| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-01-10 | Optionally fetch dataset metadata if provided during genotype fetch....* gn3/api/metadata.py (genotypes): If a dataset name is provided fetch the group it belongs to and the dataset's full and short name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-10 | Switch to gnt:belongsToSpecies in genotype queries....* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of xkos:classifiedUnder when querying for species. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-10 | Remove hard-coded dataset name....* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in probeset RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-08 | Optionally fetch dataset metadata if provided during probeset fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-06 | Remove extra gene metadata from query as it's un-necessary....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-06 | Add extra keys to the Probeset's json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-06 | Refactor gene symbol handling and add references to probeset....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-01-06 | Use gnt:geneSymbol property to fetch genes in Probeset RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-15 | Update RDF ProbeSet query....* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-15 | First frame and then compact probeset results....* gn3/api/metadata.py: Reshape the data in a nice way by first framing and compacting the json-ld result. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-15 | Update ProbeSet's context....* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-15 | Update BASE_CONTEXT entries....* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt", "gnc"... (BASE_CONTEXT): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Fix typo in GoTree prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Add optional property for platform info in dataset representation....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Fetch normalization metadata correctly....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Fix typo in platform prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Refactor metadata mappings for improved dataset representation....* gn3/api/metadata.py: (DATASET_CONTEXT): Remove "ex:" prefixes. Add new prefixes for citation, platform, GoTree, tissueInfo, contactWebUrl and contactName. (datasets): Update query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-12-07 | Update phenotype queries to use gnt:belongsToGroup....* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-30 | Add a phenotype's chromosome location to the Phenotype fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-30 | Place publication details on a sub-graph of its own....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-30 | Replace LRS with lodScore....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Remove unused variable "args"....* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Attach phenotype endpoints to one function....* gn3/api/metadata.py (phenotypes): Add "/phenotypes/<group>/<name>" to this endpoint. (fetch_phenotype_by_group): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Use "dcat:Dataset" when framing when fetching phenotypes....* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in json-ld context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Construct a more semantic graph for phenotypes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Remove unused argument during template substitution....* gn3/api/metadata.py (phenotypes): Delete "name" from template substitution. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Replace "ex:" prefix with a semantic prefix when fetching phenotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add "ex:species" to phenotypes json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Return distinct results after a dataset search....* gn3/api/metadata.py (search_datasets): Return distinct search results. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add ex:pages and ex:hits to the search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | First fram and compact the jsonld results during dataset search....* gn3/api/metadata.py (search_datasets): Replace query_and_frame with query_frame_and_compact. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Add "inbredSet" to the dataset's search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Fetch a dataset's contributors in RDF....* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors." (datasets): Fetch a dataset's contributors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-11-27 | Fetch dataset specifics in RDF....* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics". (datasets): Fetch a dataset's specifics. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Refactor to use new rdf.query_* abstractions....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Fix pylint error....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Refactor to use new rdf.query_* abstractions....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Make implicit optional type hints PEP 484 compliant....Ran the command: pipx run no_implicit_optional ./ in the root directory. | Munyoki Kilyungi |
| 2023-10-27 | Abstract out (sparql) CONSTRUCT into a function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Delete unused imports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Remove duplicate key in dictionary....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/probesets/:name"....* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Delete duplicate function....* gn3/api/metadata.py (genotypes): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/groups/:name"....* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/group"....* gn3/api/metadata.py (groups): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/species/:name"....* gn3/api/metadata.py (fetch_group_by_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/species"....* gn3/api/metadata.py (list_species): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/genewikis/ncbi/:symbol"....* gn3/api/metadata.py (get_ncbi_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/genewikis/gn/:symbol"....* gn3/api/metadata.py (get_gn_genewiki_entries): New end-point. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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