| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-06-12 | Replace citations to source from Datasets instead of InfoFiles | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Rename sql-alias of GN notes during dataset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Add rdf defs for datasetOfSpecies | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Add publicationTitle to dataset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Make geoSeries a link during dataset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Minor identation fix | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Add organization to dataset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Use NCBI taxonomy browser instead of uniprot | Munyoki 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> | |||
| 2023-06-12 | Cast longtext fields to fix broket utf-8 characters | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Remove dead comments | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Remove "^[Nn]one$" from some fields from the InfoFiles table | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Default to InfoFiles with the Dataset being a fallback for citations | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-12 | Make ((g/ph)enotype/probeset)Dataset subset of Dataset | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Dump OMIM as a normal string without any annotation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Fix broken utf-8 strings in abstract field | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Add probeset as an extra prefix | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Delete unused prefixes | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Replace species with inbredSet metadata when dumping info-files | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Only dump public data | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Allow upleading all files in a directory to virtuoso | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Replace PUT with a POST when uploading data in virtuoso | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Sanitize a probeset's description | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Update the probeset's identifier(object) | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Make a probeset's tissue multiset | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Make a probeset's alias a multiset | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-30 | Move probeset metadata used for a given experiment to it's own dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Use a phenotype's abbreviation as it's name | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Make tissue a multi-set during the probeset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Remove some metadata from the probeset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Create a new probesetfreeze dump | Munyoki Kilyungi | |
| This way, the probeset dump will become smaller. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Allow load-rdf script to read in data from a dir | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Return an empty string if a dataset doesn't have a name | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Remove unnecessary fields from probeset dump | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Sanitize a generif entry from GN | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Add genotype dump | Munyoki 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> | |||
| 2023-05-26 | Fix broken utf-8 chars when dumping an investigator's names | Munyoki 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> | |||
| 2023-05-26 | Remove an investigator's email/phone from dump for privacy reasons | Munyoki Kilyungi | |
| * examples/dump-dataset-metadata.scm (dump-investigators) <foaf:phone, foad:mbox>: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Update a dataset's subject identifier to be a gn url | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Annotate createtime field correctly with xsd:date | Munyoki Kilyungi | |
| * examples/dump-phenotype.scm (dump-publishfreeze): Use xsd:date to annotate PublishFreeze's CreateTime field. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Replace broken char-sets with an empty string | Munyoki Kilyungi | |
| * dump/strings.scm (sanitize-rdf-string): Add extra elements---broken chars---to replace with "". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Replace dump.scm with separete dumps for several tables | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Re-organize dumping macros and associated functions | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Update how info-page-files are dumped | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Update how publications are dumped | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Dump phenotypes | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Delete dump-published-phenotypes | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | When a field is null during annotation, return an empty string | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Always use "~a" to output like "display" | Munyoki Kilyungi | |
| Replacing "~s" with "~a" will print utf-8 characters correctly. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Return an empty string if args passed to ontology is empty | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-05-26 | Replace chars not allowed in RDF | Munyoki Kilyungi | |
| * dump.scm (sanitize-rdf-string): New function Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
 |
index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
| aboutsummaryrefslogtreecommitdiff |