diff options
Diffstat (limited to 'examples/classification.scm')
| -rwxr-xr-x | examples/classification.scm | 175 |
1 files changed, 41 insertions, 134 deletions
diff --git a/examples/classification.scm b/examples/classification.scm index 7f89be8..130bec8 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -14,69 +14,24 @@ ;; 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 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:set) - (gnc:resource_classification_scheme xkos:levels gnc:population_category) - (gnc:population_category a xkos:ClassificationLevel) - (gnc:population_category skos:inScheme gnc:resource_classification_scheme) - (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 "4") - (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: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 "2")) +(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 +(define-transformer gnc:set->gn:set (tables (InbredSet) - "WHERE public > 0") - (schema-triples - (gnc:set a xkos:ClassificationLevel) - (gnc:set skos:inScheme gnc:resource_classification_scheme) - (gnc:set xkos:nextLevel gnc:population_category) - (gnc:set xkos:previousLevel gnc:species) - (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 "3")) + "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: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)) +(define-transformer gnc:species->metadata + (tables (Species) + "WHERE Name != 'monkey'") (triples (string->identifier "" (remap-species-identifiers (field Species Fullname))) (set rdf:type 'gnc:species) @@ -89,33 +44,17 @@ 'taxon: (field Species TaxonomyId))))) -(define-transformer species-fan-out +(define-transformer gnc:species->gn:set (tables (InbredSet (left-join Species "ON InbredSet.SpeciesId=Species.Id")) - "WHERE public > 0") - (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.")) + "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 species-families-list +(define-transformer gn:family->gn:species/metadata (tables (Species) - "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)) + "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)))) @@ -124,49 +63,26 @@ (annotate-field (field Species OrderId) '^^xsd:integer)))) -(define-transformer species-families-fanout - (tables (Species)) - (schema-triples - (gnt:has_family_order_id a owl:DatatypeProperty)) +(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")) - "WHERE public > 0") - (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")) + "WHERE public > 0 AND Species.Name != 'monkey'") (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") (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 dct:description (annotate-field (field InbredSet description) + (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 "_")) @@ -174,9 +90,9 @@ (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) -(define-transformer inbredset-population* +(define-transformer gn:set->gn:population (tables (InbredSet) - "WHERE Family IS NOT NULL") + "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) @@ -186,14 +102,9 @@ (set gnt:has_reference_population (string->identifier "population" (field InbredSet Family) #:separator "_")))) -(define-transformer inbredset-population-list +(define-transformer gn:population->metadata (tables (InbredSet) - "WHERE Family IS NOT NULL 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")) + "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)) @@ -202,27 +113,23 @@ (annotate-field (field InbredSet FamilyOrder) '^^xsd:integer)))) -(define-transformer inbredset-population-fanout +(define-transformer gn:population->gn:set (tables (InbredSet) - "WHERE Family IS NOT NULL") + "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 population-category-inbredset +(define-transformer gnc:population_category->gn:population (tables (InbredSet) - "WHERE public > 0 GROUP BY Family") + "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 family-category-species +(define-transformer gnc:taxonomic_family->gn:family (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")) + "WHERE Name != 'monkey' GROUP BY Family") (triples "gnc:taxonomic_family" (set gnt:has_taxonomic_family (string->identifier "family" (field Species Family) #:separator "_")))) @@ -242,7 +149,7 @@ read))) (with-documentation - (name "Species Metadata") + (name "GN Classification Hierarchy") (connection %connection-settings) (table-metadata? #f) (prefixes @@ -260,18 +167,18 @@ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") ("taxon:" "<http://purl.uniprot.org/taxonomy/>"))) (inputs - (list classification-scheme-species - classification-scheme-set - species - species-fan-out - inbred-set - inbredset-population* - species-families-list - species-families-fanout - inbredset-population-list - inbredset-population-fanout - population-category-inbredset - family-category-species)) + (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)))) |