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#! /usr/bin/env guile
!#
(use-modules (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 gn:molecular-traits->gn:datasets
(tables (Tissue))
(schema-triples
(gnc:molecular_trait a owl:Class)
(gnc:molecular_trait a skos:Concept)
(gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479)
(gnc:molecular_trait rdfs:label "Molecular Trait. This describes a melecular trait of a given species. We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups."))
(triples (string->identifier "trait" (field Tissue Short_Name) #:separator "_")
(set rdf:type 'gnc:molecular_trait)
(set skos:prefLabel (field Tissue Name))
(set skos:altLabel (field Tissue Short_Name))))
(define-transformer gnc:molecular_trait->gn:molecular_trait
(tables (Tissue))
(triples "gnc:molecular_trait"
(set skos:member (string->identifier "trait" (field Tissue Short_Name) #:separator "_"))))
(define-transformer gn:set->gn:dataset
(tables (Species
(inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
(inner-join ProbeFreeze "ON ProbeFreeze.InbredSetId = InbredSet.Id")
(inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
(inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
"WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, Tissue.Short_Name")
(schema-triples
(gnt:has_probeset_data rdf:type owl:ObjectProperty)
(gnt:has_probeset_data rdfs:label "this resources has this probeset data.")
(gnt:has_probeset_data rdfs:comment "Associates a resource with this probeset data.")
(gnt:has_probeset_data rdfs:domain gnc:set)
(gnt:has_probeset_data rdfs:range gnc:molecular_trait)
(gnt:has_probeset_data rdfs:subPropertyOf dct:relation))
(triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
(multiset gnt:has_probeset_data
(map (cut string->identifier "dataset" <> #:separator "_")
(string-split
(field ("GROUP_CONCAT(ProbeSetFreeze.Name SEPARATOR ',')"
dataset_name))
#\,)))))
(define-transformer gn:dataset->set/species/molecular_trait
(tables (Species
(inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
(inner-join ProbeFreeze "ON ProbeFreeze.InbredSetId = InbredSet.Id")
(inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
(inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
"WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
(schema-triples
(gnt:has_molecular_trait rdf:type owl:ObjectProperty)
(gnt:has_molecular_trait rdfs:domain gnc:set)
(gnt:has_molecular_trait rdfs:range gnc:molecular_trait)
(gnt:has_molecular_trait rdfs:label "has molecular trait"))
(triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_")
(set gnt:has_strain
(string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
(set gnt:has_species
(string->identifier "" (remap-species-identifiers (field Species Fullname))))
(set gnt:has_molecular_trait
(string->identifier "trait" (field Tissue Short_Name) #:separator "_"))))
(define-transformer gn:dataset->metadata
(tables (ProbeSetFreeze
(inner-join ProbeFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
(inner-join InbredSet "ON InbredSet.Id = ProbeFreeze.InbredSetId")
(inner-join Species "ON InbredSet.SpeciesId = Species.Id")
(inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id")
(inner-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(inner-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(inner-join Datasets "ON InfoFiles.DatasetId = Datasets.DatasetId")
(left-join GeneChip "ON GeneChip.Id = InfoFiles.GeneChipId"))
"WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
(schema-triples
(gnt:uses_genechip a owl:ObjectProperty)
(gnt:uses_genechip rdfs:domain dcat:Dataset)
(gnt:uses_genechip skos:definition "The Platform this resource uses for it's molecular traits.")
(gnt:uses_normalization_method rdfs:comment "The normalization method used for the molecular traits in this dataset")
(gnt:uses_normalization_method rdfs:domain dcat:Dataset)
(gnt:uses_normalization_method rdfs:label "Averaging method used for the molecular traits in this dataset.")
(gnt:uses_normalization_method rdfs:range gnc:avg_method))
(triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_")
(set dct:created (annotate-field (field ProbeSetFreeze CreateTime) '^^xsd:datetime))
(set gnt:uses_normalization_method
(string->identifier "avg_method" (field AvgMethod Name AvgMethodName) #:separator "_"))
(set gnt:has_strain
(string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
(set gnt:has_species
(string->identifier "" (remap-species-identifiers (field Species Fullname))))
(set gnt:has_molecular_trait
(string->identifier "trait" (field Tissue Short_Name) #:separator "_"))
(set gnt:uses_genechip
(string->identifier "platform" (field GeneChip Name) #:separator "_"))))
(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 "Molecular Traits")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("dcat:" "<http://www.w3.org/ns/dcat#>")
("gn:" "<http://rdf.genenetwork.org/v1/id/>")
("obo:" "<http://purl.obolibrary.org/obo/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("dct:" "<http://purl.org/dc/terms/>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
(inputs
(list
gn:dataset->metadata
gn:dataset->set/species/molecular_trait
gn:molecular-traits->gn:datasets
gn:set->gn:dataset
gnc:molecular_trait->gn:molecular_trait))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
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