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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>
2023-10-20Alias Publication.Id to PublicationIdMunyoki Kilyungi
Using "(field Publication Id)" will somehow default to PublishXRef.Id. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Use InbredSetCode instead of Name when creating a trait name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Check (Publish/Geno)Freeze for InbredSet if NULL in InfoFiles.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Remove un-necessary WHERE clause when dumping phenotypes.Munyoki Kilyungi
* examples/phenotype.scm (phenotypes): Delete "WHERE" clause. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-19Add missing xkos prefix in phenotype dump.Munyoki Kilyungi
* examples/phenotype.scm (with-documentation): Add "xkos:" to prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-17Index text when loading data.Munyoki Kilyungi
* load-rdf.scm (bulk-load-data): Remove "quit;". This will be done after indexing. (index-data): New function (main): Add index-data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-17Replace skos:prefLabel with rdfs:label for genotypes.Munyoki Kilyungi
* examples/genotype.scm (genotypes)[triples]: Replace skos:prefLabel with rdfs:label.
2023-10-16Group genotype labels together.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-16Add a prefLabel for gnc:Probeset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-16Fix typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-03Classify pheno/genotype and probeset datasets using dcat:Dataset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-28quit after bulk-loading triples.Munyoki Kilyungi
* load-rdf.scm (bulk-load-data): Add "quit;" to bulk-load-data command. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Add genbank dump.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Update generif metadata dump.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Filter out empty symbols when dumping generif metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Delete this probeset-data tranformMunyoki Kilyungi
* examples/probeset-data.scm: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Add extra mappings for broken utf-8 characters to be replacedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Add an extra alias to InbredSet.InbredSetNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Remodel how GeneRIF metadata is transformedMunyoki Kilyungi
* examples/generif.scm: Import (ice-9 format). (genewiki-symbols): Transform symbols and their names only. This way there's no need to transform the symbol names in the other names thereby preventing duplication. (gn-genewiki-entries): Use format strings to create the comment blank-node. (ncbi-genewiki-entries): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Set string->identifier to defaut to "" sep and string-capitalizeMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how generif metadata is dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Update how strains are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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