From efde1c08d7578496b3daf2fcf660d66b14dfbd95 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 2 Feb 2026 18:26:08 +0300 Subject: Move all ontology to one place. Signed-off-by: Munyoki Kilyungi --- examples/classification.scm | 95 ------------- examples/datasets.scm | 48 ------- examples/molecular-traits-datasets.scm | 24 ---- examples/ontology.scm | 241 +++++++++++++++++++++++++++++++++ examples/phenotype-datasets.scm | 7 - examples/phenotype.scm | 33 ----- 6 files changed, 241 insertions(+), 207 deletions(-) create mode 100755 examples/ontology.scm (limited to 'examples') diff --git a/examples/classification.scm b/examples/classification.scm index 0a9631d..b664807 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -17,30 +17,6 @@ (define-transformer gnc:species->gn:species (tables (Species) "WHERE Name != 'monkey'") - (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:population_category) - (gnc:resource_classification_scheme xkos:levels gnc:set) - (gnc:population_category a xkos:ClassificationLevel) - (gnc:population_category skos:inScheme gnc:resource_classification_scheme) - (gnc:population_category xkos:previousLevel gnc:species) - (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 "3") - (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:population_category) - (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")) (triples "gnc:species" (set skos:member (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) @@ -48,13 +24,6 @@ (define-transformer gnc:set->gn:set (tables (InbredSet) "WHERE public > 0 AND FullName NOT LIKE '%monkey%'") - (schema-triples - (gnc:set a xkos:ClassificationLevel) - (gnc:set skos:inScheme gnc:resource_classification_scheme) - (gnc:set xkos:previousLevel gnc:population_category) - (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 "4")) (triples "gnc:set" (set skos:member (string->identifier @@ -63,22 +32,6 @@ (define-transformer gnc:species->metadata (tables (Species) "WHERE Name != 'monkey'") - (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)) (triples (string->identifier "" (remap-species-identifiers (field Species Fullname))) (set rdf:type 'gnc:species) @@ -95,12 +48,6 @@ (tables (InbredSet (left-join Species "ON InbredSet.SpeciesId=Species.Id")) "WHERE public > 0 AND Species.Name != 'monkey'") - (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.")) (triples (string->identifier "" (remap-species-identifiers (field Species Fullname))) (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) @@ -108,15 +55,6 @@ (define-transformer gn:family->gn:species/metadata (tables (Species) "WHERE Name != 'monkey' 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)) (triples (string->identifier "family" (field Species Family) #:separator "_") (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) @@ -128,8 +66,6 @@ (define-transformer gn:family->gn:species (tables (Species) "WHERE Name != 'monkey'") - (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)))))) @@ -141,28 +77,6 @@ (left-join MappingMethod "ON InbredSet.MappingMethodId=MappingMethod.Id")) "WHERE public > 0 AND Species.Name != 'monkey'") - (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")) (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") (set rdf:type 'gnc:set) (set rdfs:label (field InbredSet FullName)) @@ -191,11 +105,6 @@ (define-transformer gn:population->metadata (tables (InbredSet) "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%' 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")) (triples (string->identifier "population" (field InbredSet Family) #:separator "_") (set rdf:type 'gnc:reference_population) (set rdfs:label (field InbredSet Family)) @@ -221,10 +130,6 @@ (define-transformer gnc:taxonomic_family->gn:family (tables (Species) "WHERE Name != 'monkey' 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:taxonomic_family" (set gnt:has_taxonomic_family (string->identifier "family" (field Species Family) #:separator "_")))) diff --git a/examples/datasets.scm b/examples/datasets.scm index 8abb84f..55d8c35 100755 --- a/examples/datasets.scm +++ b/examples/datasets.scm @@ -21,54 +21,6 @@ ;; Skip monkey datasets "WHERE InfoFiles.InfoPageName NOT LIKE 'INIA_MacFas_%'" "GROUP BY Datasets.DatasetId") - (schema-triples - (gnt:has_case_info a owl:ObjectProperty) - (gnt:has_case_info rdfs:comment "Information about the cases used in this platform") - (gnt:has_case_info rdfs:domain dcat:Dataset) - (gnt:has_case_info rdfs:label "About Case") - (gnt:has_citation a owl:ObjectProperty) - (gnt:has_citation rdfs:comment "Citation for this dataset") - (gnt:has_citation rdfs:domain dcat:Dataset) - (gnt:has_citation rdfs:label "Citation") - (gnt:has_contributors a owl:ObjectProperty) - (gnt:has_contributors rdfs:comment "Contributors of this resource") - (gnt:has_contributors rdfs:comment "Contributors of this resource") - (gnt:has_contributors rdfs:domain dcat:Dataset) - (gnt:has_contributors rdfs:label "Contributors") - (gnt:has_data_processing_info a owl:ObjectProperty) - (gnt:has_data_processing_info rdfs:comment "Information about how this dataset was processed") - (gnt:has_data_processing_info rdfs:domain dcat:Dataset) - (gnt:has_data_processing_info rdfs:label "About Data Processing") - (gnt:has_experiment_design a owl:ObjectProperty) - (gnt:has_experiment_design rdfs:comment "Experiment Design for this resource") - (gnt:has_experiment_design rdfs:domain dcat:Dataset) - (gnt:has_experiment_design rdfs:label "Experiment Design") - (gnt:has_experiment_design_info a owl:ObjectProperty) - (gnt:has_experiment_design_info rdfs:comment "Information about how the experiment was designed") - (gnt:has_experiment_design_info rdfs:domain dcat:Dataset) - (gnt:has_experiment_design_info rdfs:label "Experiment Design") - (gnt:has_experiment_type a owl:ObjectProperty) - (gnt:has_experiment_type rdfs:comment "Information about the experiment type") - (gnt:has_experiment_type rdfs:domain dcat:Dataset) - (gnt:has_experiment_type rdfs:label "Experiment Type Metadata") - (gnt:has_platform_info a owl:ObjectProperty) - (gnt:has_platform_info rdfs:comment "Information about the platform that was used with this dataset") - (gnt:has_platform_info rdfs:domain dcat:Dataset) - (gnt:has_platform_info rdfs:label "About Platform") - (gnt:has_samples a owl:ObjectProperty) - (gnt:has_samples rdfs:domain dcat:Dataset) - (gnt:has_samples rdfs:label "Samples") - (gnt:has_specifics a owl:ObjectProperty) - (gnt:has_specifics rdfs:comment "Has specifics") - (gnt:has_specifics rdfs:domain dcat:Dataset) - (gnt:has_specifics rdfs:label "Specifics") - (gnt:has_summary a owl:ObjectProperty) - (gnt:has_summary rdfs:comment "Summary information about dataset") - (gnt:has_summary rdfs:domain dcat:Dataset) - (gnt:has_summary rdfs:label "Summary") - (gnt:has_tissue_info a owl:ObjectProperty) - (gnt:has_tissue_info rdfs:domain dcat:Dataset) - (gnt:has_tissue_info rdfs:label "Metadata about Tissue for this resource")) (triples (string->identifier "dataset" (field InfoFiles InfoPageName) #:separator "_") (set rdf:type 'dcat:Dataset) (set dct:title (normalize-string-field (field InfoFiles InfoPageName))) diff --git a/examples/molecular-traits-datasets.scm b/examples/molecular-traits-datasets.scm index 77bba08..98b55c6 100755 --- a/examples/molecular-traits-datasets.scm +++ b/examples/molecular-traits-datasets.scm @@ -14,11 +14,6 @@ (define-transformer gn:molecular-trait->gn:dataset (tables (Tissue)) - (schema-triples - (gnc:molecular_trait a owl:Class) - (gnc:molecular_trait a skos:Concept) - (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479) - (gnc:molecular_trait rdfs:label "Molecular Trait. This describes a melecular trait of a given species. We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups.")) (triples (string->identifier "trait" (field Tissue Short_Name) #:separator "_") (set rdf:type 'gnc:molecular_trait) (set skos:prefLabel (field Tissue Name)) @@ -36,13 +31,6 @@ (inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id") (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id")) "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, Tissue.Short_Name") - (schema-triples - (gnt:has_probeset_data rdf:type owl:ObjectProperty) - (gnt:has_probeset_data rdfs:label "this resources has this probeset data.") - (gnt:has_probeset_data rdfs:comment "Associates a resource with this probeset data.") - (gnt:has_probeset_data rdfs:domain gnc:set) - (gnt:has_probeset_data rdfs:range gnc:molecular_trait) - (gnt:has_probeset_data rdfs:subPropertyOf dct:relation)) (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") (multiset gnt:has_probeset_data (map (cut string->identifier "dataset" <> #:separator "_") @@ -62,18 +50,6 @@ (inner-join Datasets "ON InfoFiles.DatasetId = Datasets.DatasetId") (left-join GeneChip "ON GeneChip.Id = InfoFiles.GeneChipId")) "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'") - (schema-triples - (gnt:has_molecular_trait rdf:type owl:ObjectProperty) - (gnt:has_molecular_trait rdfs:domain gnc:set) - (gnt:has_molecular_trait rdfs:range gnc:molecular_trait) - (gnt:has_molecular_trait rdfs:label "has molecular trait") - (gnt:uses_genechip a owl:ObjectProperty) - (gnt:uses_genechip rdfs:domain dcat:Dataset) - (gnt:uses_genechip skos:definition "The Platform this resource uses..") - (gnt:uses_normalization_method rdfs:comment "The normalization method used for the molecular traits in this dataset") - (gnt:uses_normalization_method rdfs:domain dcat:Dataset) - (gnt:uses_normalization_method rdfs:label "Averaging method used for the molecular traits in this dataset.") - (gnt:uses_normalization_method rdfs:range gnc:avg_method)) (triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_") (set dct:created (annotate-field (field ProbeSetFreeze CreateTime) '^^xsd:datetime)) (set gnt:uses_normalization_method diff --git a/examples/ontology.scm b/examples/ontology.scm new file mode 100755 index 0000000..56d2779 --- /dev/null +++ b/examples/ontology.scm @@ -0,0 +1,241 @@ +#! /usr/bin/env guile +!# + +(use-modules (ice-9 getopt-long) + (transform triples) + (transform schema) + (transform special-forms)) + +(let* ((option-spec + '((settings (single-char #\s) (value #t)) + (output (single-char #\o) (value #t)) + (documentation (single-char #\d) (value #t)))) + (options (getopt-long (command-line) option-spec)) + (settings (option-ref options 'settings #f)) + (output (option-ref options 'output #f)) + (documentation (option-ref options 'documentation #f)) + (%connection-settings (call-with-input-file settings read))) + (with-output-to-file output + (lambda () + ;; Define all GN ontology in one place. + (prefix "dcat:" "") + (prefix "dct:" "") + (prefix "gn:" "") + (prefix "owl:" "") + (prefix "gnc:" "") + (prefix "gnt:" "") + (prefix "obo:" "") + (prefix "sdmx-measure:" "") + (prefix "skos:" "") + (prefix "rdf:" "") + (prefix "rdfs:" "") + (prefix "xsd:" "") + (prefix "qb:" "") + (prefix "xkos:" "") + (prefix "pubmed:" "") + (prefix "schema:" "") + (newline) + (triple 'gnc:population_category 'a 'xkos:ClassificationLevel) + (triple 'gnc:population_category 'rdfs:label "Population Category") + (triple 'gnc:population_category 'skos:inScheme 'gnc:resource_classification_scheme) + (triple 'gnc:population_category 'skos:prefLabel "Species") + (triple 'gnc:population_category 'xkos:depth "3") + (triple 'gnc:population_category 'xkos:nextLevel 'gnc:set) + (triple 'gnc:population_category 'xkos:previousLevel 'gnc:species) + (triple 'gnc:reference_population 'a 'skos:Concept) + (triple 'gnc:reference_population 'skos:definition "A genetic population") + (triple 'gnc:reference_population 'skos:inScheme 'gnc:population_category) + (triple 'gnc:reference_population 'skos:prefLabel "Reference population") + (triple 'gnc:resource_classification_scheme 'a 'skos:ConceptScheme) + (triple 'gnc:resource_classification_scheme 'skos:definition "A hierarchical classification scheme for organizing GeneNetwork resources by dataset type, resource set (inbredset group), or species.") + (triple 'gnc:resource_classification_scheme 'skos:prefLabel "GeneNetwork Resource Classification Scheme") + (triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:population_category) + (triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:set) + (triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:species) + (triple 'gnc:resource_classification_scheme 'xkos:levels 'gnc:taxonomic_family) + (triple 'gnc:resource_classification_scheme 'xkos:numberOfLevels "4") + (triple 'gnc:set 'a 'xkos:ClassificationLevel) + (triple 'gnc:set 'skos:definition "A category representing groups of genetically related strains or individuals (inbred sets, recombinant inbred lines, etc.).") + (triple 'gnc:set 'skos:inScheme 'gnc:resource_classification_scheme) + (triple 'gnc:set 'skos:prefLabel "InbredSet Group") + (triple 'gnc:set 'xkos:depth "4") + (triple 'gnc:set 'xkos:previousLevel 'gnc:population_category) + (triple 'gnc:species 'a 'xkos:ClassificationLevel) + (triple 'gnc:species 'skos:definition "A classification level that that associates a given resource to a species in GeneNetwork.") + (triple 'gnc:species 'skos:inScheme 'gnc:resource_classification_scheme) + (triple 'gnc:species 'skos:prefLabel "Species") + (triple 'gnc:species 'xkos:depth "2") + (triple 'gnc:species 'xkos:nextLevel 'gnc:population_category) + (triple 'gnc:species 'xkos:previousLevel 'gnc:taxonomic_family) + (triple 'gnc:taxonomic_family 'a 'xkos:ClassificationLevel) + (triple 'gnc:taxonomic_family 'skos:definition "An organizational classification level used in GeneNetwork to group resources into families.") + (triple 'gnc:taxonomic_family 'skos:inScheme 'gnc:resource_classification_scheme) + (triple 'gnc:taxonomic_family 'skos:prefLabel "Family") + (triple 'gnc:taxonomic_family 'xkos:depth "1") + (triple 'gnc:taxonomic_family 'xkos:nextLevel 'gnc:species) + (triple 'gnt:assigned_species 'a 'owl:ObjectProperty) + (triple 'gnt:assigned_species 'rdfs:domain 'gnc:set) + (triple 'gnt:assigned_species 'rdfs:label "These families have been assigned to these species") + (triple 'gnt:genetic_type 'a 'owl:DatatypeProperty) + (triple 'gnt:genetic_type 'rdfs:domain 'gnc:set) + (triple 'gnt:genetic_type 'rdfs:label "has genetic type") + (triple 'gnt:genetic_type 'rdfs:range 'xsd:string) + (triple 'gnt:genetic_type 'skos:definition "Describes the genetic architecture of a resource set (e.g., intercross, riset).") + (triple 'gnt:has_family_order_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_family_order_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_family_order_id 'rdfs:range 'xsd:integer) + (triple 'gnt:has_set_code 'a 'owl:DatatypeProperty) + (triple 'gnt:has_set_code 'rdfs:domain 'gnc:set) + (triple 'gnt:has_set_code 'rdfs:label "has set code") + (triple 'gnt:has_set_code 'rdfs:range 'xsd:string) + (triple 'gnt:has_set_code 'skos:definition "Provides a unique identifier code for a resource set.") + (triple 'gnt:has_species 'a 'owl:ObjectProperty) + (triple 'gnt:has_species 'rdf:comment "This resource belongs to this species") + (triple 'gnt:has_species 'rdfs:label "belongs to species") + (triple 'gnt:has_species 'rdfs:range 'gnc:species) + (triple 'gnt:has_strain 'a 'owl:ObjectProperty) + (triple 'gnt:has_strain 'rdf:comment "Indicates the group the resources belongs to") + (triple 'gnt:has_strain 'rdfs:domain 'gnc:species) + (triple 'gnt:has_strain 'rdfs:label "this resource belongs to this strain.") + (triple 'gnt:has_strain 'rdfs:range 'gnc:set) + (triple 'gnt:has_strain 'schema:domainIncludes 'dcat:Dataset) + (triple 'gnt:has_strain 'schema:domainIncludes 'gnc:species) + (triple 'gnt:has_strain 'skos:definition "Lists all strains that belong to this resource.") + (triple 'gnt:has_taxonomic_family 'a 'owl:ObjectProperty) + (triple 'gnt:has_taxonomic_family 'rdfs:label "has family") + (triple 'gnt:has_taxonomic_family 'schema:domainIncludes 'gnc:set) + (triple 'gnt:has_taxonomic_family 'schema:domainIncludes 'gnc:species) + (triple 'gnt:has_taxonomic_family 'skos:definition "Links a species to its taxonomic family") + (triple 'gnt:has_uniprot_taxon_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_uniprot_taxon_id 'rdfs:label "has uniprot taxonomic id") + (triple 'gnt:population_category 'skos:definition "Classification of genetic populations by breeding design and data aggregation.") + (triple 'gnt:short_name 'a 'owl:DatatypeProperty) + (triple 'gnt:short_name 'rdfs:domain 'gnc:species) + (triple 'gnt:short_name 'rdfs:label "has short name") + (triple 'gnt:short_name 'skos:definition "The short name of a given resource") + (triple 'gnt:uses_mapping_method 'a 'owl:ObjectProperty) + (triple 'gnt:uses_mapping_method 'rdfs:comment "The method used to map genetic or experimental data for this resource.") + (triple 'gnt:uses_mapping_method 'rdfs:domain 'gnc:set) + (triple 'gnt:uses_mapping_method 'rdfs:label "mapping method") + (triple 'gnt:uses_mapping_method 'rdfs:range 'gnc:mapping_method) + + ;; Describing Datasets + (triple 'gnc:molecular_trait 'a 'owl:Class) + (triple 'gnc:molecular_trait 'a 'skos:Concept) + (triple 'gnc:molecular_trait 'rdfs:label "Molecular Trait. This describes a melecular trait of a given species. We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups.") + (triple 'gnc:molecular_trait 'rdfs:subClassOf 'obo:UBERON_0000479) + (triple 'gnt:has_case_info 'a 'owl:ObjectProperty) + (triple 'gnt:has_case_info 'rdfs:comment "Information about the cases used in this platform") + (triple 'gnt:has_case_info 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_case_info 'rdfs:label "About Case") + (triple 'gnt:has_citation 'a 'owl:ObjectProperty) + (triple 'gnt:has_citation 'rdfs:comment "Citation for this dataset") + (triple 'gnt:has_citation 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_citation 'rdfs:label "Citation") + (triple 'gnt:has_contributors 'a 'owl:ObjectProperty) + (triple 'gnt:has_contributors 'rdfs:comment "Contributors of this resource") + (triple 'gnt:has_contributors 'rdfs:comment "Contributors of this resource") + (triple 'gnt:has_contributors 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_contributors 'rdfs:label "Contributors") + (triple 'gnt:has_data_processing_info 'a 'owl:ObjectProperty) + (triple 'gnt:has_data_processing_info 'rdfs:comment "Information about how this dataset was processed") + (triple 'gnt:has_data_processing_info 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_data_processing_info 'rdfs:label "About Data Processing") + (triple 'gnt:has_experiment_design 'a 'owl:ObjectProperty) + (triple 'gnt:has_experiment_design 'rdfs:comment "Experiment Design for this resource") + (triple 'gnt:has_experiment_design 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_experiment_design 'rdfs:label "Experiment Design") + (triple 'gnt:has_experiment_design_info 'a 'owl:ObjectProperty) + (triple 'gnt:has_experiment_design_info 'rdfs:comment "Information about how the experiment was designed") + (triple 'gnt:has_experiment_design_info 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_experiment_design_info 'rdfs:label "Experiment Design") + (triple 'gnt:has_experiment_type 'a 'owl:ObjectProperty) + (triple 'gnt:has_experiment_type 'rdfs:comment "Information about the experiment type") + (triple 'gnt:has_experiment_type 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_experiment_type 'rdfs:label "Experiment Type Metadata") + (triple 'gnt:has_molecular_trait 'rdf:type 'owl:ObjectProperty) + (triple 'gnt:has_molecular_trait 'rdfs:domain 'gnc:set) + (triple 'gnt:has_molecular_trait 'rdfs:label "has molecular trait") + (triple 'gnt:has_molecular_trait 'rdfs:range 'gnc:molecular_trait) + (triple 'gnt:has_phenotype_data 'rdf:type 'owl:ObjectProperty) + (triple 'gnt:has_phenotype_data 'rdfs:comment "Associates a resource with its phenotype data.") + (triple 'gnt:has_phenotype_data 'rdfs:domain 'gnc:set) + (triple 'gnt:has_phenotype_data 'rdfs:label "this resources has this phenotype data.") + (triple 'gnt:has_phenotype_data 'rdfs:range 'dcat:Dataset) + (triple 'gnt:has_phenotype_data 'rdfs:subPropertyOf 'dct:relation) + (triple 'gnt:has_platform_info 'a 'owl:ObjectProperty) + (triple 'gnt:has_platform_info 'rdfs:comment "Information about the platform that was used with this dataset") + (triple 'gnt:has_platform_info 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_platform_info 'rdfs:label "About Platform") + (triple 'gnt:has_probeset_data 'rdf:type 'owl:ObjectProperty) + (triple 'gnt:has_probeset_data 'rdfs:comment "Associates a resource with this probeset data.") + (triple 'gnt:has_probeset_data 'rdfs:domain 'gnc:set) + (triple 'gnt:has_probeset_data 'rdfs:label "this resources has this probeset data.") + (triple 'gnt:has_probeset_data 'rdfs:range 'gnc:molecular_trait) + (triple 'gnt:has_probeset_data 'rdfs:subPropertyOf 'dct:relation) + (triple 'gnt:has_samples 'a 'owl:ObjectProperty) + (triple 'gnt:has_samples 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_samples 'rdfs:label "Samples") + (triple 'gnt:has_specifics 'a 'owl:ObjectProperty) + (triple 'gnt:has_specifics 'rdfs:comment "Has specifics") + (triple 'gnt:has_specifics 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_specifics 'rdfs:label "Specifics") + (triple 'gnt:has_summary 'a 'owl:ObjectProperty) + (triple 'gnt:has_summary 'rdfs:comment "Summary information about dataset") + (triple 'gnt:has_summary 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_summary 'rdfs:label "Summary") + (triple 'gnt:has_tissue_info 'a 'owl:ObjectProperty) + (triple 'gnt:has_tissue_info 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_tissue_info 'rdfs:label "Metadata about Tissue for this resource") + (triple 'gnt:uses_genechip 'a 'owl:ObjectProperty) + (triple 'gnt:uses_genechip 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:uses_genechip 'skos:definition "The Platform this resource uses..") + (triple 'gnt:uses_normalization_method 'rdfs:comment "The normalization method used for the molecular traits in this dataset") + (triple 'gnt:uses_normalization_method 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:uses_normalization_method 'rdfs:label "Averaging method used for the molecular traits in this dataset.") + (triple 'gnt:uses_normalization_method 'rdfs:range 'gnc:avg_method) + + ;; Describing phenotypes + (triple 'gnc:phenotype 'a 'owl:Class) + (triple 'gnc:phenotype 'a 'skos:Concept) + (triple 'gnc:phenotype 'rdfs:label "A phenotype.") + (triple 'gnc:phenotype 'a 'owl:Class) + (triple 'gnc:phenotype 'a 'skos:Concept) + (triple 'gnc:phenotype 'rdfs:label "A phenotype.") + (triple 'gnt:lab_code 'a 'owl:ObjectProperty) + (triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:submitter 'a 'owl:ObjectProperty) + (triple 'gnt:submitter 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN") + (triple 'gnt:trait_id 'a 'owl:ObjectProperty) + (triple 'gnt:trait_id 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:trait_id 'skos:definition "This is the unique trait id assigned from GeneNetwork") + (triple 'gnt:abbreviation 'a 'owl:ObjectProperty) + (triple 'gnt:abbreviation 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:abbreviation 'skos:definition "The abbreviation used for this resource") + (triple 'gnt:lab_code 'a 'owl:ObjectProperty) + (triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:submitter 'a 'owl:ObjectProperty) + (triple 'gnt:submitter 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN") + (triple 'gnt:mean 'a 'rdf:Property) + (triple 'gnt:mean 'a 'qb:MeasureProperty) + (triple 'gnt:mean 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:mean 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:mean 'rdfs:range 'xsd:double) + (triple 'gnt:lod_score 'a 'rdf:Property) + (triple 'gnt:lod_score 'a 'qb:MeasureProperty) + (triple 'gnt:lod_score 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:lod_score 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:lod_score 'rdfs:range 'xsd:double) + (triple 'gnt:lod_score 'rdfs:label "Peak -logP") + (triple 'gnt:lod_score 'skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.") + (triple 'gnt:locus 'a 'rdf:Property) + (triple 'gnt:locus 'a 'qb:MeasureProperty) + (triple 'gnt:locus 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:locus 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:locus 'rdfs:range 'rdfs:Literal) + (triple 'gnt:additive 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:additive 'rdfs:range 'xsd:double) + (triple 'gnt:sequence 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:sequence 'rdfs:range 'xsd:integer)))) diff --git a/examples/phenotype-datasets.scm b/examples/phenotype-datasets.scm index 9354926..e29025c 100755 --- a/examples/phenotype-datasets.scm +++ b/examples/phenotype-datasets.scm @@ -20,13 +20,6 @@ (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")) "WHERE PublishFreeze.public > 0 GROUP BY Datasets.DatasetId") - (schema-triples - (gnt:has_phenotype_data rdf:type owl:ObjectProperty) - (gnt:has_phenotype_data rdfs:label "this resources has this phenotype data.") - (gnt:has_phenotype_data rdfs:comment "Associates a resource with its phenotype data.") - (gnt:has_phenotype_data rdfs:domain gnc:set) - (gnt:has_phenotype_data rdfs:range dcat:Dataset) - (gnt:has_phenotype_data rdfs:subPropertyOf dct:relation)) (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") (set gnt:has_phenotype_data (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")))) diff --git a/examples/phenotype.scm b/examples/phenotype.scm index 03eec45..d3ef4ba 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -19,39 +19,6 @@ (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))) - (schema-triples - (gnt:trait_id a owl:ObjectProperty) - (gnt:trait_id rdfs:domain gnc:phenotype) - (gnt:trait_id skos:definition "This is the unique trait id assigned from GeneNetwork") - (gnt:abbreviation a owl:ObjectProperty) - (gnt:abbreviation rdfs:domain gnc:phenotype) - (gnt:abbreviation skos:definition "The abbreviation used for this resource") - (gnt:labCode a owl:ObjectProperty) - (gnt:labCode rdfs:domain gnc:phenotype) - (gnt:submitter a owl:ObjectProperty) - (gnt:submitter rdfs:domain gnc:phenotype) - (gnt:submitter skos:definition "A person who submitted this resource to GN") - (gnt:mean a rdf:Property) - (gnt:mean a qb:MeasureProperty) - (gnt:mean rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:mean rdfs:domain gnc:phenotype) - (gnt:mean rdfs:range xsd:double) - (gnt:lod_score a rdf:Property) - (gnt:lod_score a qb:MeasureProperty) - (gnt:lod_score rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:lod_score rdfs:domain gnc:phenotype) - (gnt:lod_score rdfs:range xsd:double) - (gnt:lod_score rdfs:label "Peak -logP") - (gnt:lod_score skos:definition "Statistical measurement assessing the likelihood of genetic linkage between traits or genetic markers.") - (gnt:locus a rdf:Property) - (gnt:locus a qb:MeasureProperty) - (gnt:locus rdfs:subPropertyOf sdmx-measure:obsValue) - (gnt:locus rdfs:domain gnc:phenotype) - (gnt:locus rdfs:range rdfs:Literal) - (gnt:additive rdfs:domain gnc:phenotype) - (gnt:additive rdfs:range xsd:double) - (gnt:sequence rdfs:domain gnc:phenotype) - (gnt:sequence rdfs:range xsd:integer)) (triples (string->identifier "trait" (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" -- cgit 1.4.1