Move all ontology to one place.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

6 files changed, 241 insertions, 207 deletions

diff --git a/examples/classification.scm b/examples/classification.scm
index 0a9631d..b664807 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -17,30 +17,6 @@
 (define-transformer gnc:species->gn:species
   (tables (Species)
           "WHERE Name != 'monkey'")
-  (schema-triples
-   (gnc:resource_classification_scheme a skos:ConceptScheme)
-   (gnc:resource_classification_scheme skos:prefLabel "GeneNetwork Resource Classification Scheme")
-   (gnc:resource_classification_scheme skos:definition "A hierarchical classification scheme for organizing GeneNetwork resources by dataset type, resource set (inbredset group), or species.")
-   (gnc:resource_classification_scheme xkos:numberOfLevels "4")
-   (gnc:resource_classification_scheme xkos:levels gnc:taxonomic_family)
-   (gnc:resource_classification_scheme xkos:levels gnc:species)
-   (gnc:resource_classification_scheme xkos:levels gnc:population_category)
-   (gnc:resource_classification_scheme xkos:levels gnc:set)
-   (gnc:population_category a xkos:ClassificationLevel)
-   (gnc:population_category skos:inScheme gnc:resource_classification_scheme)
-   (gnc:population_category xkos:previousLevel gnc:species)
-   (gnc:population_category xkos:nextLevel gnc:set)
-   (gnc:population_category skos:prefLabel "Species")
-   (gnc:population_category rdfs:label "Population Category")
-   (gnc:population_category xkos:depth "3")
-   (gnt:population_category skos:definition "Classification of genetic populations by breeding design and data aggregation.")
-   (gnc:species a xkos:ClassificationLevel)
-   (gnc:species skos:inScheme gnc:resource_classification_scheme)
-   (gnc:species xkos:previousLevel gnc:taxonomic_family)
-   (gnc:species xkos:nextLevel gnc:population_category)
-   (gnc:species skos:prefLabel "Species")
-   (gnc:species skos:definition "A classification level that that associates a given resource to a species in GeneNetwork.")
-   (gnc:species xkos:depth "2"))
   (triples "gnc:species"
     (set skos:member
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
@@ -48,13 +24,6 @@
 (define-transformer gnc:set->gn:set
   (tables (InbredSet)
           "WHERE public > 0 AND FullName NOT LIKE '%monkey%'")
-  (schema-triples
-   (gnc:set a xkos:ClassificationLevel)
-   (gnc:set skos:inScheme gnc:resource_classification_scheme)
-   (gnc:set xkos:previousLevel gnc:population_category)
-   (gnc:set skos:prefLabel "InbredSet Group")
-   (gnc:set skos:definition "A category representing groups of genetically related strains or individuals (inbred sets, recombinant inbred lines, etc.).")
-   (gnc:set xkos:depth "4"))
   (triples "gnc:set"
     (set skos:member
          (string->identifier
@@ -63,22 +32,6 @@
 (define-transformer gnc:species->metadata
   (tables (Species)
           "WHERE Name != 'monkey'")
-  (schema-triples
-   (gnt:has_uniprot_taxon_id a owl:ObjectProperty)
-   (gnt:has_uniprot_taxon_id rdfs:label "has uniprot taxonomic id")
-   (gnt:has_taxonomic_family a owl:ObjectProperty)
-   (gnt:has_taxonomic_family rdfs:label "has family")
-   (gnt:has_taxonomic_family skos:definition "Links a species to its taxonomic family")
-   (gnt:has_taxonomic_family schema:domainIncludes gnc:species)
-   (gnt:has_taxonomic_family schema:domainIncludes gnc:set)
-   (gnt:short_name a owl:DatatypeProperty)
-   (gnt:short_name rdfs:label "has short name")
-   (gnt:short_name rdfs:domain gnc:species)
-   (gnt:short_name skos:definition "The short name of a given resource")
-   (gnt:has_species a owl:ObjectProperty)
-   (gnt:has_species rdf:comment "This resource belongs to this species")
-   (gnt:has_species rdfs:label "belongs to species")
-   (gnt:has_species rdfs:range gnc:species))
   (triples
       (string->identifier "" (remap-species-identifiers (field Species Fullname)))
     (set rdf:type 'gnc:species)
@@ -95,12 +48,6 @@
   (tables (InbredSet
            (left-join Species "ON InbredSet.SpeciesId=Species.Id"))
           "WHERE public > 0 AND Species.Name != 'monkey'")
-  (schema-triples
-   (gnt:has_strain a owl:ObjectProperty)
-   (gnt:has_strain rdfs:range gnc:set)
-   (gnt:has_strain rdfs:domain gnc:species)
-   (gnt:has_strain rdfs:label "this resource belongs to this strain.")
-   (gnt:has_strain skos:definition "Lists all strains that belong to this resource."))
   (triples (string->identifier "" (remap-species-identifiers (field Species Fullname)))
     (set gnt:has_strain
          (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
@@ -108,15 +55,6 @@
 (define-transformer gn:family->gn:species/metadata
   (tables (Species)
           "WHERE Name != 'monkey' GROUP BY FAMILY")
-  (schema-triples
-   (gnc:taxonomic_family a xkos:ClassificationLevel)
-   (gnc:taxonomic_family skos:inScheme gnc:resource_classification_scheme)
-   (gnc:taxonomic_family skos:prefLabel "Family")
-   (gnc:taxonomic_family skos:definition "An organizational classification level used in GeneNetwork to group resources into families.")
-   (gnc:taxonomic_family xkos:depth "1")
-   (gnc:taxonomic_family xkos:nextLevel gnc:species)
-   (gnt:has_family_order_id a owl:DatatypeProperty)
-   (gnt:has_family_order_id rdfs:range xsd:integer))
   (triples (string->identifier "family" (field Species Family) #:separator "_")
     (set gnt:has_species
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))
@@ -128,8 +66,6 @@
 (define-transformer gn:family->gn:species
   (tables (Species)
           "WHERE Name != 'monkey'")
-  (schema-triples
-   (gnt:has_family_order_id a owl:DatatypeProperty))
   (triples (string->identifier "family" (field Species Family) #:separator "_")
     (set gnt:has_species
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
@@ -141,28 +77,6 @@
            (left-join MappingMethod
                       "ON InbredSet.MappingMethodId=MappingMethod.Id"))
           "WHERE public > 0 AND Species.Name != 'monkey'")
-  (schema-triples
-   (gnt:genetic_type a owl:DatatypeProperty)
-   (gnt:genetic_type rdfs:label "has genetic type")
-   (gnt:genetic_type skos:definition "Describes the genetic architecture of a resource set (e.g., intercross, riset).")
-   (gnt:genetic_type rdfs:domain gnc:set)
-   (gnt:genetic_type rdfs:range xsd:string)
-   (gnt:has_set_code a owl:DatatypeProperty)
-   (gnt:has_set_code rdfs:label "has set code")
-   (gnt:has_set_code skos:definition "Provides a unique identifier code for a resource set.")
-   (gnt:has_set_code rdfs:domain gnc:set)
-   (gnt:has_set_code rdfs:range xsd:string)
-   (gnt:uses_mapping_method a owl:ObjectProperty)
-   (gnt:uses_mapping_method rdfs:label "mapping method")
-   (gnt:uses_mapping_method rdfs:domain gnc:set)
-   (gnt:uses_mapping_method rdfs:range gnc:mapping_method)
-   (gnt:uses_mapping_method rdfs:comment "The method used to map genetic or experimental data for this resource.")
-   (gnt:has_strain a owl:ObjectProperty)
-   (gnt:has_strain rdf:comment "Indicates the group the resources belongs to")
-   (gnt:has_strain schema:domainIncludes dcat:Dataset)
-   (gnt:has_strain schema:domainIncludes gnc:species)
-   (gnt:has_strain rdfs:range gnc:set)
-   (gnt:has_strain rdfs:label "belongs-to-group"))
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
     (set rdf:type 'gnc:set)
     (set rdfs:label (field InbredSet FullName))
@@ -191,11 +105,6 @@
 (define-transformer gn:population->metadata
   (tables (InbredSet)
           "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%' GROUP BY Family")
-  (schema-triples
-   (gnc:reference_population a skos:Concept)
-   (gnc:reference_population skos:inScheme gnc:population_category)
-   (gnc:reference_population skos:prefLabel "Reference population")
-   (gnc:reference_population skos:definition "A genetic population"))
   (triples (string->identifier "population" (field InbredSet Family) #:separator "_")
     (set rdf:type 'gnc:reference_population)
     (set rdfs:label (field InbredSet Family))
@@ -221,10 +130,6 @@
 (define-transformer gnc:taxonomic_family->gn:family
   (tables (Species)
           "WHERE Name != 'monkey' GROUP BY Family")
-  (schema-triples
-   (gnt:assigned_species rdfs:domain gnc:set)
-   (gnt:assigned_species a owl:ObjectProperty)
-   (gnt:assigned_species rdfs:label "These families have been assigned to these species"))
   (triples "gnc:taxonomic_family"
     (set gnt:has_taxonomic_family
          (string->identifier "family" (field Species Family) #:separator "_"))))
diff --git a/examples/datasets.scm b/examples/datasets.scm
index 8abb84f..55d8c35 100755
--- a/examples/datasets.scm
+++ b/examples/datasets.scm
@@ -21,54 +21,6 @@
           ;; Skip monkey datasets
           "WHERE InfoFiles.InfoPageName NOT LIKE 'INIA_MacFas_%'"
           "GROUP BY Datasets.DatasetId")
-  (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: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"))
   (triples (string->identifier "dataset" (field InfoFiles InfoPageName) #:separator "_")
     (set rdf:type 'dcat:Dataset)
     (set dct:title (normalize-string-field (field InfoFiles InfoPageName)))
diff --git a/examples/molecular-traits-datasets.scm b/examples/molecular-traits-datasets.scm
index 77bba08..98b55c6 100755
--- a/examples/molecular-traits-datasets.scm
+++ b/examples/molecular-traits-datasets.scm
@@ -14,11 +14,6 @@
 
 (define-transformer gn:molecular-trait->gn:dataset
   (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))
@@ -36,13 +31,6 @@
            (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 "_")
@@ -62,18 +50,6 @@
            (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: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")
-   (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 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
diff --git a/examples/ontology.scm b/examples/ontology.scm
new file mode 100755
index 0000000..56d2779
--- /dev/null
+++ b/examples/ontology.scm
@@ -0,0 +1,241 @@
+#! /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 'a 'owl:Class)
+      (triple 'gnc:phenotype 'a 'skos:Concept)
+      (triple 'gnc:phenotype 'rdfs:label "A phenotype.")
+      (triple 'gnt:lab_code 'a 'owl:ObjectProperty)
+      (triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype)
+      (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:trait_id 'a 'owl:ObjectProperty)
+      (triple 'gnt:trait_id 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:trait_id 'skos:definition "This is the unique trait id assigned from GeneNetwork")
+      (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:lab_code 'a 'owl:ObjectProperty)
+      (triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype)
+      (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:mean 'a 'rdf:Property)
+      (triple 'gnt:mean 'a 'qb:MeasureProperty)
+      (triple 'gnt:mean 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:mean 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:mean 'rdfs:range 'xsd:double)
+      (triple 'gnt:lod_score 'a 'rdf:Property)
+      (triple 'gnt:lod_score 'a 'qb:MeasureProperty)
+      (triple 'gnt:lod_score 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:lod_score 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:lod_score 'rdfs:range 'xsd:double)
+      (triple 'gnt:lod_score 'rdfs:label "Peak -logP")
+      (triple 'gnt:lod_score 'skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.")
+      (triple 'gnt:locus 'a 'rdf:Property)
+      (triple 'gnt:locus 'a 'qb:MeasureProperty)
+      (triple 'gnt:locus 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:locus 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:locus 'rdfs:range 'rdfs:Literal)
+      (triple 'gnt:additive 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:additive 'rdfs:range 'xsd:double)
+      (triple 'gnt:sequence 'rdfs:domain 'gnc:phenotype)
+      (triple 'gnt:sequence 'rdfs:range 'xsd:integer))))
diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm
index 9354926..e29025c 100755
--- a/examples/phenotype-datasets.scm
+++ b/examples/phenotype-datasets.scm
@@ -20,13 +20,6 @@
            (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId")
            (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id"))
           "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId")
-  (schema-triples
-   (gnt:has_phenotype_data rdf:type owl:ObjectProperty)
-   (gnt:has_phenotype_data rdfs:label "this resources has this phenotype data.")
-   (gnt:has_phenotype_data rdfs:comment "Associates a resource with its phenotype data.")
-   (gnt:has_phenotype_data rdfs:domain gnc:set)
-   (gnt:has_phenotype_data rdfs:range dcat:Dataset)
-   (gnt:has_phenotype_data rdfs:subPropertyOf dct:relation))
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
     (set gnt:has_phenotype_data (string->identifier "dataset" (field PublishFreeze Name) #:separator "_"))))
 
diff --git a/examples/phenotype.scm b/examples/phenotype.scm
index 03eec45..d3ef4ba 100755
--- a/examples/phenotype.scm
+++ b/examples/phenotype.scm
@@ -19,39 +19,6 @@
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
            (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
            (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")))
-  (schema-triples
-   (gnt:trait_id a owl:ObjectProperty)
-   (gnt:trait_id rdfs:domain gnc:phenotype)
-   (gnt:trait_id skos:definition "This is the unique trait id assigned from GeneNetwork")
-   (gnt:abbreviation a owl:ObjectProperty)
-   (gnt:abbreviation rdfs:domain gnc:phenotype)
-   (gnt:abbreviation skos:definition "The abbreviation used for this resource")
-   (gnt:labCode a owl:ObjectProperty)
-   (gnt:labCode rdfs:domain gnc:phenotype)
-   (gnt:submitter a owl:ObjectProperty)
-   (gnt:submitter rdfs:domain gnc:phenotype)
-   (gnt:submitter skos:definition "A person who submitted this resource to GN")
-   (gnt:mean a rdf:Property)
-   (gnt:mean a qb:MeasureProperty)
-   (gnt:mean rdfs:subPropertyOf sdmx-measure:obsValue)
-   (gnt:mean rdfs:domain gnc:phenotype)
-   (gnt:mean rdfs:range xsd:double)
-   (gnt:lod_score a rdf:Property)
-   (gnt:lod_score a qb:MeasureProperty)
-   (gnt:lod_score rdfs:subPropertyOf sdmx-measure:obsValue)
-   (gnt:lod_score rdfs:domain gnc:phenotype)
-   (gnt:lod_score rdfs:range xsd:double)
-   (gnt:lod_score rdfs:label "Peak -logP")
-   (gnt:lod_score skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.")
-   (gnt:locus a rdf:Property)
-   (gnt:locus a qb:MeasureProperty)
-   (gnt:locus rdfs:subPropertyOf sdmx-measure:obsValue)
-   (gnt:locus rdfs:domain gnc:phenotype)
-   (gnt:locus rdfs:range rdfs:Literal)
-   (gnt:additive rdfs:domain gnc:phenotype)
-   (gnt:additive rdfs:range xsd:double)
-   (gnt:sequence rdfs:domain gnc:phenotype)
-   (gnt:sequence rdfs:range xsd:integer))
   (triples (string->identifier
             "trait"
             (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"