct•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Add foaf prefix when transforming generif data•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Update how gn-specific genewiki entries are transformed•••Each comment is identified using a unique uuid so that we can identify
it's metadata I.e time, author, symbol, etc.
| Munyoki Kilyungi |
2023-08-23 | Add extra utility fn for removing duplicates•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-23 | Add an extra module for generating unique ids•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Replace gnt:traitName with rdfs:label•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Delete gnt:hasAcknowledgement from InfoFiles•••We fetch all our metadata from the Datasets table.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Add missing function•••* examples/dataset-metadata.scm (remap-species-identifiers): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Remove hard-coded paths•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Rename dump -> transform•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Remove "dump-" prefix•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Rename define-dump -> define-transformer•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Replace inbredSet with set as the string-identifier•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-21 | Move dumps related to datasets to one place•••* examples/dump-dataset-metadata.scm: Add dump-gene-chip,
dump-publishfreeze, dump-genofreeze, dump-probesetfreeze
* examples/dump-genotype.scm: Delete dump-genofreeze.
* examples/dump-phenotype.scm: Delete dump-publishfreeze.
* examples/dump-probesetfreeze.scm: Delete file
| Munyoki Kilyungi |
2023-08-21 | Rename inbredSet -> set•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-19 | Add traitName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-19 | Point ttl path to /export/data/genenetwork-virtuoso/•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-19 | Rename inbredSet identifier•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-19 | Add short name of an inbredSet as an altName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-17 | Rename gnt:species -> gnt:belongsToSpecies•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-17 | Update genotype rdf transformation•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-08-17 | Update how phenotypes are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |