Refine species/indbredset: labels, definitions, and property types.

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

1 files changed, 72 insertions, 36 deletions

diff --git a/examples/classification.scm b/examples/classification.scm
index 77d672e..b3c6acf 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -18,25 +18,38 @@
   (tables (Species))
   (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 "3")
    (gnc:resource_classification_scheme xkos:levels gnc:dataset_type)
    (gnc:resource_classification_scheme xkos:levels gnc:set)
    (gnc:resource_classification_scheme xkos:levels gnc:species)
    (gnc:dataset_type a xkos:ClassificationLevel)
+   (gnc:dataset_type skos:prefLabel "Dataset Type")
    (gnc:dataset_type skos:definition "Classification level describing the biological or experimental nature of a dataset.   A dataset can either be a probeSet, a genotype or a phenotype.")
    (gnc:dataset_type xkos:depth "1")
+   (gnc:dataset_type xkos:nextLevel gnc:set)
    (gnc:dataset_type skos:member gnc:probeset)
    (gnc:dataset_type skos:member gnc:genotype)
    (gnc:dataset_type skos:member gnc:phenotype)
-   (gnc:probeset skos:definition "A category that lists all the probesets contained in GN.")
-   (gnc:probeset skos:note "Since the probeset are too many to be listed, we don't include them at the moment in RDF.")
-   (gnc:genotype skos:definition "A category that lists all the genotypes contained in GeneNetwork.")
-   (gnc:phenotype skos:definition "A category that lists all the phenotypes contained in GeneNetwork.")
+   (gnc:probeset a skos:Concept)
+   (gnc:probeset skos:prefLabel "Transcriptomic Datasets")
+   (gnc:probeset skos:altLabel "ProbeSet")
+   (gnc:probeset skos:definition "A category representing microarray or sequencing probe sets that measure gene expression or other molecular traits.")
+   (gnc:probeset skos:note "Individual probe sets are too numerous to list explicitly in this ontology but are available through the GeneNetwork API.")
+   (gnc:genotype a skos:Concept)
+   (gnc:genotype skos:prefLabel "Genotype Datasets")
+   (gnc:genotype skos:altLabel "Genotype")
+   (gnc:genotype skos:definition "A category representing genetic marker or variant datasets used for genetic mapping.")
+   (gnc:phenotype a skos:Concept)
+   (gnc:phenotype skos:prefLabel "Phenotype Datasets")
+   (gnc:phenotype skos:altLabel "Phenotype")
+   (gnc:phenotype skos:definition "A category representing measured traits or phenotypes for genetic analysis.")
    (gnc:species a xkos:ClassificationLevel)
-   (gnc:species skos:definition "A category that lists all the species in GeneNetwork.")
-   (gnc:species xkos:depth "3")
-   (gnc:species xkos:specializes gnc:set))
+   (gnc:species xkos:previousLevel gnc:set)
+   (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 "3"))
   (triples "gnc:species"
     (set skos:member
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
@@ -45,9 +58,11 @@
   (tables (InbredSet))
   (schema-triples
    (gnc:set a xkos:ClassificationLevel)
-   (gnc:set skos:definition "A category that lists all the inbred set groups contained in GeneNetwork.")
-   (gnc:set xkos:depth "2")
-   (gnc:set xkos:generalizes gnc:species))
+   (gnc:set xkos:nextLevel gnc:species)
+   (gnc:set xkos:previousLevel gnc:dataset_type)
+   (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 "2"))
   (triples "gnc:set"
     (set skos:member
          (string->identifier
@@ -56,26 +71,31 @@
 (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:has_uniprot_taxon_id a owl:ObjectProperty)
+   (gnt:has_uniprot_taxon_id rdfs:label "has uniprot taxonomic id")
+   (gnt:has_family a owl:DatatypeProperty)
+   (gnt:has_family rdfs:label "has family")
+   (gnt:has_family rdfs:range xsd:string)
+   (gnt:has_family skos:definition "Links a species to its taxonomic family")
+   (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:belongs_to_species a rdf:property)
+   (gnt:belongs_to_species a owl:ObjectProperty)
    (gnt:belongs_to_species rdf:comment "This resource belongs to this species")
-   (gnt:belongs_to_species rdf:label "belongsToSpecies"))
+   (gnt:belongs_to_species rdfs:label "belongs to species")
+   (gnt:belongs_to_species rdfs:range gnc:species))
   (triples
       (string->identifier "" (remap-species-identifiers (field Species Fullname)))
-    (set skos:inScheme 'gnc:resource_classification_scheme)
+    (set rdfs: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_family (field Species Family))
+    (set gnt:has_uniprot_taxon_id (ontology
+                                   'taxon:
+                                   (field Species TaxonomyId)))))
 
 (define-transformer inbred-set
   (tables (InbredSet
@@ -83,26 +103,39 @@
            (left-join MappingMethod
                       "ON InbredSet.MappingMethodId=MappingMethod.Id")))
   (schema-triples
-   (gnt:genetic_type a owl:ObjectProperty)
+   (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:code a owl:ObjectProperty)
-   (gnt:code 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)
    ;; 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"))
+   (gnt:has_family rdfs:domain gnc:set)
+   (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:belongs_to_group a owl:ObjectProperty)
+   (gnt:belongs_to_group rdf:comment "Indicates the group the resources belongs to")
+   (gnt:belongs_to_group schema:domainIncludes dcat:Dataset)
+   (gnt:belongs_to_group schema:domainIncludes gnc:species)
+   (gnt:belongs_to_group rdfs:range gnc:set)
+   (gnt:belongs_to_group rdfs:label "belongs-to-group"))
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
-    (set skos:inScheme 'gnc:resource_classification_scheme)
+    (set rdfs: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:has_family (field InbredSet Family))
+    (set gnt:uses_mapping_method
+         (string->identifier "mapping_method" (field MappingMethod Name) #:separator "_"))
+    (set gnt:has_set_code (field InbredSet InbredSetCode))
+    (set gnt:belongs_to_species
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
 
 
@@ -124,12 +157,15 @@
    (connection %connection-settings)
    (table-metadata? #f)
    (prefixes
-    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+    '(("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("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/>")))