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authorMunyoki Kilyungi2023-07-18 17:32:19 +0300
committerMunyoki Kilyungi2023-07-21 14:36:41 +0300
commit4026ee70a5b705bd53fd0c8d08e88c8953587fea (patch)
tree70abc1bdfc232ad1323c03eb749217b6e4fe7ec1
parent5f5f425f2084168c87101ae5e95037bce3fa8c1b (diff)
downloadgn-transform-databases-4026ee70a5b705bd53fd0c8d08e88c8953587fea.tar.gz
Dump phenotypes with documentation.
-rwxr-xr-xexamples/dump-phenotype.scm50
1 files 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:" "<http://purl.obolibrary.org/obo/CHEBI_>")
- (prefix "dct:" "<http://purl.org/dc/terms/>")
- (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
- (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
- (prefix "gn:" "<http://genenetwork.org/>")
- (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
- (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
- (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
- (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
- (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
- (prefix "omim:" "<https://www.omim.org/entry/>")
- (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
- (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
- (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
- (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
- (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
- (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
- (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/>")
- (prefix "publication:" "<http://genenetwork.org/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:" "<http://genenetwork.org/terms/>")
+ ("gn-term:" "<http://genenetwork.org/terms/>")
+ ("phenotype:" "<http://genenetwork.org/phenotype/>")
+ ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+ ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+ ("dataset:" "<http://genenetwork.org/dataset/>")
+ ("publication:" "<http://genenetwork.org/publication/>")))
+ (inputs
+ (list dump-publishfreeze
+ dump-phenotype))
+ (outputs
+ '(#:documentation "./docs/dump-phenotype.md"
+ #:rdf "./verified-data/dump-phenotype.ttl")))