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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(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-genofreeze
(tables (GenoFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
(left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE GenoFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL")
(schema-triples
(gn:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn:genotypeDataset rdfs:subPropertyOf gn:dataset)
(gn:shortName rdfs:range rdfs:Literal))
(triples (ontology
'dataset:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field GenoFreeze Name)
'pre "_" 'post))
(set rdf:type 'gn:genotypeDataset)
(set gn:name (field GenoFreeze Name))
(set gn:fullName (field GenoFreeze FullName))
(set gn:shortName (field GenoFreeze ShortName))
(set dct:created (annotate-field
(field GenoFreeze CreateTime)
'^^xsd:date))
(set gn:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(define-dump dump-genotypes
(tables (Geno
(left-join GenoXRef "ON Geno.Id = GenoXRef.GenoId")
(left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
(schema-triples
(gn:genotypeDataset rdfs:subPropertyOf gn:dataset))
(triples
(ontology
'genotype:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev))
'pre "_" 'post))
(set rdf:type 'gn:genotype)
(set gn:name (sanitize-rdf-string (field Geno Name)))
(set gn:markerName (sanitize-rdf-string (field Geno Marker_Name)))
(set gn:chr (field Geno Chr))
(set gn:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
(set gn:sequence (annotate-field (field Geno Sequence) '^^xsd:int))
(set gn:source (field Geno Source))
(set gn:source2 (field Geno Source2))
(set gn:genotypeOfDataset
(ontology 'dataset:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
'pre "_" 'post)))
(set gn:chrNum
(annotate-field
(field ("IFNULL(Geno.chr_num, '')" chr_num))
'^^xsd:int))
(set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments)))
(set gn:cM
(annotate-field
(field ("IFNULL(GenoXRef.cM, '')" Chr_mm8))
'^^xsd:int))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-genotype.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 "taxon:" "<http://purl.uniprot.org/taxonomy/>")
(prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
(prefix "up:" "<http://purl.uniprot.org/core/>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "genotype:" "<http://genenetwork.org/genotype/>")
(prefix "dataset:" "<http://genenetwork.org/dataset/>")
(newline)
(dump-genofreeze db)
(dump-genotypes db))
#:encoding "utf8")))
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