diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/classification.scm | 72 |
1 files changed, 54 insertions, 18 deletions
diff --git a/examples/classification.scm b/examples/classification.scm index d94276a..c9d9d63 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -20,10 +20,11 @@ (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:numberOfLevels "4") (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:resource_classification_scheme xkos:levels gnc:family) (gnc:dataset_type a xkos:ClassificationLevel) (gnc:dataset_type skos:inScheme gnc:resource_classification_scheme) (gnc:dataset_type skos:prefLabel "Dataset Type") @@ -100,7 +101,7 @@ (set skos:prefLabel (field Species MenuName)) (set skos:altLabel (field Species SpeciesName)) (set gnt:short_name (field Species Name)) - (set gnt:has_family (string->identifier "family" (field Species Family))) + (set gnt:has_family (string->identifier "family" (field Species Family) #:separator "_")) (set gnt:has_uniprot_taxon_id (ontology 'taxon: (field Species TaxonomyId))))) @@ -119,11 +120,19 @@ (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) -(define-transformer species-families + +(define-transformer species-families-list (tables (Species) "GROUP BY FAMILY") (schema-triples - (gnt:has_family_order_id a owl:DatatypeProperty)) + (gnc:family a xkos:ClassificationLevel) + (gnc:family skos:inScheme gnc:resource_classification_scheme) + (gnc:family skos:prefLabel "Family") + (gnc:family skos:definition "An organizational classification level used in GeneNetwork to group resources into families.") + (gnc:family xkos:depth "4") + (gnc:family xkos:previousLevel 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)))) @@ -132,6 +141,15 @@ (annotate-field (field Species OrderId) '^^xsd:integer)))) +(define-transformer species-families-fanout + (tables (Species)) + (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)))))) + + (define-transformer inbred-set (tables (InbredSet (left-join Species "ON InbredSet.SpeciesId=Species.Id") @@ -174,28 +192,44 @@ (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) -(define-transformer inbredset-families +(define-transformer inbredset-families-list (tables (InbredSet) - "WHERE Family IS NOT NULL") + "WHERE Family IS NOT NULL GROUP BY Family") (triples (string->identifier "family" (field InbredSet Family) #:separator "_") + (set rdf:type 'gnc:family) (set rdfs:label (field InbredSet Family)) (set gnt:has_family_order_id (annotate-field (field InbredSet FamilyOrder) '^^xsd:integer)))) -(define-transformer species-families-fanout - (tables (Species)) - (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)))))) - (define-transformer inbredset-families-fanout (tables (InbredSet) "WHERE Family IS NOT NULL") (triples (string->identifier "family" (field InbredSet Family) #:separator "_") - (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + (set gnt:has_strain + (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + +(define-transformer family-category-inbredset + (tables (InbredSet) + "WHERE public > 0 GROUP BY Family") + (schema-triples + (gnt:assigned_strain rdfs:domain gnc:set) + (gnt:assigned_strain a owl:ObjectProperty) + (gnt:assigned_strain rdfs:label "These families have been assigned to these strains")) + (triples "gnc:family" + (set gnt:assigned_strain + (string->identifier "family" (field InbredSet Family) #:separator "_")))) + +(define-transformer family-category-species + (tables (Species) + "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:family" + (set gnt:assigned_species + (string->identifier "family" (field Species Family) #:separator "_")))) @@ -235,10 +269,12 @@ species species-fan-out inbred-set - species-families - inbredset-families + species-families-list species-families-fanout - inbredset-families-fanout)) + inbredset-families-list + inbredset-families-fanout + family-category-inbredset + family-category-species)) (outputs `(#:documentation ,documentation #:rdf ,output)))) |