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2023-08-30Remodel how GeneRIF metadata is transformedMunyoki Kilyungi
* 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>
2023-08-28Set string->identifier to defaut to "" sep and string-capitalizeMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how generif metadata is dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how strains are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how genotypes are transformedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Add qb: and sdmx-measure: prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update phenotype dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Replace gnc:probeset with gnc:ProbesetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how datasets are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Fix typoMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Replace gnt:belongsToSpecies/Set with xkos:classifiedUnderMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Replace gnc:Type with gnc:DatasetTypeMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Use the correct name for the SpeciesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Replace gnt:belongsToSpecies with xkos:classifiedUnderMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Re-introduce gnt:shortNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Treat strings wrapped in "()" as symbolsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Rename fileMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Add new file with classification hierarchy ontologyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-25Replace gdmt: with dcat:Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-24Remove match-case for RDF-FILEMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-24Add new methods for bulk-loading dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-24Delete http methods for adding dataMunyoki Kilyungi
* 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>
2023-08-23Add all transformers as inputs to transform-with-documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Update how NCBI genewiki entries are transformedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Update how symbols from GeneRIF_BASIC are transformedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Delete blank-node constructMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Add foaf prefix when transforming generif dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Update how gn-specific genewiki entries are transformedMunyoki Kilyungi
Each comment is identified using a unique uuid so that we can identify it's metadata I.e time, author, symbol, etc.
2023-08-23Add extra utility fn for removing duplicatesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Add an extra module for generating unique idsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Replace gnt:traitName with rdfs:labelMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Delete gnt:hasAcknowledgement from InfoFilesMunyoki Kilyungi
We fetch all our metadata from the Datasets table. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Add missing functionMunyoki Kilyungi
* examples/dataset-metadata.scm (remap-species-identifiers): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Remove hard-coded pathsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Rename dump -> transformMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Remove "dump-" prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Rename define-dump -> define-transformerMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Replace inbredSet with set as the string-identifierMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Move dumps related to datasets to one placeMunyoki Kilyungi
* 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
2023-08-21Rename inbredSet -> setMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-19Add traitNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-19Point ttl path to /export/data/genenetwork-virtuoso/Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-19Rename inbredSet identifierMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-19Add short name of an inbredSet as an altNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-17Rename gnt:species -> gnt:belongsToSpeciesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-17Update genotype rdf transformationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-17Update how phenotypes are transformedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Rename gnt:molecularTrait -> gnt:hasTissueMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Add missing skos prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Add "probeset_" prefix to probesetsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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