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| author | Munyoki Kilyungi | 2023-05-22 10:51:20 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-05-26 08:40:22 +0300 |
| commit | 2363e578a834d4017ef4e320fa7da553376c61cf (patch) | |
| tree | b31605a0548cc1134e91481f7a1e9ee9efed80ed /examples | |
| parent | dbbbf859b187c80545d923c2f712f0c755843a8f (diff) | |
| download | gn-transform-databases-2363e578a834d4017ef4e320fa7da553376c61cf.tar.gz | |
Update a dataset's subject identifier to be a gn url
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-dataset-metadata.scm | 7 | ||||
| -rwxr-xr-x | examples/dump-phenotype.scm | 7 |
2 files changed, 11 insertions, 3 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index aa7a5f2..e4f8334 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -130,8 +130,10 @@ (gn:contributors rdfs:range rdfs:Literal) (gn:citation rdfs:range rdfs:Literal) (gn:acknowledgment rdfs:range rdfs:Literal)) - (triples (string->identifier "dataset" - (field InfoFiles InfoPageName)) + (triples (ontology 'dataset: + (regexp-substitute/global #f "[^A-Za-z0-9:]" + (field InfoFiles InfoPageName) + 'pre "_" 'post)) ;; Add GeneChipName and GeoPlatform: ;; GeneChip.GeneChipName AS gene_chip_name ;; GeneChip.GeoPlatform AS geo_platform @@ -214,6 +216,7 @@ (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") (prefix "up:" "<http://purl.uniprot.org/core/>") (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (prefix "dataset:" "<http://genenetwork.org/dataset/>") (newline) (dump-info-files db) (dump-investigators db)) diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index 242e835..08d5127 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -89,7 +89,11 @@ (set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float)) (set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal)) (set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int)) - (set gn:phenotypeOfDataset (string->identifier "dataset" (field PublishFreeze Name))) + (set gn:phenotypeOfDataset + (ontology 'dataset: + (regexp-substitute/global #f "[^A-Za-z0-9:]" + (field PublishFreeze Name) + 'pre "_" 'post))) (set gn:phenotypeOfPublication (let ((pmid (field ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" @@ -127,6 +131,7 @@ (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") (prefix "up:" "<http://purl.uniprot.org/core/>") (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (prefix "dataset:" "<http://genenetwork.org/dataset/>") (newline) (dump-publishfreeze db) (dump-phenotypes db)) |