aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
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>
2023-12-14Remove "remap-species-identifiers" from generif transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Link extra resources to genes and trim gene symbols.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Refactor symbol identifier in strains.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Add GeneList metadata RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Remove some resource links from ProbeSet RDF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-14Use correct identifier for the AvgMethod table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-04Replace xkos:classifiedUnder -> gnt:belongsToGroup.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-04Replace xkos:classifiedUnder -> gnt:belongsToSpecies for species.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-04Replace xkos:classifiendUnder with gnt:belongsToGroup for groups.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-04Fix typo in publishfreeze transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Trim the contributor's name when transforming phenotype metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Add a label to the "gnt:lodScore" term.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Set a phenotype's gnt:locus to a genotype.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Replace LRS with LOD Score.Munyoki Kilyungi
* examples/phenotype.scm (phenotypes): Replace gnt:LRS with gnt:lodScore. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-24Move remap-species-identifier to strings.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22"Add special-case for blank Chr field".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Construct URIs for external data in RDF ProbeSet transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add extra joins for GeneList and GeneList_rn33.Munyoki Kilyungi
These tables are referenced when constructing URIs for mouse and rat data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Delete some RDF prefixes when transforming ProbeSet metadata.Munyoki Kilyungi
External resources are explicitly defined so we don't need these prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add 'lower-case-and-replace-spaces' functionMunyoki Kilyungi
* transform/strings.scm (lower-case-and-replace-spaces): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Remove unused properties during ProbeSet RDF transform.Munyoki Kilyungi
The removed terms are actually used when constructing terms. Most of this values are NULL anyways. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add Species join when during RDF ProbeSet transform.Munyoki Kilyungi
We add the species join since when constructing resource links, this table is required. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Add extra gnt:location term when transforming ProbeSet metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Add strand position when transforming ProbeSet metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-21Delete un-necessary predicates from ProbeSet transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-20Add "gnt:belongsToSpecies" and "gnt:belongsToGroup" gn terms.Munyoki Kilyungi
These terms are useful when constructing a graph for framing purposes in json-ld. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-17Remove "FamilyOrder" join when transforming Species table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-17Capitalize InbredSetName id's consistently.Munyoki Kilyungi
2023-11-17Make species identifiers consistent.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-17Revert "Make Phenotypy InbredSet classification consistent."Munyoki Kilyungi
This reverts commit 092b9b4967133fc5a04d9fbf2255f4ce07dedb8b.
2023-11-17Make Phenotypy InbredSet classification consistent.Munyoki Kilyungi
* examples/phenotype.scm (phenotypes): Remove "separator" and "proc" args. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-20Use the correct URL for "gnt:" prefix.Munyoki Kilyungi
* examples/phenotype.scm (option-spec): Replace http://genenetwork.org/terms/ with http://genenetwork.org/term/. * examples/publication.scm (option-spec): Ditto. * examples/tissue.scm (option-spec): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-19 06:07:39 +0000