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2024-02-08Fix how the dataset directory is constructed....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-08Remove "string->identifier" for the dataset directory name....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-08Use correct format string literal when printing out sql results....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-08Update local git-repo directory....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-02-08Add a basic guile script to transform stored rtf data to files....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-08Add InfoFiles.Experiment_Type metadata....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-05Correct formatting for the gnt:location predicate for ProbeSets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Fix typo with pantherLink ResourceLink....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Use correct property for classifying pantherLink as a resource....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Delete duplicate entries for gnc:biogpsLink/gnc:gtexLink....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Update handling of RGD_ID field in genelist metadata transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Replace gnt:symbol with gnt:geneSymbol....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Refactor 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
2023-12-22Replace gnc:GeneSymbol with gnc:Gene....A GeneSymbol != Gene. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Use gnt:geneSymbol instead of rdfs:label/gnt:symbol....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Use gnt:hasGeneId instead of gnt:gene/dct:references....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-22Move 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
2023-12-20Set up as Guix channel for CI....* .guix-channel, .guix/gn-transform-databases-package.scm, guix.scm: New files. Arun Isaac
2023-12-20Use guile to run tests....Disuse run64. * Makefile (RUN64): Delete variable. (GUILE): New variable. (check): Use GUILE to run tests. Arun Isaac
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....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
2023-12-15Use URI encoding for OMIM and homologene resource link handling....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Refactor Uniprot and GeneId handling in ProbeSet RDF transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Add missing "gene:" prefix in ProbeSet RDF transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Trim gene symbol rdfs:label for the GeneList_rn33 table....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Use URI encoding for symbol-based resource link URLs....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Remove "remap-species-identifiers" from generif transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Link extra resources to genes and trim gene symbols....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Refactor symbol identifier in strains.scm....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Add GeneList metadata RDF transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Remove some resource links from ProbeSet RDF transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-14Use correct identifier for the AvgMethod table....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-04Replace xkos:classifiedUnder -> gnt:belongsToGroup....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-04Replace xkos:classifiedUnder -> gnt:belongsToSpecies for species....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-04Replace xkos:classifiendUnder with gnt:belongsToGroup for groups....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-04Fix typo in publishfreeze transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Trim the contributor's name when transforming phenotype metadata....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Add a label to the "gnt:lodScore" term....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Set a phenotype's gnt:locus to a genotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Replace LRS with LOD Score....* examples/phenotype.scm (phenotypes): Replace gnt:LRS with gnt:lodScore. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-24Move remap-species-identifier to strings.scm....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22"Add special-case for blank Chr field"....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Construct URIs for external data in RDF ProbeSet transform....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Add extra joins for GeneList and GeneList_rn33....These tables are referenced when constructing URIs for mouse and rat data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Delete some RDF prefixes when transforming ProbeSet metadata....External resources are explicitly defined so we don't need these prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Add 'lower-case-and-replace-spaces' function...* transform/strings.scm (lower-case-and-replace-spaces): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Remove unused properties during ProbeSet RDF transform....The removed terms are actually used when constructing terms. Most of this values are NULL anyways. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-22Add Species join when during RDF ProbeSet transform....We add the species join since when constructing resource links, this table is required. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-01 23:14:08 +0000