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2024-07-10Rename script: Give file a more relevant name.Frederick Muriuki Muriithi
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-10Replace "dump" -> "transform" where relevant.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-10Remove the "generif-data-file" from the documentation.Munyoki Kilyungi
Right now, we get the generif metadata from the GeneRIF_BASIC table. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-10Provide sample JSON file and update instruction in docsFrederick Muriuki Muriithi
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>
2024-05-20Add pointers to git metadata in RDF for the dataset metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-15manifest.scm: Use upstream ccwl.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-15Use a set to represent a phenotype's owner.Munyoki Kilyungi
The owners in the database is not a consistent comma separated list. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-15Replace rdfs:label with gnt:traitId for Phenotypes.Munyoki Kilyungi
2024-02-15Refactor how changes are committed and pushed.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-15Remove call to string-append when defining dir-name local var.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-15Filter out files that only have "None".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-14Capitalize the first string of every path.Munyoki Kilyungi
This is done to match the RDF identifier. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Convert extra dataset metadata to text-files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Remove more fields from dataset's RDF output.Munyoki Kilyungi
These are: "Experiment_Type", "Contributors" & "Citation" which are already in RTF form. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Fix missplaced parens.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-09Re-add triplets that describe dataset terms.Munyoki Kilyungi
These triplets will be re-used when constructing the json-ld endpoints for GN3. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-09Update push and reset git commands.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-09Use correct path to the datasets directory.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Delete rdf triplets from dataset transform.Munyoki Kilyungi
These triplets are now stored as text files and versioned in git. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Add method for commiting changes to the gn-docs git repo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Delete unused variable in the getopts arglist.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Fix typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Fix how the dataset directory is constructed.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Remove "string->identifier" for the dataset directory name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Use correct format string literal when printing out sql results.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Update local git-repo directory.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-08Add a basic guile script to transform stored rtf data to files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Add InfoFiles.Experiment_Type metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-05Correct formatting for the gnt:location predicate for ProbeSets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Fix typo with pantherLink ResourceLink.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Use correct property for classifying pantherLink as a resource.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Delete duplicate entries for gnc:biogpsLink/gnc:gtexLink.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Update handling of RGD_ID field in genelist metadata transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Replace gnt:symbol with gnt:geneSymbol.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Refactor gene metadata RDF transform.Munyoki Kilyungi
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>
2023-12-22Replace gnc:GeneSymbol with gnc:Gene.Munyoki Kilyungi
A GeneSymbol != Gene. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Use gnt:geneSymbol instead of rdfs:label/gnt:symbol.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Use gnt:hasGeneId instead of gnt:gene/dct:references.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-22Move gnt:hasGeneId definitions to genelist.scmMunyoki Kilyungi
* examples/generif.scm: Move definitions for gnt:hasGeneId from here to... * examples/genelist.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-20Set up as Guix channel for CI.Arun Isaac
* .guix-channel, .guix/gn-transform-databases-package.scm, guix.scm: New files.
2023-12-20Use guile to run tests.Arun Isaac
Disuse run64. * Makefile (RUN64): Delete variable. (GUILE): New variable. (check): Use GUILE to run tests.
2023-12-20Set correct top level module directory.Arun Isaac
2023-12-20Fix srfi-26 import typo.Arun Isaac
2023-12-15Preserve gene symbol case when used as an identifer.Munyoki Kilyungi
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>
2023-12-15Use URI encoding for OMIM and homologene resource link handling.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Refactor Uniprot and GeneId handling in ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Add missing "gene:" prefix in ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Trim gene symbol rdfs:label for the GeneList_rn33 table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Use URI encoding for symbol-based resource link URLs.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-24 00:11:39 +0000