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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))))
(define-dump dump-probeset
(tables (ProbeSet
(left-join ProbeSetXRef "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
(left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
(triples (ontology 'gn:probeset_ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
name)))
(set gn:probesetOfDataset
(string->identifier
"dataset"
(field ProbeSetFreeze Name)))
(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: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))
(set gn:locus (field ProbeSetXRef Locus))
(set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
(set gn:name (field ProbeSet Name))
(set gn:symbol (field ProbeSet Symbol))
(set gn:description (field ProbeSet description))
(set gn:chr (field ProbeSet Chr))
(set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gn:chr_2016 (field ProbeSet Chr_2016))
(set gn:mb_2016 (annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016)) '^^xsd:double))
(set gn:alias (string-trim-both (field ProbeSet alias)))
(set gn:generif (ontology 'generif: (field ProbeSet GeneId)))
(set gn:genbank (ontology 'nuccore: (field ProbeSet GenbankId)))
(set gn:snp (field ("IFNULL(ProbeSet.SNP, '')" SNP)))
(set gn:blatSeq (string-trim-both (field ProbeSet BlatSeq)))
(set gn:targetSeq (field ProbeSet TargetSeq))
(set gn:unigene (field ProbeSet UniGeneId))
(set gn:strandProbe (field ProbeSet Strand_Probe))
(set gn:strandGene (field ProbeSet Strand_Gene))
(set gn:omim (ontology 'omim: (field ProbeSet OMIM)))
(set gn:comments (sanitize-rdf-string (field ProbeSet comments)))
(set gn:targetRegion (field ProbeSet Probe_set_target_region))
(set gn:specificity (annotate-field
(field ("IFNULL(ProbeSet.Probe_set_specificity, '')" Probe_set_specificity))
'^^xsd:double))
(set gn:blatScore (annotate-field
(field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')" Probe_set_BLAT_score))
'^^xsd:double))
(set gn:blatMbStart (annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')" Probe_set_Blat_Mb_start))
'^^xsd:double))
(set gn:blatMbend (annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')" Probe_set_Blat_Mb_end))
'^^xsd:double))
(set gn:blatMbStart2016
(annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')" Probe_set_Blat_Mb_start_2016)) '^^xsd:double))
(set gn:blatMbend2016
(annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_2016, '')" Probe_set_Blat_Mb_end_2016)) '^^xsd:double))
(set gn:strand (field ProbeSet Probe_set_strand))
(set gn:noteByRW (field ProbeSet Probe_set_Note_by_RW))
(set gn:flag (field ProbeSet flag))
(set gn:symbolH (field ProbeSet Symbol_H))
(set gn:descriptionH (field ProbeSet Description_H))
(set gn:chromosomeH (field ProbeSet chromosome_H))
(set gn:mbH (annotate-field (field ProbeSet MB_H) '^^xsd:double))
(set gn:aliasH (field ProbeSet alias_H))
(set gn:geneIdH (field ProbeSet GeneId_H))
(set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num)))
(set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num)))
(set gn:probeTargetDescription (field ProbeSet Probe_Target_Description))
(set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId)))
(set gn:ENSEMBLGeneId (string-trim-both
(field ProbeSet ENSEMBLGeneId)))
(set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8)))
(set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8)))
(set gn:probeSetBlatMbStart_mm8
(annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_mm8, '')" Probe_set_Blat_Mb_start_mm8))
'^^xsd:double))
(set gn:probeSetBlatMbEnd_mm8
(annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_mm8, '')" Probe_set_Blat_Mb_end_mm8))
'^^xsd:double))
(set gn:homoloGeneID (ontology
'homologene:
(field ProbeSet HomoloGeneID)))
(set gn:biotype_ENS (field ProbeSet Biotype_ENS))
(set gn:proteinName (field ProbeSet ProteinName))
(set gn:uniProtReference (ontology 'uniprot:
(field ProbeSet UniProtID)))
(set gn:flybase_Id (field ProbeSet Flybase_Id))
(set gn:RGD_ID (field ("IFNULL(ProbeSet.RGD_ID, '')" RGD_ID)))
(set gn:hgnc (ontology
'hgnc: (field ProbeSet HGNC_ID)))
(set gn:HMDB_ID (field ProbeSet HMDB_ID))
(set gn:confidence (field ("IFNULL(ProbeSet.Confidence, '')" Confidence)))
(set gn:chebi_ID (ontology
'chebi:
(field
("IFNULL(ProbeSet.ChEBI_ID, '')"
ChEBI_ID))))
(set gn:CASNumber (field ProbeSet CAS_number))
(set gn:PubChemID (ontology
'pubchem:
(field
("IFNULL(ProbeSet.PubChem_ID, '')"
PubChem_ID))))
(set gn:chemSpiderID (field ("IFNULL(ProbeSet.ChemSpider_ID, '')" ChemSpider_ID)))
(set gn:uniiID (field ProbeSet UNII_ID))
(set gn:ECNumber (field ProbeSet EC_number))
(set gn:keggID (ontology 'kegg:
(field ProbeSet KEGG_ID)))
(set gn:molecularWeight (annotate-field (field ProbeSet Molecular_Weight) '^^xsd:double))
(set gn:nugowikiID (field ("IFNULL(ProbeSet.Nugowiki_ID, '')" Nugowiki_ID)))
(set gn:type (field ProbeSet Type))
(set gn:tissue (field ProbeSet Tissue))
(set gn:primaryName (field ProbeSet PrimaryName))
(set gn:secondaryNames (field ProbeSet SecondaryNames))
(set gn:peptideSequence (field ProbeSet PeptideSequence))))
;; Molecular Traits are also referred to as ProbeSets
(define-dump dump-probesetfreeze
(tables (ProbeSetFreeze
(left-join ProbeFreeze "USING (ProbeFreezeId)")
(left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(left-join InbredSet "ON ProbeFreeze.InbredSetId=InbredSet.Id")
(left-join Tissue "USING (TissueId)"))
"WHERE ProbeSetFreeze.public > 0 GROUP BY ProbeFreeze.Id")
(schema-triples
(gn:molecularTrait rdfs:range rdfs:Literal))
(triples
(string->identifier "dataset" (field ProbeSetFreeze Name))
(set rdf:type 'gn:dataset)
(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-probeset.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#>")
(newline)
(dump-gene-chip db)
(dump-probeset db)
(dump-probesetfreeze db))
#:encoding "utf8")))
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