From 4026ee70a5b705bd53fd0c8d08e88c8953587fea Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 18 Jul 2023 17:32:19 +0300 Subject: Dump phenotypes with documentation. --- examples/dump-phenotype.scm | 50 +++++++++++++++++---------------------------- 1 file changed, 19 insertions(+), 31 deletions(-) diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index e4d20c9..33577ce 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -111,34 +111,22 @@ (ontology 'publication: pmid)))))) -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-phenotype.ttl") - (lambda () - (prefix "chebi:" "") - (prefix "dct:" "") - (prefix "foaf:" "") - (prefix "generif:" "") - (prefix "gn:" "") - (prefix "hgnc:" "") - (prefix "homologene:" "") - (prefix "kegg:" "") - (prefix "molecularTrait:" "") - (prefix "nuccore:" "") - (prefix "omim:" "") - (prefix "owl:" "") - (prefix "phenotype:" "") - (prefix "pubchem:" "") - (prefix "pubmed:" "") - (prefix "rdf:" "") - (prefix "rdfs:" "") - (prefix "uniprot:" "") - (prefix "up:" "") - (prefix "xsd:" "") - (prefix "dataset:" "") - (prefix "publication:" "") - (newline) - (dump-publishfreeze db) - (dump-phenotypes db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "Phenotypes Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("gn-id:" "") + ("gn-term:" "") + ("phenotype:" "") + ("rdf:" "") + ("rdfs:" "") + ("xsd:" "") + ("dataset:" "") + ("publication:" ""))) + (inputs + (list dump-publishfreeze + dump-phenotype)) + (outputs + '(#:documentation "./docs/dump-phenotype.md" + #:rdf "./verified-data/dump-phenotype.ttl"))) -- cgit v1.2.3