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#! /usr/bin/env guile
!#
(use-modules (srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 regex)
(dump strings)
(dump sql)
(dump triples)
(dump special-forms))
(define %connection-settings
(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))
(triples (string->identifier "platform" (field GeneChip Name))
(set rdf:type 'gn:platform)
(set gn:name (field GeneChip GeneChipName))
(set gn:geoPlatform
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
;; Molecular Traits are also referred to as ProbeSets
(define-dump dump-probesetfreeze
(tables (ProbeSetFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join ProbeFreeze "USING (ProbeFreezeId)")
(left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
(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:probesetDataset rdf:subClassOf gn:dataset))
(triples
(ontology 'probeset:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post))
(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 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
(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")))
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