From 16ebe166618b7e36d92bcc6c3e497dcfa188ce90 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 19 Jul 2023 20:23:58 +0300
Subject: Dump probesetfreeze metadata using new metadata
---
examples/dump-probesetfreeze.scm | 77 +++++++++++++++++++---------------------
1 file changed, 36 insertions(+), 41 deletions(-)
(limited to 'examples')
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index 0be81ac..a45fd0a 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -16,18 +16,15 @@
(call-with-input-file (list-ref (command-line) 1)
read))
-(define %dump-directory
- (list-ref (command-line) 2))
-
(define-dump dump-gene-chip
(tables (GeneChip))
(schema-triples
- (gn:name rdfs:range rdfs:Literal))
+ (gn-term:name rdfs:range rdfs:Literal))
(triples (string->identifier "platform" (field GeneChip Name))
(set rdf:type 'gn:platform)
- (set gn:name (field GeneChip GeneChipName))
- (set gn:geoPlatform
+ (set gn-term:name (field GeneChip GeneChipName))
+ (set gn-term:geoPlatform
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
@@ -41,48 +38,46 @@
(left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
"WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
(schema-triples
- (gn:avgMethod rdfs:range rdfs:Literal)
- (gn:dataScale rdfs:range rdfs:Literal)
+ (gn-term:avgMethod rdfs:range rdfs:Literal)
+ (gn-term:dataScale rdfs:range rdfs:Literal)
(gn:probesetDataset rdf:subClassOf gn:dataset))
(triples
- (ontology 'probeset:
- (regexp-substitute/global #f "[^A-Za-z0-9:]"
- (field ProbeSetFreeze Name)
- 'pre "_" 'post))
+ (string->identifier
+ ""
+ (regexp-substitute/global
+ #f "[^A-Za-z0-9:]"
+ (field ProbeSetFreeze Name)
+ 'pre "_" 'post)
+ #:separator ""
+ #:proc string-capitalize-first)
(set rdf:type 'gn:probesetDataset)
- (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
- (set gn:fullName (field ProbeSetFreeze FullName))
- (set gn:shortName (field ProbeSetFreeze ShortName))
+ (set gn-term:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
+ (set gn-term:fullName (field ProbeSetFreeze FullName))
+ (set gn-term:shortName (field ProbeSetFreeze ShortName))
(set dct:created (annotate-field
(field ProbeSetFreeze CreateTime)
'^^xsd:datetime))
- (set gn:dataScale (field ProbeSetFreeze DataScale))
- (set gn:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
- (set gn:datasetOfInbredSet
+ (set gn-term:dataScale (field ProbeSetFreeze DataScale))
+ (set gn-term:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
+ (set gn-term:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
-(call-with-target-database
- %connection-settings
- (lambda (db)
- (with-output-to-file (string-append %dump-directory "dump-probesetfreeze.ttl")
- (lambda ()
- (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 "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
- (prefix "gn:" "<http://genenetwork.org/>")
- (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
- (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
- (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 "probeset:" "<http://genenetwork.org/probeset/>")
- (newline)
- (dump-gene-chip db)
- (dump-probesetfreeze db))
- #:encoding "utf8")))
+(dump-with-documentation
+ (name "Probeset freeze metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+ '(("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
+ ("gn:" "<http://genenetwork.org/id/>")
+ ("gn-term:" "<http://genenetwork.org/term/>")
+ ("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#>")))
+ (inputs
+ (list dump-gene-chip
+ dump-probesetfreeze))
+ (outputs
+ '(#:documentation "./docs/dump-gene-chip.md"
+ #:rdf "./verified-data/dump-probesetfreeze.ttl")))
--
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