| Age | Commit message (Expand) | Author |
|---|---|---|
| 2023-05-30 | Add probeset as an extra prefix•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Delete unused prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Replace species with inbredSet metadata when dumping info-files•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Only dump public data•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Allow upleading all files in a directory to virtuoso•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Replace PUT with a POST when uploading data in virtuoso•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Sanitize a probeset's description•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Update the probeset's identifier(object)•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Make a probeset's tissue multiset•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Make a probeset's alias a multiset•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Move probeset metadata used for a given experiment to it's own dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Use a phenotype's abbreviation as it's name•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Make tissue a multi-set during the probeset dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Remove some metadata from the probeset dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Create a new probesetfreeze dump•••This way, the probeset dump will become smaller. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Allow load-rdf script to read in data from a dir•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Return an empty string if a dataset doesn't have a name•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Remove unnecessary fields from probeset dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Sanitize a generif entry from GN•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Add genotype dump•••* 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> | Munyoki Kilyungi |
| 2023-05-26 | Fix broken utf-8 chars when dumping an investigator's names•••* 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> | Munyoki Kilyungi |
| 2023-05-26 | Remove an investigator's email/phone from dump for privacy reasons•••* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:phone, foad:mbox>: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Update a dataset's subject identifier to be a gn url•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Annotate createtime field correctly with xsd:date•••* examples/dump-phenotype.scm (dump-publishfreeze): Use xsd:date to annotate PublishFreeze's CreateTime field. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Replace broken char-sets with an empty string•••* dump/strings.scm (sanitize-rdf-string): Add extra elements---broken chars---to replace with "". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Replace dump.scm with separete dumps for several tables•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Re-organize dumping macros and associated functions•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Update how info-page-files are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Update how publications are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Dump phenotypes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Delete dump-published-phenotypes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | When a field is null during annotation, return an empty string•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Always use "~a" to output like "display"•••Replacing "~s" with "~a" will print utf-8 characters correctly. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Return an empty string if args passed to ontology is empty•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Replace chars not allowed in RDF•••* dump.scm (sanitize-rdf-string): New function Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Dump molecular traits, also referred to as Probesets•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Update how inbred-set in dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Fix how a symbol is displayed in the final RDF•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-26 | Update how Species are dumped•••* dump.scm (dump-species): Rename gn:menuName to gn:displayName. Add gn:family and up:organism triplets. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Delete "operation" from fields•••Nested raw queries: ((field (query alias)) alias) are now supported so an "operation is not needed". * dump.scm (field->key, field->assoc-ref): Delete ((field table column operation alias) alias)) Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Simplify pattern matching when checking for a node•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Wrap the password in quotes•••The password can contain special characters. As such, wrap it in quotes. * load-rdf.scm (delete-graph): Replace "~a" with "~s". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Update GeneRIF prefix•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Add species data to generif entries•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Dump genewiki symbol•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Annotate gn:geneWikiEntry as a class and add a comment•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Dump species, symbols and indicate generif type when a geneid = 0•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Separate NCBI and GN wikientries in dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Add dublin-core and uniprot prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-04-05 | Avoid prefixing 'pubmed: to an empty string•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
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