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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))
;; Only dump publish freeze entries that were not dumped from the InfoFiles page
(define-dump dump-publishfreeze
(tables (PublishFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
(left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
"WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
(schema-triples
(gn:datasetOfInbredSet rdfs:range gn:inbredSet)
(gn:name rdfs:range rdfs:Literal)
(gn:fullName rdfs:range rdfs:Literal)
(gn:shortName rdfs:range rdfs:Literal)
(gn:createTime rdfs:range rdfs:Literal)
(gn:phenotypeDataset rdf:subClassOf gn:dataset))
(triples (string->identifier "dataset" (field PublishFreeze Name))
(set rdf:type 'gn:phenotypeDataset)
(set gn:name (field PublishFreeze Name))
(set gn:fullName (field PublishFreeze FullName))
(set gn:shortName (field PublishFreeze ShortName))
(set dct:created (annotate-field
(field PublishFreeze CreateTime)
'^^xsd:date))
(set gn:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(define-dump dump-phenotypes
(tables (Phenotype
(left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
(schema-triples
(gn:phenotypeDataset rdfs:subPropertyOf gn:dataset))
(triples (ontology 'phenotype:
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, ':')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
'pre "_" 'post))
(set rdf:type 'gn:phenotype)
(set gn:name (sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100))"
PhenotypeName))))
;; There is no row with an empty post-publication description so
;; use this field as the main publication description
(set gn:publicationDescription
(sanitize-rdf-string
(field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
postPubDescr))))
(set gn:originalDescription (sanitize-rdf-string
(delete-substrings
(field Phenotype Original_description)
"Original post publication description: ")))
(set gn:prePublicationDescription
(sanitize-rdf-string
(field
("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
prePubDesc))))
(set gn:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
(set gn:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
(set gn:labCode (field Phenotype Lab_code))
(set gn:submitter (sanitize-rdf-string (field Phenotype Submitter)))
(set gn:owner (sanitize-rdf-string (field Phenotype Owner)))
(set gn:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
(set gn:locus (field PublishXRef Locus))
(set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
(set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
(set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
(set gn:phenotypeOfDataset
(ontology 'dataset:
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("IFNULL(PublishFreeze.Name, '')" DatasetName))
'pre "_" 'post)))
(set gn:phenotypeOfPublication
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
pmid)))
(publication-id (field Publication Id)))
(if (string-null? pmid)
(string->identifier "publication"
(number->string publication-id))
(ontology 'pubmed: pmid))))))
(call-with-target-database
%connection-settings
(lambda (db)
(with-output-to-file (string-append %dump-directory "dump-phenotype.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 "dataset:" "<http://genenetwork.org/dataset/>")
(newline)
(dump-publishfreeze db)
(dump-phenotypes db))
#:encoding "utf8")))
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