#! /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."))))