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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>
2023-08-15Rename dump-probeset-metadata -> dump-probeset-dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Remove "xsd:double" annotationMunyoki Kilyungi
A probeset' specificity and BLAT_score can be 0. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Dump probeset summary statsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Rename probeset dataset nameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Introduce phenotype/genotype/probeset Dataset as a categoryMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Return "" for non-empty strings in string->identifier/annotate-fieldMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Update probeset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Update how probesetfreeze metadata is dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Replace "used" with "uses" in ontologyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Update how genotypes are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Use prism, fabio and dct ontologies to represent a publicationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Dump publishfreeze dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Remove explicity cast when dumping strainsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-15Delete explicit sql-level utf-8 conversionsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-12Add comment on Strain tablePjotr Prins
2023-08-12Git repoPjotr Prins
2023-08-12Add git clonePjotr Prins
2023-08-12Add LICENSEPjotr Prins
2023-08-11Use correct encoding when writing to a fileMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-09Update how phenotypes are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-09Add new line before dump titleMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Update phenotype and publishfreeze dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Replace gnt:name/shortName with skos:label/altLabelMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Update publish-freeze dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Update how published datasets are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Replace gdmt:hasTitleInfo with skos:prefLabelMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Fix typoMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Update tissue dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Dump molecular traitsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-07Add extra metadata to gnc: and gnt: itemsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-04Annotate terms related to speciesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-04Add gnt:shortName to species dumpMunyoki Kilyungi
2023-08-04Updated species.ttl and sorted entriesPjotr Prins
2023-08-02Re-model how datasets are fetchedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-02Correct the associations between subject and objectMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-02Introduce a vCard prefix to store metadata about an investigatorMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-02README: add link to gemtextPjotr Prins
2023-08-02Added missing prefix to species.ttlPjotr Prins
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