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2023-08-30Delete this probeset-data tranform•••* examples/probeset-data.scm: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-30Add extra mappings for broken utf-8 characters to be replaced•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-30Add an extra alias to InbredSet.InbredSetName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-30Remodel 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
2023-08-28Set string->identifier to defaut to "" sep and string-capitalize•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Update how generif metadata is dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Update how strains are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Update how genotypes are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Add qb: and sdmx-measure: prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Update phenotype dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Replace gnc:probeset with gnc:Probeset•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Update how datasets are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Fix typo•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Replace gnt:belongsToSpecies/Set with xkos:classifiedUnder•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Replace gnc:Type with gnc:DatasetType•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Use the correct name for the Species•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Replace gnt:belongsToSpecies with xkos:classifiedUnder•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Re-introduce gnt:shortName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Treat strings wrapped in "()" as symbols•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Rename file•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-28Add new file with classification hierarchy ontology•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-25Replace gdmt: with dcat:•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-24Remove match-case for RDF-FILE•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-24Add new methods for bulk-loading data•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-24Delete 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
2023-08-23Add all transformers as inputs to transform-with-documentation•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Update how NCBI genewiki entries are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Update how symbols from GeneRIF_BASIC are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Delete blank-node construct•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Add foaf prefix when transforming generif data•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Update 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
2023-08-23Add extra utility fn for removing duplicates•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-23Add an extra module for generating unique ids•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Replace gnt:traitName with rdfs:label•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Delete gnt:hasAcknowledgement from InfoFiles•••We fetch all our metadata from the Datasets table. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Add missing function•••* examples/dataset-metadata.scm (remap-species-identifiers): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Remove hard-coded paths•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Rename dump -> transform•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Remove "dump-" prefix•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Rename define-dump -> define-transformer•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Replace inbredSet with set as the string-identifier•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-21Move 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
2023-08-21Rename inbredSet -> set•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-19Add traitName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-19Point ttl path to /export/data/genenetwork-virtuoso/•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-19Rename inbredSet identifier•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-19Add short name of an inbredSet as an altName•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-17Rename gnt:species -> gnt:belongsToSpecies•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-17Update genotype rdf transformation•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-17Update how phenotypes are transformed•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
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