diff options
| -rwxr-xr-x | examples/genelist.scm | 22 | ||||
| -rwxr-xr-x | examples/ontology.scm | 164 | ||||
| -rwxr-xr-x | examples/probesets-experiment-metadata.scm | 2 |
3 files changed, 159 insertions, 29 deletions
diff --git a/examples/genelist.scm b/examples/genelist.scm index 5048bf2..ecd5cad 100755 --- a/examples/genelist.scm +++ b/examples/genelist.scm @@ -30,34 +30,34 @@ (gnc:transcript rdfs:domain gnc:gene_symbol) (gnt:transcript a owl:ObjectProperty) (gnc:transcript rdfs:comments "The gene transcript of this resource") - (gnc:ebi_gwas_link rdfs:Class gnc:ResourceLink) + (gnc:ebi_gwas_link rdfs:Class gnc:resource_link) (gnc:ebi_gwas_link rdfs:label "EBI GWAS") (gnc:ebi_gwas_link rdfs:comments "EBI GWAS") - (gnc:protein_atlas_link rdfs:Class gnc:ResourceLink) + (gnc:protein_atlas_link rdfs:Class gnc:resource_link) (gnc:protein_atlas_link rdfs:label "Protein Atlas") (gnc:protein_atlas_link rdfs:comments "Human Protein Atlas") - (gnc:genemania_link rdfs:Class gnc:ResourceLink) + (gnc:genemania_link rdfs:Class gnc:resource_link) (gnc:genemania_link rdfs:label "GeneMANIA") (gnc:genemania_link rdfs:comments "GeneMANIA") - (gnc:gemma_link rdfs:Class gnc:ResourceLink) + (gnc:gemma_link rdfs:Class gnc:resource_link) (gnc:gemma_link rdfs:label "Gemma") (gnc:gemma_link rdfs:comments "Meta-analysis of gene expression data") - (gnc:biogps_link rdfs:Class gnc:ResourceLink) + (gnc:biogps_link rdfs:Class gnc:resource_link) (gnc:biogps_link rdfs:label "BioGPS") (gnc:biogps_link rdfs:comments "Expression across many tissues and cell types") - (gnc:aba_link rdfs:Class gnc:ResourceLink) + (gnc:aba_link rdfs:Class gnc:resource_link) (gnc:aba_link rdfs:label "ABA") (gnc:aba_link rdfs:comments "Allen Brain Atlas") - (gnc:panther_link rdfs:Class gnc:ResourceLink) + (gnc:panther_link rdfs:Class gnc:resource_link) (gnc:panther_link rdfs:label "PANTHER") (gnc:panther_link rdfs:comments "Gene and protein data resources from Celera-ABI") - (gnc:panther_link rdfs:Class gnc:ResourceLink) + (gnc:panther_link rdfs:Class gnc:resource_link) (gnc:panther_link rdfs:label "STRING") (gnc:panther_link rdfs:comments "Protein interactions: known and inferred") - (gnc:gtex_link rdfs:Class gnc:ResourceLink) + (gnc:gtex_link rdfs:Class gnc:resource_link) (gnc:gtex_link rdfs:label "GTEx Portal") (gnc:gtex_link rdfs:comments "GTEx Portal") - (gnc:rgd_link rdfs:Class gnc:ResourceLink) + (gnc:rgd_link rdfs:Class gnc:resource_link) (gnc:rgd_link rdfs:label "Rat Genome DB") (gnc:rgd_link rdfs:comments "Rat Genome DB") (gnc:has_kg_id rdfs:domain gnc:gene_symbol) @@ -279,7 +279,7 @@ "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=" (string-trim-both symbol) - "a gnc:PantherLink")) + "a gnc:panther_link")) ""))) (set dct:references (let ((symbol (string-trim-both (field GeneList_rn33 geneSymbol)))) diff --git a/examples/ontology.scm b/examples/ontology.scm index f2b54cc..07e1759 100755 --- a/examples/ontology.scm +++ b/examples/ontology.scm @@ -25,6 +25,7 @@ (prefix "gnc:" "<http://rdf.genenetwork.org/v1/category/>") (prefix "gnt:" "<http://rdf.genenetwork.org/v1/term/>") (prefix "obo:" "<http://purl.obolibrary.org/obo/>") + (prefix "bfo:" "<http://purl.obolibrary.org/obo/BFO_>") (prefix "sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>") (prefix "skos:" "<http://www.w3.org/2004/02/skos/core#>") (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") @@ -35,6 +36,19 @@ (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") (prefix "schema:" "<https://schema.org/>") (newline) + ;; Minimal BFO bridge for GN terms. + (triple 'gnc:resource_entity 'a 'owl:Class) + (triple 'gnc:resource_entity 'rdfs:label "GeneNetwork resource entity") + (triple 'gnc:resource_entity 'rdfs:subClassOf 'bfo:0000001) + (triple 'gnc:material_resource 'a 'owl:Class) + (triple 'gnc:material_resource 'rdfs:label "GeneNetwork material resource") + (triple 'gnc:material_resource 'rdfs:subClassOf 'bfo:0000040) + (triple 'gnc:material_resource 'rdfs:subClassOf 'gnc:resource_entity) + (triple 'gnc:information_resource 'a 'owl:Class) + (triple 'gnc:information_resource 'rdfs:label "GeneNetwork information resource") + (triple 'gnc:information_resource 'rdfs:subClassOf 'bfo:0000031) + (triple 'gnc:information_resource 'rdfs:subClassOf 'gnc:resource_entity) + (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) @@ -73,6 +87,10 @@ (triple 'gnc:taxonomic_family 'skos:prefLabel "Family") (triple 'gnc:taxonomic_family 'xkos:depth "1") (triple 'gnc:taxonomic_family 'xkos:nextLevel 'gnc:species) + (triple 'gnc:strain 'a 'owl:Class) + (triple 'gnc:strain 'rdfs:subClassOf 'gnc:material_resource) + (triple 'gnc:mapping_method 'a 'skos:ConceptScheme) + (triple 'gnc:avg_method 'a 'skos:ConceptScheme) (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") @@ -82,7 +100,6 @@ (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) @@ -118,12 +135,27 @@ (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) + (triple 'gnt:has_reference_population 'a 'owl:ObjectProperty) + (triple 'gnt:has_reference_population 'schema:domainIncludes 'gnc:set) + (triple 'gnt:has_reference_population 'schema:domainIncludes 'gnc:population_category) + (triple 'gnt:has_reference_population 'rdfs:range 'gnc:reference_population) + (triple 'gnt:has_population_order_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_population_order_id 'rdfs:domain 'gnc:reference_population) + (triple 'gnt:has_population_order_id 'rdfs:range 'xsd:integer) + (triple 'gnt:alias 'a 'owl:DatatypeProperty) + (triple 'gnt:alias 'rdfs:domain 'gnc:strain) + (triple 'gnt:gene 'a 'owl:DatatypeProperty) + (triple 'gnt:gene 'rdfs:domain 'gnc:gene_symbol) ;; 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 'gnc:molecular_trait 'rdfs:subClassOf 'gnc:information_resource) + (triple 'gnc:molecular_trait_metadata 'a 'owl:Class) + (triple 'gnc:molecular_trait_metadata 'rdfs:subClassOf 'gnc:information_resource) + (triple 'gnc:gene_chip 'a 'skos:ConceptScheme) (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) @@ -163,6 +195,9 @@ (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_phenotype_trait 'a 'owl:ObjectProperty) + (triple 'gnt:has_phenotype_trait 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_phenotype_trait 'rdfs:range 'gnc:phenotype_trait) (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) @@ -194,21 +229,32 @@ (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) + (triple 'gnt:has_probeset 'a 'owl:ObjectProperty) + (triple 'gnt:has_probeset 'rdfs:domain 'gnc:molecular_trait_metadata) + (triple 'gnt:has_probeset 'rdfs:range 'gnc:probeset) ;; Describing phenotypes (triple 'gnc:phenotype 'a 'owl:Class) (triple 'gnc:phenotype 'a 'skos:Concept) (triple 'gnc:phenotype 'rdfs:label "A phenotype.") + (triple 'gnc:phenotype 'rdfs:subClassOf 'gnc:information_resource) (triple 'gnc:phenotype_trait 'a 'owl:Class) (triple 'gnc:phenotype_trait 'a 'skos:Concept) (triple 'gnc:phenotype_trait 'rdfs:label "A phenotype trait.") - (triple 'gnt:abbreviation 'a 'owl:ObjectProperty) + (triple 'gnc:phenotype_trait 'rdfs:subClassOf 'gnc:information_resource) + (triple 'gnt:abbreviation 'a 'owl:DatatypeProperty) (triple 'gnt:abbreviation 'rdfs:domain 'gnc:phenotype) (triple 'gnt:abbreviation 'skos:definition "The abbreviation used for this resource") + (triple 'gnt:has_phenotype 'a 'owl:ObjectProperty) + (triple 'gnt:has_phenotype 'rdfs:domain 'gnc:phenotype_trait) + (triple 'gnt:has_phenotype 'rdfs:range 'gnc:phenotype) (triple 'gnt:additive 'rdfs:domain 'gnc:phenotype) (triple 'gnt:additive 'rdfs:range 'xsd:double) - (triple 'gnt:lab_code 'a 'owl:ObjectProperty) + (triple 'gnt:lab_code 'a 'owl:DatatypeProperty) (triple 'gnt:lab_code 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:has_lab_code 'a 'owl:DatatypeProperty) + (triple 'gnt:has_lab_code 'rdfs:domain 'gnc:phenotype) + (triple 'gnt:has_lab_code 'rdfs:subPropertyOf 'gnt:lab_code) (triple 'gnt:locus 'a 'qb:MeasureProperty) (triple 'gnt:locus 'a 'rdf:Property) (triple 'gnt:locus 'rdfs:domain 'gnc:phenotype) @@ -226,9 +272,24 @@ (triple 'gnt:mean 'rdfs:domain 'gnc:phenotype) (triple 'gnt:mean 'rdfs:range 'xsd:double) (triple 'gnt:mean 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:se 'a 'qb:MeasureProperty) + (triple 'gnt:se 'a 'rdf:Property) + (triple 'gnt:se 'rdfs:domain 'gnc:molecular_trait_metadata) + (triple 'gnt:se 'rdfs:range 'xsd:double) + (triple 'gnt:se 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:pvalue 'a 'qb:MeasureProperty) + (triple 'gnt:pvalue 'a 'rdf:Property) + (triple 'gnt:pvalue 'rdfs:domain 'gnc:molecular_trait_metadata) + (triple 'gnt:pvalue 'rdfs:range 'xsd:double) + (triple 'gnt:pvalue 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:h2 'a 'qb:MeasureProperty) + (triple 'gnt:h2 'a 'rdf:Property) + (triple 'gnt:h2 'rdfs:domain 'gnc:molecular_trait_metadata) + (triple 'gnt:h2 'rdfs:range 'xsd:double) + (triple 'gnt:h2 'rdfs:subPropertyOf 'sdmx-measure:obsValue) (triple 'gnt:sequence 'rdfs:domain 'gnc:phenotype) (triple 'gnt:sequence 'rdfs:range 'xsd:integer) - (triple 'gnt:submitter 'a 'owl:ObjectProperty) + (triple 'gnt:submitter 'a 'owl:DatatypeProperty) (triple 'gnt:submitter 'rdfs:domain 'gnc:phenotype) (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN") (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN") @@ -240,6 +301,9 @@ (triple 'gnc:dna_marker 'a 'owl:Class) (triple 'gnc:dna_marker 'a 'skos:Concept) (triple 'gnc:dna_marker 'rdfs:label "A DNA Marker or SNP") + (triple 'gnc:dna_marker 'rdfs:subClassOf 'gnc:material_resource) + (triple 'gnc:marker 'a 'owl:Class) + (triple 'gnc:marker 'rdfs:subClassOf 'gnc:dna_marker) (triple 'gnt:has_genotype_files 'rdfs:label "This resource has these genotype files") (triple 'gnt:has_genotype_files 'rdfs:domain 'dcat:Dataset) (triple 'gnt:has_genotype_data 'rdf:type 'owl:ObjectProperty) @@ -248,16 +312,19 @@ (triple 'gnt:has_genotype_data 'rdfs:domain 'gnc:set) (triple 'gnt:has_genotype_data 'rdfs:range 'dcat:Dataset) (triple 'gnt:has_genotype_data 'rdfs:subPropertyOf 'dct:relation) - (triple 'gnt:has_marker_count 'rdf:type 'owl:ObjectProperty) + (triple 'gnt:has_marker_count 'rdf:type 'owl:DatatypeProperty) (triple 'gnt:has_marker_count 'rdfs:label "this resources has N number of dna markers/SNPs.") - (triple 'gnt:has_marker_count 'rdfs:domain 'xsd:integer) - (triple 'gnt:has_marker_count 'rdfs:range 'dcat:Dataset) + (triple 'gnt:has_marker_count 'rdfs:domain 'dcat:Dataset) + (triple 'gnt:has_marker_count 'rdfs:range 'xsd:integer) (triple 'gnt:chr 'a 'qb:MeasureProperty) (triple 'gnt:chr 'a 'rdf:Property) (triple 'gnt:chr 'rdfs:label "Chromosome") (triple 'gnt:chr 'rdfs:domain 'gnc:marker) (triple 'gnt:chr 'rdfs:range 'rdfs:Literal) (triple 'gnt:chr 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnt:chromosome 'a 'owl:DatatypeProperty) + (triple 'gnt:chromosome 'rdfs:subPropertyOf 'gnt:chr) + (triple 'gnt:chromosome 'rdfs:range 'rdfs:Literal) (triple 'gnt:mb 'rdfs:label "Megabase") (triple 'gnt:mb 'rdfs:domain 'gnc:marker) (triple 'gnt:mb 'rdfs:range 'rdfs:Literal) @@ -270,31 +337,39 @@ (triple 'gnt:source 'rdfs:domain 'gnc:marker) (triple 'gnt:source 'rdfs:range 'rdfs:Literal) (triple 'gnt:source 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + (triple 'gnc:nucleotide 'a 'owl:Class) + (triple 'gnc:nucleotide 'rdfs:subClassOf 'gnc:material_resource) + (triple 'gnt:has_sequence 'a 'owl:DatatypeProperty) + (triple 'gnt:has_sequence 'rdfs:domain 'gnc:nucleotide) + (triple 'gnt:has_sequence 'rdfs:range 'xsd:string) ;; Probesets (triple 'gnc:probeset 'a 'owl:Class) (triple 'gnc:probeset 'a 'skos:Concept) (triple 'gnc:probeset 'rdfs:label "A probeset") + (triple 'gnc:probeset 'rdfs:subClassOf 'gnc:material_resource) (triple 'gnt:has_target_id 'a 'owl:ObjectProperty) (triple 'gnt:has_target_id 'rdfs:label "The target id for this probeset") (triple 'gnt:has_target_id 'rdfs:domain 'gnc:probeset) - (triple 'gnt:symbol 'a 'owl:ObjectProperty) + (triple 'gnt:symbol 'a 'owl:DatatypeProperty) (triple 'gnt:symbol 'rdfs:domain 'gnc:probeset) - (triple 'gnt:targets_region 'a 'owl:ObjectProperty) + (triple 'gnt:targets_region 'a 'owl:DatatypeProperty) (triple 'gnt:targets_region 'rdfs:label "The target region") (triple 'gnt:targets_region 'rdfs:domain 'gnc:probeset) + (triple 'gnt:mb_mm8 'a 'owl:DatatypeProperty) (triple 'gnt:mb_mm8 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_specificity 'a 'owl:ObjectProperty) + (triple 'gnt:mb_mm8 'rdfs:range 'xsd:double) + (triple 'gnt:has_specificity 'a 'owl:DatatypeProperty) (triple 'gnt:has_specificity 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_blat_score 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_score 'a 'owl:DatatypeProperty) (triple 'gnt:has_blat_score 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_blat_mb_start 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_mb_start 'a 'owl:DatatypeProperty) (triple 'gnt:has_blat_mb_start 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_blat_mb_end 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_mb_end 'a 'owl:DatatypeProperty) (triple 'gnt:has_blat_mb_end 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_blat_seq 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_seq 'a 'owl:DatatypeProperty) (triple 'gnt:has_blat_seq 'rdfs:domain 'gnc:probeset) - (triple 'gnt:has_target_seq 'a 'owl:ObjectProperty) + (triple 'gnt:has_target_seq 'a 'owl:DatatypeProperty) (triple 'gnt:has_target_seq 'rdfs:domain 'gnc:probeset) (triple 'gnt:has_homologene_id 'a 'owl:ObjectProperty) (triple 'gnt:has_homologene_id 'rdfs:domain 'gnc:probeset) @@ -310,15 +385,70 @@ (triple 'gnt:has_chebi_id 'rdfs:domain 'gnc:probeset) ;; RIF + (triple 'gnc:gene 'a 'rdfs:Class) + (triple 'gnc:gene 'rdfs:subClassOf 'gnc:material_resource) + (triple 'gnc:gene_symbol 'a 'rdfs:Class) + (triple 'gnc:gene_symbol 'rdfs:subClassOf 'gnc:information_resource) + (triple 'gnc:transcript 'a 'rdfs:Class) + (triple 'gnc:transcript 'rdfs:subClassOf 'gnc:information_resource) + (triple 'gnc:resource_link 'a 'rdfs:Class) + (triple 'gnc:aba_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:biogps_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:ebi_gwas_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:gemma_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:genemania_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:gtex_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:panther_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:protein_atlas_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:rgd_link 'rdfs:subClassOf 'gnc:resource_link) + (triple 'gnc:has_kg_id 'a 'owl:DatatypeProperty) + (triple 'gnc:has_kg_id 'rdfs:domain 'gnc:gene) + (triple 'gnc:has_unigen_id 'a 'owl:DatatypeProperty) + (triple 'gnc:has_unigen_id 'rdfs:domain 'gnc:gene) + (triple 'gnc:has_protein_id 'a 'owl:DatatypeProperty) + (triple 'gnc:has_protein_id 'rdfs:domain 'gnc:gene) + (triple 'gnc:has_align_id 'a 'owl:DatatypeProperty) + (triple 'gnc:has_align_id 'rdfs:domain 'gnc:gene) (triple 'gnc:gene_wiki_entry 'a 'rdfs:Class) + (triple 'gnc:gene_wiki_entry 'rdfs:subClassOf 'gnc:information_resource) (triple 'gnc:gn_wiki_entry 'rdfs:subClassOf 'gnc:gene_wiki_entry) - (triple 'gnt:initial 'a 'owl:ObjectProperty) + (triple 'gnt:initial 'a 'owl:DatatypeProperty) (triple 'gnt:initial 'rdfs:domain 'gnc:gene_wiki_entry) (triple 'gnt:initial 'skos:definition "Optional user or project code or your initials") - (triple 'gnt:reason 'a 'owl:ObjectProperty) + (triple 'gnt:reason 'a 'owl:DatatypeProperty) (triple 'gnt:reason 'rdfs:domain 'gnc:gene_wiki_entry) (triple 'gnt:reason 'skos:definition "The reason why this resource was modified") + (triple 'gnt:belongs_to_category 'a 'owl:DatatypeProperty) + (triple 'gnt:belongs_to_category 'rdfs:domain 'gnc:gene_wiki_entry) + (triple 'gnt:has_gene_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_gene_id 'schema:domainIncludes 'gnc:gene) + (triple 'gnt:has_gene_id 'schema:domainIncludes 'gnc:ncbi_wiki_entry) + (triple 'gnt:gene_symbol 'a 'owl:DatatypeProperty) + (triple 'gnt:gene_symbol 'rdfs:domain 'gnc:gene) (triple 'gnc:gn_wiki_entry 'rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork") (triple 'gnt:gene_symbol 'rdfs:domain 'gnc:gn_wiki_entry) + (triple 'gnt:transcript 'a 'owl:ObjectProperty) + (triple 'gnt:transcript 'rdfs:domain 'gnc:gene) + (triple 'gnt:transcript 'rdfs:range 'gnc:transcript) + (triple 'gnt:strand 'a 'owl:DatatypeProperty) + (triple 'gnt:strand 'rdfs:domain 'gnc:gene) + (triple 'gnt:strand 'rdfs:range 'xsd:string) + (triple 'gnt:tx_start 'a 'owl:DatatypeProperty) + (triple 'gnt:tx_start 'rdfs:domain 'gnc:gene) + (triple 'gnt:tx_start 'rdfs:range 'xsd:double) + (triple 'gnt:tx_end 'a 'owl:DatatypeProperty) + (triple 'gnt:tx_end 'rdfs:domain 'gnc:gene) + (triple 'gnt:tx_end 'rdfs:range 'xsd:double) + (triple 'gnt:has_align_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_align_id 'rdfs:domain 'gnc:gene) + (triple 'gnt:has_protein_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_protein_id 'rdfs:domain 'gnc:gene) + (triple 'gnt:has_rgd_id 'a 'owl:DatatypeProperty) + (triple 'gnt:has_rgd_id 'rdfs:domain 'gnc:gene) + (triple 'gnt:has_geo_series_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_geo_series_id 'rdfs:domain 'skos:Concept) + (triple 'gnt:has_go_tree_value 'a 'owl:DatatypeProperty) + (triple 'gnt:has_go_tree_value 'rdfs:domain 'skos:Concept) + (triple 'gnt:has_go_tree_value 'rdfs:range 'xsd:string) (triple 'gnc:ncbi_wiki_entry 'rdfs:subClassOf 'gnc:gene_wiki_entry) (triple 'gnc:ncbi_wiki_entry 'rdfs:comment "Represents GeneRIF Entries obtained from NCBI")))) diff --git a/examples/probesets-experiment-metadata.scm b/examples/probesets-experiment-metadata.scm index 8706c3c..b2eb93e 100755 --- a/examples/probesets-experiment-metadata.scm +++ b/examples/probesets-experiment-metadata.scm @@ -34,7 +34,7 @@ #:separator "_")) (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) '^^xsd:double)) - (set gnt:SE (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se)) + (set gnt:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se)) '^^xsd:double)) (set gnt:locus (sanitize-rdf-string (field ProbeSetXRef Locus))) (set gnt:lod_score (annotate-field |