| Age | Commit message (Expand) | Author |
|---|
| 2024-07-19 | Add comment.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-15 | Add missing RIF symbols.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-10 | Replace "FIXME" with relevant info in the docs.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-10 | Unfill paragraphs.•••Don't break paragraphs. It makes future edits easier to diff.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-10 | Document running actual transformation scripts•••Document an example command to invoke to enable the actual
transformation of the data to be done.
This will need to be cleaned up, and the commands will also need to
check for the appropriate arguments before attempting to run in the
first place.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Frederick Muriuki Muriithi |
| 2024-07-10 | Rename script: Give file a more relevant name.•••Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Frederick Muriuki Muriithi |
| 2024-07-10 | Replace "dump" -> "transform" where relevant.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-10 | Remove the "generif-data-file" from the documentation.•••Right now, we get the generif metadata from the GeneRIF_BASIC table.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-07-10 | Provide sample JSON file and update instruction in docs•••The documentation for generating a transformation of a JSON file into
a Terse RDF Triple Language (Turtle) form was incomplete. This commit
provides a sample JSON file that can be used to demonstrate the
working of the code.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Frederick Muriuki Muriithi |
| 2024-05-20 | Add pointers to git metadata in RDF for the dataset metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-05-15 | manifest.scm: Use upstream ccwl.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-05-15 | Use a set to represent a phenotype's owner.•••The owners in the database is not a consistent comma separated list.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-05-15 | Replace rdfs:label with gnt:traitId for Phenotypes. | Munyoki Kilyungi |
| 2024-02-15 | Refactor how changes are committed and pushed.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-15 | Remove call to string-append when defining dir-name local var.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-15 | Filter out files that only have "None".•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-14 | Capitalize the first string of every path.•••This is done to match the RDF identifier.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Convert extra dataset metadata to text-files.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Remove more fields from dataset's RDF output.•••These are: "Experiment_Type", "Contributors" & "Citation" which are
already in RTF form.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Fix missplaced parens.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-09 | Re-add triplets that describe dataset terms.•••These triplets will be re-used when constructing the json-ld endpoints
for GN3.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-09 | Update push and reset git commands.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-09 | Use correct path to the datasets directory.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Delete rdf triplets from dataset transform.•••These triplets are now stored as text files and versioned in git.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Add method for commiting changes to the gn-docs git repo.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Delete unused variable in the getopts arglist.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Fix typo.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Fix how the dataset directory is constructed.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Remove "string->identifier" for the dataset directory name.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Use correct format string literal when printing out sql results.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Update local git-repo directory.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-08 | Add a basic guile script to transform stored rtf data to files.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-08 | Add InfoFiles.Experiment_Type metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-05 | Correct formatting for the gnt:location predicate for ProbeSets.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Fix typo with pantherLink ResourceLink.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Use correct property for classifying pantherLink as a resource.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Delete duplicate entries for gnc:biogpsLink/gnc:gtexLink.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Update handling of RGD_ID field in genelist metadata transform.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Replace gnt:symbol with gnt:geneSymbol.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Refactor gene metadata RDF transform.•••In the case of the GeneList_rn33 table, the table id is used, since
there is no other way to uniquely identify a gene using the other
fields. See the following for more details:
https://issues.genenetwork.org/issues/transform-genelist-to-rdf
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Replace gnc:GeneSymbol with gnc:Gene.•••A GeneSymbol != Gene.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Use gnt:geneSymbol instead of rdfs:label/gnt:symbol.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Use gnt:hasGeneId instead of gnt:gene/dct:references.•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-22 | Move gnt:hasGeneId definitions to genelist.scm•••* examples/generif.scm: Move definitions for gnt:hasGeneId from here to...
* examples/genelist.scm: ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-20 | Set up as Guix channel for CI.•••* .guix-channel, .guix/gn-transform-databases-package.scm, guix.scm:
New files.
| Arun Isaac |
| 2023-12-20 | Use guile to run tests.•••Disuse run64.
* Makefile (RUN64): Delete variable.
(GUILE): New variable.
(check): Use GUILE to run tests.
| Arun Isaac |
| 2023-12-20 | Set correct top level module directory. | Arun Isaac |
| 2023-12-20 | Fix srfi-26 import typo. | Arun Isaac |
| 2023-12-15 | Preserve gene symbol case when used as an identifer.•••Genes with varying casing (e.g., Shh, SHH) result in
`string->identifier` capitalizing the first letter by default. This
creates inconsistencies in gene symbols, leading to different
predicates and objects for the same entity, introducing errors.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
