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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")
(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")
(left-join GeneChip "ON GeneChip.Id = InfoFiles.GeneChipId"))
"WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
(schema-triples
(gnt:has_case_info a owl:ObjectProperty)
(gnt:has_case_info rdfs:comment "Information about the cases used in this platform")
(gnt:has_case_info rdfs:domain dcat:Dataset)
(gnt:has_case_info rdfs:label "About Case")
(gnt:has_citation a owl:ObjectProperty)
(gnt:has_citation rdfs:comment "Citation for this dataset")
(gnt:has_citation rdfs:domain dcat:Dataset)
(gnt:has_citation rdfs:label "Citation")
(gnt:has_contributors a owl:ObjectProperty)
(gnt:has_contributors rdfs:comment "Contributors of this resource")
(gnt:has_contributors rdfs:comment "Contributors of this resource")
(gnt:has_contributors rdfs:domain dcat:Dataset)
(gnt:has_contributors rdfs:label "Contributors")
(gnt:has_data_processing_info a owl:ObjectProperty)
(gnt:has_data_processing_info rdfs:comment "Information about how this dataset was processed")
(gnt:has_data_processing_info rdfs:domain dcat:Dataset)
(gnt:has_data_processing_info rdfs:label "About Data Processing")
(gnt:has_experiment_design a owl:ObjectProperty)
(gnt:has_experiment_design rdfs:comment "Experiment Design for this resource")
(gnt:has_experiment_design rdfs:domain dcat:Dataset)
(gnt:has_experiment_design rdfs:label "Experiment Design")
(gnt:has_experiment_design_info a owl:ObjectProperty)
(gnt:has_experiment_design_info rdfs:comment "Information about how the experiment was designed")
(gnt:has_experiment_design_info rdfs:domain dcat:Dataset)
(gnt:has_experiment_design_info rdfs:label "Experiment Design")
(gnt:has_experiment_type a owl:ObjectProperty)
(gnt:has_experiment_type rdfs:comment "Information about the experiment type")
(gnt:has_experiment_type rdfs:comment "Information about the experiment type")
(gnt:has_experiment_type rdfs:domain dcat:Dataset)
(gnt:has_experiment_type rdfs:label "Experiment Type Metadata")
(gnt:has_platform_info a owl:ObjectProperty)
(gnt:has_platform_info rdfs:comment "Information about the platform that was used with this dataset")
(gnt:has_platform_info rdfs:domain dcat:Dataset)
(gnt:has_platform_info rdfs:label "About Platform")
(gnt:has_samples a owl:ObjectProperty)
(gnt:has_samples rdfs:domain dcat:Dataset)
(gnt:has_samples rdfs:label "Samples")
(gnt:has_specifics a owl:ObjectProperty)
(gnt:has_specifics rdfs:comment "Has specifics")
(gnt:has_specifics rdfs:domain dcat:Dataset)
(gnt:has_specifics rdfs:label "Specifics")
(gnt:has_summary a owl:ObjectProperty)
(gnt:has_summary rdfs:comment "Summary information about dataset")
(gnt:has_summary rdfs:domain dcat:Dataset)
(gnt:has_summary rdfs:label "Summary")
(gnt:has_tissue_info a owl:ObjectProperty)
(gnt:has_tissue_info rdfs:domain dcat:Dataset)
(gnt:has_tissue_info rdfs:label "Metadata about Tissue for this resource")
(gnt:uses_genechip a owl:ObjectProperty)
(gnt:uses_genechip rdfs:domain dcat:Dataset)
(gnt:uses_genechip skos:definition "The Platform this resource uses")
(gnt:uses_normalization_method rdfs:comment "The method used to map genetic or experimental data for this resource.")
(gnt:uses_normalization_method rdfs:domain dcat:Dataset)
(gnt:uses_normalization_method rdfs:label "Averaging method")
(gnt:uses_normalization_method rdfs:range gnc:avg_method))
(gnt:uses_normalization_method a owl:ObjectProperty)
(triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_")
(set rdf:type 'dcat:Dataset)
(set skos:prefLabel (field ProbeSetFreeze Name))
(set dct:title (normalize-string-field (field InfoFiles InfoPageName)))
(set rdfs:label (normalize-string-field (field InfoFiles InfoPageName)))
(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 "_"))
(set dct:identifier (format #f "GN~a" (field InfoFiles GN_AccesionId)))
(set gnt:has_experiment_type
(let ((experiment-type
(field InfoFiles Experiment_Type)))
(if (or (null? experiment-type) (string-blank? experiment-type))
"" (sanitize-rdf-string experiment-type))))
(set gnt:has_tissue_info
(let ((tissue-info
(field InfoFiles About_Tissue)))
(if (or (null? tissue-info) (string-blank? tissue-info))
"" (sanitize-rdf-string tissue-info))))
(set gnt:has_summary
(let* ((summary
(field InfoFiles Summary)))
(if (or (null? summary) (string-blank? summary))
"" (sanitize-rdf-string summary))))
(set gnt:has_citation
(let ((citation
(field InfoFiles Citation)))
(if (or (null? citation) (string-blank? citation))
"" (sanitize-rdf-string citation))))
(set gnt:has_samples
(let ((samples
(field InfoFiles samples)))
(if (or (null? samples) (string-blank? samples))
"" (sanitize-rdf-string samples))))
(set gnt:has_specifics
(let* ((specifics
(field InfoFiles Specifics)))
(if (or (null? specifics) (string-blank? specifics))
"" (sanitize-rdf-string specifics))))
(set gnt:has_case_info
(let ((cases
(field InfoFiles About_Cases)))
(if (or (null? cases) (string-blank? cases))
"" (sanitize-rdf-string cases))))
(set gnt:has_platform_info
(let* ((platform
(field InfoFiles About_Array_Platform)))
(if (or (null? platform) (string-blank? platform))
"" (sanitize-rdf-string platform))))
(set gnt:has_data_processing_info
(let* ((processing
(field InfoFiles About_Data_Values_Processing)))
(if (or (null? processing) (string-blank? processing))
"" (sanitize-rdf-string processing))))
(set gnt:has_experiment_type
(let ((experiment-type
(field InfoFiles Experiment_Type)))
(if (or (null? experiment-type) (string-blank? experiment-type))
"" (sanitize-rdf-string experiment-type))))
(set gnt:has_experiment_design
(let ((experiment-design
(field InfoFiles Overall_Design)))
(if (or (null? experiment-design) (string-blank? experiment-design))
"" (sanitize-rdf-string experiment-design))))
(set gnt:has_contributors
(let ((contributors
(field InfoFiles Contributor)))
(if (or (null? contributors) (string-blank? contributors))
"" (sanitize-rdf-string contributors))))))
(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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