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-rwxr-xr-xexamples/classification.scm187
1 files changed, 114 insertions, 73 deletions
diff --git a/examples/classification.scm b/examples/classification.scm
index e3da8da..130bec8 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -14,97 +14,126 @@
 
 
 ;; Classification Scheme
-(define-transformer classification-scheme-species
-  (tables (Species))
-  (schema-triples
-   (gnc:resource_classification_scheme a skos:ConceptScheme)
-   (gnc:resource_classification_scheme skos:prefLabel "GeneNetwork Classification Scheme For Resources which are either defines as a dataset, an inbred group, or a species.")
-   (gnc:resource_classification_scheme xkos:numberOfLevels "3")
-   (gnc:resource_classification_scheme xkos:levels "( gnc:dataset_type gnc:set gnc:species )")
-   (gnc:dataset_type a xkos:ClassificationLevel)
-   (gnc:dataset_type skos:prefLabel "The Type of a Dataset which can be a ProbeSet, Genotype, or Phenotype")
-   (gnc:dataset_type xkos:depth "1")
-   (gnc:dataset_type skos:member gnc:probeset)
-   (gnc:dataset_type skos:member gnc:genotype)
-   (gnc:dataset_type skos:member gnc:phenotype)
-   (gnc:probeset skos:prefLabel "mRNA Assay Datasets")
-   (gnc:probeset skos:altLabel "ProbeSet")
-   (gnc:genotype skos:prefLabel "Genotype")
-   (gnc:genotype skos:altLabel "DNA Markers and SNPs")
-   (gnc:phenotype skos:prefLabel "Phenotype")
-   (gnc:phenotype skos:altLabel "Traits and Cofactors")
-   (gnc:species a xkos:ClassificationLevel)
-   (gnc:species skos:prefLabel "The species in which this resource belongs")
-   (gnc:species xkos:depth "3")
-   (gnc:species xkos:specializes gnc:set))
+(define-transformer gnc:species->gn:species
+  (tables (Species)
+          "WHERE Name != 'monkey'")
   (triples "gnc:species"
     (set skos:member
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
 
-(define-transformer classification-scheme-set
-  (tables (InbredSet))
-  (schema-triples
-   (gnc:set a xkos:ClassificationLevel)
-   (gnc:set skos:prefLabel "The Type of Set, Ie InbredSet/OutbredSet that a resource can belong to")
-   (gnc:set xkos:depth "2")
-   (gnc:set xkos:generalizes gnc:species))
+(define-transformer gnc:set->gn:set
+  (tables (InbredSet)
+          "WHERE public > 0 AND FullName NOT LIKE '%monkey%'")
   (triples "gnc:set"
     (set skos:member
          (string->identifier
           "set" (field InbredSet Name InbredSetName) #:separator "_"))))
 
-(define-transformer species
-  (tables (Species))
-  (schema-triples
-   (gnt:family a owl:ObjectProperty)
-   (gnt:family rdfs:domain gnc:species)
-   (gnt:family skos:definition "This resource belongs to this family")
-   (gnt:short_name a owl:ObjectProperty)
-   (gnt:short_name rdfs:domain gnc:species)
-   (gnt:short_name skos:definition "The short name of a given resource")
-   (gnt:belongs_to_species a rdf:property)
-   (gnt:belongs_to_species rdf:comment "This resource belongs to this species")
-   (gnt:belongs_to_species rdf:label "belongsToSpecies"))
+(define-transformer gnc:species->metadata
+  (tables (Species)
+          "WHERE Name != 'monkey'")
   (triples
       (string->identifier "" (remap-species-identifiers (field Species Fullname)))
-    (set skos:inScheme 'gnc:resource_classification_scheme)
+    (set rdf:type 'gnc:species)
     (set rdfs:label (remap-species-identifiers (field Species Fullname)))
     (set skos:prefLabel (field Species MenuName))
     (set skos:altLabel (field Species SpeciesName))
     (set gnt:short_name (field Species Name))
-    (set gnt:family (field Species Family))
-    (set skos:notation (ontology
-                        'taxon:
-                        (field Species TaxonomyId)))))
+    (set gnt:has_taxonomic_family (string->identifier "family" (field Species Family) #:separator "_"))
+    (set gnt:has_uniprot_taxon_id (ontology
+                                   'taxon:
+                                   (field Species TaxonomyId)))))
+
+(define-transformer gnc:species->gn:set
+  (tables (InbredSet
+           (left-join Species "ON InbredSet.SpeciesId=Species.Id"))
+          "WHERE public > 0 AND Species.Name != 'monkey'")
+  (triples (string->identifier "" (remap-species-identifiers (field Species Fullname)))
+    (set gnt:has_strain
+         (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
+
+(define-transformer gn:family->gn:species/metadata
+  (tables (Species)
+          "WHERE Name != 'monkey' GROUP BY FAMILY")
+  (triples (string->identifier "family" (field Species Family) #:separator "_")
+    (set gnt:has_species
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
+    (set rdfs:label (field Species Family))
+    (set gnt:has_family_order_id
+         (annotate-field (field Species OrderId)
+                         '^^xsd:integer))))
+
+(define-transformer gn:family->gn:species
+  (tables (Species)
+          "WHERE Name != 'monkey'")
+  (triples (string->identifier "family" (field Species Family) #:separator "_")
+    (set gnt:has_species
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
+
 
-(define-transformer inbred-set
+(define-transformer gn:set->metadata
   (tables (InbredSet
            (left-join Species "ON InbredSet.SpeciesId=Species.Id")
            (left-join MappingMethod
-                      "ON InbredSet.MappingMethodId=MappingMethod.Id")))
-  (schema-triples
-   (gnt:genetic-type a owl:ObjectProperty)
-   (gnt:genetic-type rdfs:domain gnc:set)
-   (gnt:code a owl:ObjectProperty)
-   (gnt:code rdfs:domain gnc:set)
-   ;; Already defined as an owl prop in species
-   (gnt:family rdfs:domain gnc:set)
-   (gnt:mapping_method a owl:ObjectProperty)
-   (gnt:mapping_method rdfs:domain gnc:set)
-   (gnt:belongs_to_group a rdf:property)
-   (gnt:belongs_to_group rdf:comment "This resource given to this group")
-   (gnt:belongs_to_group rdf:label "belongs-to-group"))
+                      "ON InbredSet.MappingMethodId=MappingMethod.Id"))
+          "WHERE public > 0 AND Species.Name != 'monkey'")
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
-    (set skos:inScheme 'gnc:resource_classification_scheme)
+    (set rdf:type 'gnc:set)
     (set rdfs:label (field InbredSet FullName))
     (set skos:prefLabel (field InbredSet Name InbredSetName))
-    (set gnt:genetic-type (field InbredSet GeneticType))
-    (set gnt:family (field InbredSet Family))
-    (set gnt:mapping_method (field MappingMethod Name))
-    (set gnt:code (field InbredSet InbredSetCode))
-    (set xkos:generalizes
+    (set gnt:genetic_type (field InbredSet GeneticType))
+    (set dct:description (annotate-field (sanitize-rdf-string (field InbredSet description))
+                                         '^^rdf:HTML))
+    (set gnt:uses_mapping_method
+         (string->identifier "mapping_method" (field MappingMethod Name) #:separator "_"))
+    (set gnt:has_set_code (field InbredSet InbredSetCode))
+    (set gnt:has_species
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
 
+(define-transformer gn:set->gn:population
+  (tables (InbredSet)
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%'")
+  (schema-triples
+   (gnt:has_reference_population rdfs:domain gnc:set)
+   (gnt:has_reference_population a owl:ObjectProperty)
+   (gnt:has_reference_population rdfs:comment "This group belongs to this population category.")
+   (gnt:has_reference_population rdfs:label "belongs to population category."))
+  (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
+    (set gnt:has_reference_population
+         (string->identifier "population" (field InbredSet Family) #:separator "_"))))
+
+(define-transformer gn:population->metadata
+  (tables (InbredSet)
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%' GROUP BY Family")
+  (triples (string->identifier "population" (field InbredSet Family) #:separator "_")
+    (set rdf:type 'gnc:reference_population)
+    (set rdfs:label (field InbredSet Family))
+    (set skos:member 'gnc:population_category)
+    (set gnt:has_population_order_id
+         (annotate-field (field InbredSet FamilyOrder)
+                         '^^xsd:integer))))
+
+(define-transformer gn:population->gn:set
+  (tables (InbredSet)
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%'")
+  (triples (string->identifier "population" (field InbredSet Family) #:separator "_")
+    (set gnt:has_strain
+         (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
+
+(define-transformer gnc:population_category->gn:population
+  (tables (InbredSet)
+          "WHERE public > 0 AND FullName NOT LIKE '%monkey%' GROUP BY Family")
+  (triples "gnc:population_category"
+    (set gnt:has_reference_population
+         (string->identifier "population" (field InbredSet Family) #:separator "_"))))
+
+(define-transformer gnc:taxonomic_family->gn:family
+  (tables (Species)
+          "WHERE Name != 'monkey' GROUP BY Family")
+  (triples "gnc:taxonomic_family"
+    (set gnt:has_taxonomic_family
+         (string->identifier "family" (field Species Family) #:separator "_"))))
+
 
 
 (let* ((option-spec
@@ -120,24 +149,36 @@
           read)))
 
   (with-documentation
-   (name "Species Metadata")
+   (name "GN Classification Hierarchy")
    (connection %connection-settings)
    (table-metadata? #f)
    (prefixes
-    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+    '(("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
       ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
       ("owl:" "<http://www.w3.org/2002/07/owl#>")
       ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+      ("schema:" "<https://schema.org/>")
       ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
       ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
       ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
       ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
       ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
    (inputs
-    (list classification-scheme-species
-          classification-scheme-set
-          species
-          inbred-set))
+    (list gnc:species->gn:species
+          gnc:set->gn:set
+          gnc:species->metadata
+          gnc:species->gn:set
+          gn:family->gn:species/metadata
+          gn:family->gn:species
+          gn:set->metadata
+          gn:set->gn:population
+          gn:population->metadata
+          gn:population->gn:set
+          gnc:population_category->gn:population
+          gnc:taxonomic_family->gn:family))
    (outputs
     `(#:documentation ,documentation
       #:rdf ,output))))
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-02-07 11:22:12 +0000