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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))
;; These are phenotype datasets that don't have Infofile metadata
(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.InfoFileId IS NULL")
(triples
(string->identifier
""
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field PublishFreeze Name)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:phenotypeDataset)
(set rdfs:label (field PublishFreeze Name))
(set skos:prefLabel (field PublishFreeze FullName))
(set skos:altLabel (field PublishFreeze ShortName))
(set dct:created (annotate-field
(field PublishFreeze CreateTime)
'^^xsd:date))
(set gnt:belongsToInbredSet
(string->identifier
"" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first))))
(define-dump dump-phenotypes
(tables (Phenotype
(left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
;; We need this join so as to construct the trait's skos:altLabel
(left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
(left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name"))
;; Only dump public traits; Ignore "hanging" traits
;; I.e. traits that have no associated vectors
"WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL")
(schema-triples
(gnc:phenotype a skos:Concept)
(gnc:phenotype skos:description "This is a set of controlled terms that are used to describe a given phenotype")
(gnt:abbreviation a owl:ObjectProperty)
(gnt:abbreviation rdfs:domain gnc:phenotype)
(gnt:abbreviation skos:definition "The abbreviation used for this resource")
(gnt:labCode a owl:ObjectProperty)
(gnt:labCode rdfs:domain gnc:phenotype)
(gnt:submitter a owl:ObjectProperty)
(gnt:submitter rdfs:domain gnc:phenotype)
(gnt:submitter skos:definition "A person who submitted this resource to GN")
(gnt:mean rdfs:domain gnc:phenotype)
(gnt:mean rdfs:range xsd:double)
(gnt:LRS rdfs:domain gnc:phenotype)
(gnt:LRS rdfs:range xsd:double)
(gnt:locus rdfs:domain gnc:phenotype)
(gnt:locus rdfs:range rdfs:Literal)
(gnt:additive rdfs:domain gnc:phenotype)
(gnt:additive rdfs:range xsd:double)
(gnt:sequence rdfs:domain gnc:phenotype)
(gnt:sequence rdfs:range xsd:integer))
(triples (string->identifier
""
(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)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:phenotype)
(set skos:prefLabel (sanitize-rdf-string
(field
("IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)"
PhenotypeName))))
;; Add an alternative name for this resources. This is how GN
;; currently labels phenotypes
(set skos:altLabel (field
("CONCAT(InbredSet.Name, '_', PublishXRef.Id)"
phenotypeAltName)))
;; All phenotypes have a post-publication description
(set dct:description
(sanitize-rdf-string
(field Phenotype Post_publication_description)))
;; All phenotypes have a post-publication abbreviation
(set gnt:abbreviation (field Phenotype Post_publication_abbreviation))
(set gnt:labCode (field Phenotype Lab_code))
(set gnt:submitter
(sanitize-rdf-string (field Phenotype Submitter)))
(set dct:contributor (sanitize-rdf-string (field Phenotype Owner)))
(multiset dct:contributor (string-split
(sanitize-rdf-string (field Phenotype Owner))
#\,))
(set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
(set gnt:locus (field PublishXRef Locus))
(set gnt:LRS (annotate-field
(field ("IFNULL(PublishXRef.LRS, '')" lrs))
'^^xsd:double))
(set gnt:additive
(annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive))
'^^xsd:double))
(set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:integer))
(set gnt:belongsToDataset
(string->identifier
""
(regexp-substitute/global #f "[^A-Za-z0-9:]"
(field InfoFiles InfoPageName)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first))
(set dct:isReferencedBy
(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 "unpublished"
(number->string publication-id))
(ontology 'pubmed: pmid))))))
(dump-with-documentation
(name "Phenotypes Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dct:" "<http://purl.org/dc/terms/>")
("gn:" "<http://genenetwork.org/id/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("gnc:" "<http://genenetwork.org/category/>")
("gnt:" "<http://genenetwork.org/terms/>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list
dump-publishfreeze
dump-phenotypes))
(outputs
'(#:documentation "./docs/dump-phenotype.md"
#:rdf "./verified-data/dump-phenotype.ttl")))
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