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#! /usr/bin/env guile
!#
(use-modules (rnrs programs)
(rnrs io ports)
(srfi srfi-1)
(srfi srfi-26)
(ice-9 getopt-long)
(ice-9 match)
(ice-9 regex)
(transform strings)
(transform sql)
(transform triples)
(transform special-forms))
(define-transformer phenotypes
(tables (PublishXRef
(left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")))
(schema-triples
(gnt:traitId a owl:ObjectProperty)
(gnt:traitId rdfs:domain gnc:Phenotype)
(gnt:traitId skos:definition "This is the unique trait id assigned from GeneNetwork")
(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 a rdf:Property)
(gnt:mean a qb:MeasureProperty)
(gnt:mean rdfs:subPropertyOf sdmx-measure:obsValue)
(gnt:mean rdfs:domain gnc:Phenotype)
(gnt:mean rdfs:range xsd:double)
(gnt:lodScore a rdf:Property)
(gnt:lodScore a qb:MeasureProperty)
(gnt:lodScore rdfs:subPropertyOf sdmx-measure:obsValue)
(gnt:lodScore rdfs:domain gnc:Phenotype)
(gnt:lodScore rdfs:range xsd:double)
(gnt:lodScore rdfs:label "Peak -logP")
(gnt:lodScore skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.")
(gnt:locus a rdf:Property)
(gnt:locus a qb:MeasureProperty)
(gnt:locus rdfs:subPropertyOf sdmx-measure:obsValue)
(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
"trait"
(field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
(set rdf:type 'gnc:Phenotype)
(set gnt:belongsToGroup
(string->identifier
"set" (field InbredSet Name InbredSetName)
#:separator ""
#:proc string-capitalize-first))
;; This is the trait's name
(set gnt:traitId
(let ((trait-id (field PublishXRef Id)))
(if (number? trait-id)
(number->string trait-id)
trait-id)))
(set skos:altLabel
(field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
;; 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)))
(multiset dct:contributor
(map string-trim-both
(string-split
(sanitize-rdf-string (field Phenotype Owner))
#\,)))
(set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
(set gnt:locus
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(sanitize-rdf-string (field PublishXRef Locus))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first))
(set gnt:lodScore (annotate-field
(field ("IFNULL((PublishXRef.LRS/4.604), '')" 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 dct:isReferencedBy
(let ((pmid (field
("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
pmid)))
(publication-id (field Publication Id PublicationId)))
(if (string-null? pmid)
(string->identifier "unpublished"
(number->string publication-id))
(ontology 'pubmed: pmid))))))
(let* ((option-spec
'((settings (single-char #\s) (value #t))
(output (single-char #\o) (value #t))
(documentation (single-char #\d) (value #t))))
(options (getopt-long (command-line) option-spec))
(settings (option-ref options 'settings #f))
(output (option-ref options 'output #f))
(documentation (option-ref options 'documentation #f))
(%connection-settings
(call-with-input-file settings
read)))
(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/term/>")
("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
("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#>")
("qb:" "<http://purl.org/linked-data/cube#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list
phenotypes))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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