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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"]
["Monkey (Macaca nemestrina)" "Macaca nemestrina"]
["Bat (Glossophaga soricina)" "Glossophaga soricina"]
[str str]))
(define-dump dump-species
(tables (Species))
(schema-triples
(gnt:name rdfs:range rdfs:Literal)
(gnt:displayName rdfs:range rdfs:Literal)
(gnt:binomialName rdfs:range rdfs:Literal)
(gnt:family rdfs:range rdfs:Literal))
(triples
(string->binomial-name (field Species FullName))
(set rdf:type 'gnc:species)
(set gnt:name (field Species SpeciesName))
(set gnt:displayName (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
(gnt:strainOfSpecies rdfs:domain gnt:strain)
(gnt:strainOfSpecies rdfs:range gn-term:species)
(gn-term:name rdfs:range rdfs:Literal)
(gn-term:alias rdfs:range rdfs:Literal)
(gn-term:symbol rdfs:range rdfs:Literal))
(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 gn-term:strainOfSpecies
(string->identifier "" (remap-species-identifiers (field Species FullName))
#:separator ""
#:proc string-capitalize-first))
;; Name, and maybe a second name
(set gn-term:name (sanitize-rdf-string (field Strain Name)))
(set gn-term:name2 (sanitize-rdf-string (field Strain Name2)))
(set gn-term:alias (sanitize-rdf-string (field Strain Alias)))
(set gn-term:symbol (field Strain Symbol))))
(define-dump dump-mapping-method
(tables (MappingMethod))
(triples
(string->identifier "mappingMethod" (field MappingMethod Name))
(set rdf:type 'gnc:mappingMethod)))
(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
(gn-term:fullName rdfs:range rdfs:Literal)
(gn-term:geneticType rdfs:range rdfs:Literal)
(gn-term:inbredSetCode rdfs:range rdfs:Literal)
(gn-term:inbredFamily rdfs:range rdfs:Literal)
(gn-term:inbredSetOfSpecies rdfs:range gn:species)
(gn-term:inbredSetType rdfs:range rdfs:Literal)
(gn-term:phenotype rdfs:range gn-term:inbredSetType)
(gn-term:genotype rdfs:range gn-term:inbredSetType)
(gn-term:inbredSetOfMappingMethod rdfs:range gn-term:mappingMethod))
(triples (string->identifier
"" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gnc:inbredSet)
(set gn-term:binomialName (field InbredSet FullName))
(set gn-term:geneticType (field InbredSet GeneticType))
(set gn-term:inbredFamily (field InbredSet Family))
(set gn-term:inbredSetOfMappingMethod (field MappingMethod Name))
(set gn-term:inbredSetCode (field InbredSet InbredSetCode))
(set gn-term:inbredSetOfSpecies
(string->binomial-name
(field Species FullName BinomialName)))
(set gn-term:genotype
(field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
(set gn-term:phenotype
(field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))
(define-dump dump-avg-method
;; The Name and Normalization fields seem to be the same. Dump only
;; the Name field.
(tables (AvgMethod))
(schema-triples
(gn-term:normalization rdfs:range rdfs:Literal))
(triples (string->identifier "avgmethod" (field AvgMethod Name))
(set rdf:type 'gnc:avgMethod)
(set gn-term:normalization (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/>")
("gnt:" "<http://genenetwork.org/term/>")
("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-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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