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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 (remap-species-identifiers str)
"This procedure remaps identifiers to standard binominal. Obviously this should
be sorted by correcting the database!"
(match str
["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
["Macaca mulatta" "Macaca nemestrina"]
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
(define-dump dump-species
(tables (Species))
(schema-triples
(gnc:species a skos:Concept)
(gnc:species skos:description "This is a set of controlled terms that are used to describe a given species")
(gnc:species skos:broader gnc:family)
(gnt:binomialName a owl:ObjectProperty)
(gnt:binomialName rdfs:domain gnc:species)
(gnt:family a owl:ObjectProperty)
(gnt:family rdfs:domain gnc:species)
(gnt:family skos:definition "This resource belongs to this family")
(gnt:organism a owl:ObjectProperty)
(gnt:organism rdfs:domain gnc:species)
(gnt:shortName a owl:ObjectProperty)
(gnt:shortName rdfs:domain gnc:species))
(triples
(string->identifier "" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:species)
(set skos:label (field Species SpeciesName))
(set skos:altLabel (field Species Name))
(set rdfs:label (field Species MenuName))
(set gnt:binomialName (field Species FullName))
(set gnt:family (field Species Family))
(set gnt:organism (ontology 'taxon: (field Species TaxonomyId)))))
(define-dump dump-strain
(tables (Strain
(left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
(schema-triples
(gnc:strain skos:broader gnc:species)
(gnt:species rdfs:domain gnc:strain)
(gnt:species skos:definition "This resource belongs to this species")
(gnt:species a owl:ObjectProperty)
(gnt:species skos:definition "This resource belongs to this species")
(gnt:alias rdfs:domain gnc:strain)
(gnt:alias a owl:ObjectProperty)
(gnt:symbol rdfs:domain gnc:strain)
(gnt:symbol a owl:ObjectProperty))
(triples (string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:strain)
(set gnt:species
(string->identifier "" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
;; Name, and maybe a second name
(set rdfs:label (sanitize-rdf-string (field Strain Name)))
(set rdfs:label (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2))))
(set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias))))
(set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol)))))
(define-dump dump-mapping-method
(tables (MappingMethod))
(schema-triples
(gnc:mappingMethod a skos:Concept)
(gnc:mappingMethod skos:definition "Terms that decribe mapping/normalization methods used in GeneNetwork"))
(triples
(string->identifier "mappingMethod" (field MappingMethod Name))
(set rdf:type 'gnc:mappingMethod)
(set rdfs:label (field MappingMethod Name))))
(define-dump dump-inbred-set
(tables (InbredSet
(left-join Species "ON InbredSet.SpeciesId=Species.Id")
(left-join MappingMethod
"ON InbredSet.MappingMethodId=MappingMethod.Id")))
(schema-triples
(gnc:inbredSet skos:broader gnc:species)
(gnc:inbredSet skos:definition "A set of terms used to describe an inbred set")
(gnt:geneticType a owl:ObjectProperty)
(gnt:geneticType rdfs:domain gnc:inbredSet)
(gnt:code a owl:ObjectProperty)
(gnt:code rdfs:domain gnc:inbredSet)
;; Already defined as an owl prop in dump-species
(gnt:family rdfs:domain gnc:inbredSet)
(gnt:phenotype a owl:ObjectProperty)
(gnt:phenotype rdfs:domain gnc:inbredSet)
(gnt:genotype a owl:ObjectProperty)
(gnt:genotype rdfs:domain gnt:inbredSet)
(gnt:mappingMethod a owl:ObjectProperty)
(gnt:mappingMethod rdfs:domain gnc:inbredSet))
(triples (string->identifier
"" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:inbredSet)
(set rdfs:label (field InbredSet FullName))
(set gnt:geneticType (field InbredSet GeneticType))
(set gnt:family (field InbredSet Family))
(set gnt:mappingMethod (field MappingMethod Name))
(set gnt:code (field InbredSet InbredSetCode))
(set gnt:species
(string->identifier "" (remap-species-identifiers (field Species Fullname))
#:separator ""
#:proc string-capitalize-first))
(set gnt:genotype
(field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
(set gnt:phenotype
(field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))
(multiset gnt:molecularTrait
(map
(lambda (x)
(string->identifier "tissue"
x))
(string-split-substring
(field ("(SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name)"
molecularTrait))
"||")))))
(define-dump dump-avg-method
;; The Name and Normalization fields seem to be the same. Dump only
;; the Name field.
(tables (AvgMethod))
(schema-triples
(gnc:avgMethod rdf:type owl:Class))
(triples (string->identifier "avgmethod" (field AvgMethod Name))
(set rdf:type 'gnc:avgMethod)
(set rdfs:label (field AvgMethod Normalization))))
(dump-with-documentation
(name "Species Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
("gnc:" "<http://genenetwork.org/category/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("gnt:" "<http://genenetwork.org/term/>")
("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#>")
("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
(inputs
(list
dump-inbred-set
dump-species
dump-strain
dump-mapping-method
dump-avg-method))
(outputs
'(#:documentation "./docs/dump-species-metadata.md"
#:rdf "./verified-data/dump-species-metadata.ttl")))
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