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2023-11-17Remove "FamilyOrder" join when transforming Species table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-17Capitalize InbredSetName id's consistently.Munyoki Kilyungi
2023-11-17Make species identifiers consistent.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-17Revert "Make Phenotypy InbredSet classification consistent."Munyoki Kilyungi
This reverts commit 092b9b4967133fc5a04d9fbf2255f4ce07dedb8b.
2023-11-17Make Phenotypy InbredSet classification consistent.Munyoki Kilyungi
* examples/phenotype.scm (phenotypes): Remove "separator" and "proc" args. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-20Use the correct URL for "gnt:" prefix.Munyoki Kilyungi
* 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>
2023-10-20Alias Publication.Id to PublicationIdMunyoki Kilyungi
Using "(field Publication Id)" will somehow default to PublishXRef.Id. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Use InbredSetCode instead of Name when creating a trait name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Check (Publish/Geno)Freeze for InbredSet if NULL in InfoFiles.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Remove un-necessary WHERE clause when dumping phenotypes.Munyoki Kilyungi
* examples/phenotype.scm (phenotypes): Delete "WHERE" clause. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Add missing xkos prefix in phenotype dump.Munyoki Kilyungi
* examples/phenotype.scm (with-documentation): Add "xkos:" to prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-17Replace skos:prefLabel with rdfs:label for genotypes.Munyoki Kilyungi
* examples/genotype.scm (genotypes)[triples]: Replace skos:prefLabel with rdfs:label.
2023-10-16Group genotype labels together.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-16Add a prefLabel for gnc:Probeset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-16Fix typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-03Classify pheno/genotype and probeset datasets using dcat:Dataset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Add genbank dump.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Update generif metadata dump.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Filter out empty symbols when dumping generif metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Delete this probeset-data tranformMunyoki Kilyungi
* examples/probeset-data.scm: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Add an extra alias to InbredSet.InbredSetNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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>
2023-08-28Rename 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>
2023-08-23Add 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>
2023-08-23Add 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.
2023-08-21Replace 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>
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