diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/classification.scm | 108 |
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/>"))) |