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2024-07-10Document running actual transformation scriptsFrederick Muriuki Muriithi
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>
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>
generated by cgit v1.2.3 (git 2.44.0) at 2024-09-19 22:02:58 +0000