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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-probeset-metadata
(tables (ProbeSetXRef
(left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
(left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id"))
"WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1")
(schema-triples
(gn:probesetData rdfs:range gn:probeset)
(gn:hasProbeset rdfs:range rdfs:Literal))
(triples
(string->identifier
"probesetData"
(field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))"
ProbeSetName)))
(set rdf:type 'gn:probesetData)
(set gn:hasProbeset
(ontology
'probeset:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
name))
'pre "_" 'post)))
(set gn:probesetOfDataset
(ontology
'probeset:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post)))
(set gn:mean
(annotate-field
(field ("IFNULL(ProbeSetXRef.mean, '')" mean))
'^^xsd:double))
(set gn:se
(annotate-field
(field ("IFNULL(ProbeSetXRef.se, '')" se))
'^^xsd:double))
(set gn:locus (field ProbeSetXRef Locus))
(set gn:LRS
(annotate-field
(field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
'^^xsd:double))
(set gn:pValue
(annotate-field
(field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
'^^xsd:double))
(set gn:additive
(annotate-field
(field ("IFNULL(ProbeSetXRef.additive, '')" additive))
'^^xsd:double))
(set gn:h2
(annotate-field
(field ("IFNULL(ProbeSetXRef.h2, '')" h2))
'^^xsd:float))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-probeset-metadata.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 "probeset:" "<http://genenetwork.org/probeset/>")
(newline)
(dump-probeset-metadata db))
#:encoding "utf8")))
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