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2023-06-12Make geoSeries a link during dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Minor identation fixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add organization to dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Use NCBI taxonomy browser instead of uniprotMunyoki Kilyungi
NCBI presents data in a user friendly way from the taxid. To get the same data from uniprot, you need a unique identify which requires an extra query to retrieve. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Cast longtext fields to fix broket utf-8 charactersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Remove dead commentsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Remove "^[Nn]one$" from some fields from the InfoFiles tableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Default to InfoFiles with the Dataset being a fallback for citationsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Make ((g/ph)enotype/probeset)Dataset subset of DatasetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Dump OMIM as a normal string without any annotationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Fix broken utf-8 strings in abstract fieldMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Add probeset as an extra prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Delete unused prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Replace species with inbredSet metadata when dumping info-filesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Only dump public dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Sanitize a probeset's descriptionMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Update the probeset's identifier(object)Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Make a probeset's tissue multisetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Make a probeset's alias a multisetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-30Move probeset metadata used for a given experiment to it's own dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Use a phenotype's abbreviation as it's nameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Make tissue a multi-set during the probeset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Remove some metadata from the probeset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Create a new probesetfreeze dumpMunyoki Kilyungi
This way, the probeset dump will become smaller. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Return an empty string if a dataset doesn't have a nameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Remove unnecessary fields from probeset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Sanitize a generif entry from GNMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Add genotype dumpMunyoki Kilyungi
* examples/dump-genotype.scm: New dump for genotypes and their associated datasets(that were not dumped from the info-files table). Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Fix broken utf-8 chars when dumping an investigator's namesMunyoki Kilyungi
* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:name, foaf:givenName>: Binary convert fields first to latin1 then utf8. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Remove an investigator's email/phone from dump for privacy reasonsMunyoki Kilyungi
* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:phone, foad:mbox>: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update a dataset's subject identifier to be a gn urlMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Annotate createtime field correctly with xsd:dateMunyoki Kilyungi
* examples/dump-phenotype.scm (dump-publishfreeze): Use xsd:date to annotate PublishFreeze's CreateTime field. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Replace dump.scm with separete dumps for several tablesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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