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#! /usr/bin/env guile
!#
(use-modules (ice-9 getopt-long)
(transform triples)
(transform schema)
(transform special-forms))
(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-output-to-file output
(lambda ()
;; Define all GN ontology in one place.
(prefix "dcat:" "<http://www.w3.org/ns/dcat#>")
(prefix "dct:" "<http://purl.org/dc/terms/>")
(prefix "gn:" "<http://rdf.genenetwork.org/v1/id/>")
(prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
(prefix "gnc:" "<http://rdf.genenetwork.org/v1/category/>")
(prefix "gnt:" "<http://rdf.genenetwork.org/v1/term/>")
(prefix "obo:" "<http://purl.obolibrary.org/obo/>")
(prefix "sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
(prefix "skos:" "<http://www.w3.org/2004/02/skos/core#>")
(prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
(prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
(prefix "qb:" "<http://purl.org/linked-data/cube#>")
(prefix "xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
(prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
(prefix "schema:" "<https://schema.org/>")
(newline)
(triple 'gnc:population_category 'a 'xkos:ClassificationLevel)
(triple 'gnc:population_category 'rdfs:label "Population Category")
(triple 'gnc:population_category 'skos:inScheme 'gnc:resource_classification_scheme)
(triple 'gnc:population_category 'skos:prefLabel "Species")
(triple 'gnc:population_category 'xkos:depth "3")
(triple 'gnc:population_category 'xkos:nextLevel 'gnc:set)
(triple 'gnc:population_category 'xkos:previousLevel 'gnc:species)
(triple 'gnc:reference_population 'a 'skos:Concept)
(triple 'gnc:reference_population 'skos:definition "A genetic population")
(triple 'gnc:reference_population 'skos:inScheme 'gnc:population_category)
(triple 'gnc:reference_population 'skos:prefLabel "Reference population")
(triple 'gnc:resource_classification_scheme 'a 'skos:ConceptScheme)
(triple 'gnc:resource_classification_scheme 'skos:definition "A hierarchical classification scheme for organizing GeneNetwork resources by dataset type, resource set (inbredset group), or species.")
(triple 'gnc:resource_classification_scheme 'skos:prefLabel "GeneNetwork Resource Classification Scheme")
(triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:population_category)
(triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:set)
(triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:species)
(triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:taxonomic_family)
(triple 'gnc:resource_classification_scheme 'xkos:numberOfLevels "4")
(triple 'gnc:set 'a 'xkos:ClassificationLevel)
(triple 'gnc:set 'skos:definition "A category representing groups of genetically related strains or individuals (inbred sets, recombinant inbred lines, etc.).")
(triple 'gnc:set 'skos:inScheme 'gnc:resource_classification_scheme)
(triple 'gnc:set 'skos:prefLabel "InbredSet Group")
(triple 'gnc:set 'xkos:depth "4")
(triple 'gnc:set 'xkos:previousLevel 'gnc:population_category)
(triple 'gnc:species 'a 'xkos:ClassificationLevel)
(triple 'gnc:species 'skos:definition "A classification level that that associates a given resource to a species in GeneNetwork.")
(triple 'gnc:species 'skos:inScheme 'gnc:resource_classification_scheme)
(triple 'gnc:species 'skos:prefLabel "Species")
(triple 'gnc:species 'xkos:depth "2")
(triple 'gnc:species 'xkos:nextLevel 'gnc:population_category)
(triple 'gnc:species 'xkos:previousLevel 'gnc:taxonomic_family)
(triple 'gnc:taxonomic_family 'a 'xkos:ClassificationLevel)
(triple 'gnc:taxonomic_family 'skos:definition "An organizational classification level used in GeneNetwork to group resources into families.")
(triple 'gnc:taxonomic_family 'skos:inScheme 'gnc:resource_classification_scheme)
(triple 'gnc:taxonomic_family 'skos:prefLabel "Family")
(triple 'gnc:taxonomic_family 'xkos:depth "1")
(triple 'gnc:taxonomic_family 'xkos:nextLevel 'gnc:species)
(triple 'gnt:assigned_species 'a 'owl:ObjectProperty)
(triple 'gnt:assigned_species 'rdfs:domain 'gnc:set)
(triple 'gnt:assigned_species 'rdfs:label "These families have been assigned to these species")
(triple 'gnt:genetic_type 'a 'owl:DatatypeProperty)
(triple 'gnt:genetic_type 'rdfs:domain 'gnc:set)
(triple 'gnt:genetic_type 'rdfs:label "has genetic type")
(triple 'gnt:genetic_type 'rdfs:range 'xsd:string)
(triple 'gnt:genetic_type 'skos:definition "Describes the genetic architecture of a resource set (e.g., intercross, riset).")
(triple 'gnt:has_family_order_id 'a 'owl:DatatypeProperty)
(triple 'gnt:has_family_order_id 'a 'owl:DatatypeProperty)
(triple 'gnt:has_family_order_id 'rdfs:range 'xsd:integer)
(triple 'gnt:has_set_code 'a 'owl:DatatypeProperty)
(triple 'gnt:has_set_code 'rdfs:domain 'gnc:set)
(triple 'gnt:has_set_code 'rdfs:label "has set code")
(triple 'gnt:has_set_code 'rdfs:range 'xsd:string)
(triple 'gnt:has_set_code 'skos:definition "Provides a unique identifier code for a resource set.")
(triple 'gnt:has_species 'a 'owl:ObjectProperty)
(triple 'gnt:has_species 'rdf:comment "This resource belongs to this species")
(triple 'gnt:has_species 'rdfs:label "belongs to species")
(triple 'gnt:has_species 'rdfs:range 'gnc:species)
(triple 'gnt:has_strain 'a 'owl:ObjectProperty)
(triple 'gnt:has_strain 'rdf:comment "Indicates the group the resources belongs to")
(triple 'gnt:has_strain 'rdfs:domain 'gnc:species)
(triple 'gnt:has_strain 'rdfs:label "this resource belongs to this strain.")
(triple 'gnt:has_strain 'rdfs:range 'gnc:set)
(triple 'gnt:has_strain 'schema:domainIncludes 'dcat:Dataset)
(triple 'gnt:has_strain 'schema:domainIncludes 'gnc:species)
(triple 'gnt:has_strain 'skos:definition "Lists all strains that belong to this resource.")
(triple 'gnt:has_taxonomic_family 'a 'owl:ObjectProperty)
(triple 'gnt:has_taxonomic_family 'rdfs:label "has family")
(triple 'gnt:has_taxonomic_family 'schema:domainIncludes 'gnc:set)
(triple 'gnt:has_taxonomic_family 'schema:domainIncludes 'gnc:species)
(triple 'gnt:has_taxonomic_family 'skos:definition "Links a species to its taxonomic family")
(triple 'gnt:has_uniprot_taxon_id 'a 'owl:ObjectProperty)
(triple 'gnt:has_uniprot_taxon_id 'rdfs:label "has uniprot taxonomic id")
(triple 'gnt:population_category 'skos:definition "Classification of genetic populations by breeding design and data aggregation.")
(triple 'gnt:short_name 'a 'owl:DatatypeProperty)
(triple 'gnt:short_name 'rdfs:domain 'gnc:species)
(triple 'gnt:short_name 'rdfs:label "has short name")
(triple 'gnt:short_name 'skos:definition "The short name of a given resource")
(triple 'gnt:uses_mapping_method 'a 'owl:ObjectProperty)
(triple 'gnt:uses_mapping_method 'rdfs:comment "The method used to map genetic or experimental data for this resource.")
(triple 'gnt:uses_mapping_method 'rdfs:domain 'gnc:set)
(triple 'gnt:uses_mapping_method 'rdfs:label "mapping method")
(triple 'gnt:uses_mapping_method 'rdfs:range 'gnc:mapping_method)
;; Describing Datasets
(triple 'gnc:molecular_trait 'a 'owl:Class)
(triple 'gnc:molecular_trait 'a 'skos:Concept)
(triple '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.")
(triple 'gnc:molecular_trait 'rdfs:subClassOf 'obo:UBERON_0000479)
(triple 'gnt:has_case_info 'a 'owl:ObjectProperty)
(triple 'gnt:has_case_info 'rdfs:comment "Information about the cases used in this platform")
(triple 'gnt:has_case_info 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_case_info 'rdfs:label "About Case")
(triple 'gnt:has_citation 'a 'owl:ObjectProperty)
(triple 'gnt:has_citation 'rdfs:comment "Citation for this dataset")
(triple 'gnt:has_citation 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_citation 'rdfs:label "Citation")
(triple 'gnt:has_contributors 'a 'owl:ObjectProperty)
(triple 'gnt:has_contributors 'rdfs:comment "Contributors of this resource")
(triple 'gnt:has_contributors 'rdfs:comment "Contributors of this resource")
(triple 'gnt:has_contributors 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_contributors 'rdfs:label "Contributors")
(triple 'gnt:has_data_processing_info 'a 'owl:ObjectProperty)
(triple 'gnt:has_data_processing_info 'rdfs:comment "Information about how this dataset was processed")
(triple 'gnt:has_data_processing_info 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_data_processing_info 'rdfs:label "About Data Processing")
(triple 'gnt:has_experiment_design 'a 'owl:ObjectProperty)
(triple 'gnt:has_experiment_design 'rdfs:comment "Experiment Design for this resource")
(triple 'gnt:has_experiment_design 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_experiment_design 'rdfs:label "Experiment Design")
(triple 'gnt:has_experiment_design_info 'a 'owl:ObjectProperty)
(triple 'gnt:has_experiment_design_info 'rdfs:comment "Information about how the experiment was designed")
(triple 'gnt:has_experiment_design_info 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_experiment_design_info 'rdfs:label "Experiment Design")
(triple 'gnt:has_experiment_type 'a 'owl:ObjectProperty)
(triple 'gnt:has_experiment_type 'rdfs:comment "Information about the experiment type")
(triple 'gnt:has_experiment_type 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_experiment_type 'rdfs:label "Experiment Type Metadata")
(triple 'gnt:has_molecular_trait 'rdf:type 'owl:ObjectProperty)
(triple 'gnt:has_molecular_trait 'rdfs:domain 'gnc:set)
(triple 'gnt:has_molecular_trait 'rdfs:label "has molecular trait")
(triple 'gnt:has_molecular_trait 'rdfs:range 'gnc:molecular_trait)
(triple 'gnt:has_phenotype_data 'rdf:type 'owl:ObjectProperty)
(triple 'gnt:has_phenotype_data 'rdfs:comment "Associates a resource with its phenotype data.")
(triple 'gnt:has_phenotype_data 'rdfs:domain 'gnc:set)
(triple 'gnt:has_phenotype_data 'rdfs:label "this resources has this phenotype data.")
(triple 'gnt:has_phenotype_data 'rdfs:range 'dcat:Dataset)
(triple 'gnt:has_phenotype_data 'rdfs:subPropertyOf 'dct:relation)
(triple 'gnt:has_platform_info 'a 'owl:ObjectProperty)
(triple 'gnt:has_platform_info 'rdfs:comment "Information about the platform that was used with this dataset")
(triple 'gnt:has_platform_info 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_platform_info 'rdfs:label "About Platform")
(triple 'gnt:has_probeset_data 'rdf:type 'owl:ObjectProperty)
(triple 'gnt:has_probeset_data 'rdfs:comment "Associates a resource with this probeset data.")
(triple 'gnt:has_probeset_data 'rdfs:domain 'gnc:set)
(triple 'gnt:has_probeset_data 'rdfs:label "this resources has this probeset data.")
(triple 'gnt:has_probeset_data 'rdfs:range 'gnc:molecular_trait)
(triple 'gnt:has_probeset_data 'rdfs:subPropertyOf 'dct:relation)
(triple 'gnt:has_samples 'a 'owl:ObjectProperty)
(triple 'gnt:has_samples 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_samples 'rdfs:label "Samples")
(triple 'gnt:has_specifics 'a 'owl:ObjectProperty)
(triple 'gnt:has_specifics 'rdfs:comment "Has specifics")
(triple 'gnt:has_specifics 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_specifics 'rdfs:label "Specifics")
(triple 'gnt:has_summary 'a 'owl:ObjectProperty)
(triple 'gnt:has_summary 'rdfs:comment "Summary information about dataset")
(triple 'gnt:has_summary 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_summary 'rdfs:label "Summary")
(triple 'gnt:has_tissue_info 'a 'owl:ObjectProperty)
(triple 'gnt:has_tissue_info 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:has_tissue_info 'rdfs:label "Metadata about Tissue for this resource")
(triple 'gnt:uses_genechip 'a 'owl:ObjectProperty)
(triple 'gnt:uses_genechip 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:uses_genechip 'skos:definition "The Platform this resource uses..")
(triple 'gnt:uses_normalization_method 'rdfs:comment "The normalization method used for the molecular traits in this dataset")
(triple 'gnt:uses_normalization_method 'rdfs:domain 'dcat:Dataset)
(triple 'gnt:uses_normalization_method 'rdfs:label "Averaging method used for the molecular traits in this dataset.")
(triple 'gnt:uses_normalization_method 'rdfs:range 'gnc:avg_method)
;; Describing phenotypes
(triple 'gnc:phenotype 'a 'owl:Class)
(triple 'gnc:phenotype 'a 'skos:Concept)
(triple 'gnc:phenotype 'rdfs:label "A phenotype.")
(triple 'gnc:phenotype_trait 'a 'owl:Class)
(triple 'gnc:phenotype_trait 'a 'skos:Concept)
(triple 'gnc:phenotype_trait 'rdfs:label "A phenotype trait.")
(triple 'gnt:abbreviation 'a 'owl:ObjectProperty)
(triple 'gnt:abbreviation 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:abbreviation 'skos:definition "The abbreviation used for this resource")
(triple 'gnt:additive 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:additive 'rdfs:range 'xsd:double)
(triple 'gnt:lab_code 'a 'owl:ObjectProperty)
(triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:locus 'a 'qb:MeasureProperty)
(triple 'gnt:locus 'a 'rdf:Property)
(triple 'gnt:locus 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:locus 'rdfs:range 'rdfs:Literal)
(triple 'gnt:locus 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
(triple 'gnt:lod_score 'a 'qb:MeasureProperty)
(triple 'gnt:lod_score 'a 'rdf:Property)
(triple 'gnt:lod_score 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:lod_score 'rdfs:label "Peak -logP")
(triple 'gnt:lod_score 'rdfs:range 'xsd:double)
(triple 'gnt:lod_score 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
(triple 'gnt:lod_score 'skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.")
(triple 'gnt:mean 'a 'qb:MeasureProperty)
(triple 'gnt:mean 'a 'rdf:Property)
(triple 'gnt:mean 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:mean 'rdfs:range 'xsd:double)
(triple 'gnt:mean 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
(triple 'gnt:sequence 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:sequence 'rdfs:range 'xsd:integer)
(triple 'gnt:submitter 'a 'owl:ObjectProperty)
(triple 'gnt:submitter 'rdfs:domain 'gnc:phenotype)
(triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN")
(triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN")
(triple 'gnt:has_phenotype_trait 'a 'owl:ObjectProperty)
(triple 'gnt:has_phenotype_trait 'rdfs:domain 'gnc:set)
(triple 'gnt:has_phenotype_trait 'skos:definition "This is the unique trait id assigned from GeneNetwork for a a phenotype. It's a combination of the set name and the phenotype's post pub abbreviation."))))
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