From 2363e578a834d4017ef4e320fa7da553376c61cf Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 22 May 2023 10:51:20 +0300 Subject: Update a dataset's subject identifier to be a gn url Signed-off-by: Munyoki Kilyungi --- examples/dump-phenotype.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'examples/dump-phenotype.scm') 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:" "") (prefix "up:" "") (prefix "xsd:" "") + (prefix "dataset:" "") (newline) (dump-publishfreeze db) (dump-phenotypes db)) -- cgit v1.2.3