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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-0
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
"LIMIT 2000000 OFFSET 0")
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:probeset rdfs:range rdfs:Literal))
(triples (ontology
'probeset:
(string-trim-both
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)"
name))
'pre "_" 'post)))
(set rdf:type 'gn:probeset)
(set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
(set gn:name (field ProbeSet Name))
(set gn:symbol (delete-substrings (field ProbeSet Symbol) "\""))
(set gn:description (sanitize-rdf-string
(field ProbeSet description)))
(set gn:chr (field ProbeSet Chr))
(set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
;; For now have the tissue, and alias as one line without
;; splitting to make the dump faster
;; (set gn:tissue (field ("IFNULL(ProbeSet.Tissue, '')" Tissue)))
;; (set gn:alias (field ProbeSet alias))
;; (set gn:generif (ontology 'generif: (field ProbeSet GeneId)))
(set gn:blatSeq (sanitize-rdf-string
(string-trim-both (field ProbeSet BlatSeq))))
(set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
;; (set gn:unigene (field ProbeSet UniGeneId))
;; (set gn:genbank (field ProbeSet GenbankId))
;; (set gn:omim (sanitize-rdf-string (string-trim-both (field ProbeSet OMIM))))
;; (set gn:RefSeq_TranscriptId (field ProbeSet RefSeq_TranscriptId))
(set gn:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))))
(define-dump dump-probeset-1
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
"LIMIT 2000000 OFFSET 2000000")
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:probeset rdfs:range rdfs:Literal))
(triples (ontology
'probeset:
(string-trim-both
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)"
name))
'pre "_" 'post)))
(set rdf:type 'gn:probeset)
(set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
(set gn:name (field ProbeSet Name))
(set gn:symbol (delete-substrings (field ProbeSet Symbol) "\""))
(set gn:description (sanitize-rdf-string
(field ProbeSet description)))
(set gn:chr (field ProbeSet Chr))
(set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gn:blatSeq (sanitize-rdf-string
(string-trim-both (field ProbeSet BlatSeq))))
(set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
(set gn:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))))
(define-dump dump-probeset-2
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
"WHERE ProbeSet.Name IS NOT NULL LIMIT 2000000 OFFSET 4000000")
(schema-triples
(gn:name rdfs:range rdfs:Literal)
(gn:probeset rdfs:range rdfs:Literal))
(triples (ontology
'probeset:
(string-trim-both
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
name))
'pre "_" 'post)))
(set rdf:type 'gn:probeset)
(set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
(set gn:name (field ProbeSet Name))
(set gn:symbol (delete-substrings (field ProbeSet Symbol) "\""))
(set gn:description (sanitize-rdf-string
(field ProbeSet description)))
(set gn:chr (field ProbeSet Chr))
(set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gn:blatSeq (sanitize-rdf-string
(string-trim-both (field ProbeSet BlatSeq))))
(set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
(set gn:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-probeset-0.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 "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-probeset-0 db))
#:encoding "utf8")
(with-output-to-file (string-append %dump-directory "dump-probeset-1.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 "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-probeset-1 db))
#:encoding "utf8")
(with-output-to-file (string-append %dump-directory "dump-probeset-2.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 "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-probeset-2 db))
#:encoding "utf8")))
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