diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/classification.scm | 11 | ||||
| -rwxr-xr-x | examples/genbank.scm | 2 | ||||
| -rwxr-xr-x | examples/genelist.scm | 6 | ||||
| -rwxr-xr-x | examples/generif.scm | 4 | ||||
| -rwxr-xr-x | examples/genotype.scm | 2 | ||||
| -rwxr-xr-x | examples/strains.scm | 2 |
6 files changed, 13 insertions, 14 deletions
diff --git a/examples/classification.scm b/examples/classification.scm index be03656..ecc071b 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -89,10 +89,10 @@ (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 owl:ObjectProperty) - (gnt:belongs_to_species rdf:comment "This resource belongs to this species") - (gnt:belongs_to_species rdfs:label "belongs to species") - (gnt:belongs_to_species rdfs:range gnc:species)) + (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) @@ -113,7 +113,6 @@ (gnt:has_strain a owl:ObjectProperty) (gnt:has_strain rdfs:range gnc:set) (gnt:has_strain rdfs:domain gnc:species) - (gnt:has_strain owl:inverseOf gnt:belongs_to_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))) @@ -159,7 +158,7 @@ (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 + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) diff --git a/examples/genbank.scm b/examples/genbank.scm index 0379921..d09b30f 100755 --- a/examples/genbank.scm +++ b/examples/genbank.scm @@ -24,7 +24,7 @@ 'genbank: (field Genbank Id)) (set gnt:has_sequence (field Genbank Sequence)) - (set gnt:belongs_to_species + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) diff --git a/examples/genelist.scm b/examples/genelist.scm index 60ae4cd..5048bf2 100755 --- a/examples/genelist.scm +++ b/examples/genelist.scm @@ -21,7 +21,7 @@ (gnc:gene_symbol a rdfs:Class) (gnc:gene_symbol rdfs:label "A gene symbol") (gnt:gene rdfs:domain gnc:gene_symbol) - (gnt:belongs_to_species rdfs:domain gnc:gene_symbol) + (gnt:has_species rdfs:domain gnc:gene_symbol) (gnc:gene a rdfs:Class) (gnc:gene rdfs:label "Gene") (gnt:has_gene_id a owl:ObjectProperty) @@ -229,7 +229,7 @@ '^^xsd:double)) (set gnt:strand (string-trim-both (field GeneList Strand))) (set - gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) + gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) (set gnt:transcript (ontology 'transcript: @@ -253,7 +253,7 @@ gene-uid) #:separator "_")) (set rdf:type 'gnc:gene) - (set gnt:belongs_to_species 'gn:Rattus_norvegicus) + (set gnt:has_species 'gn:Rattus_norvegicus) (set gnt:gene_symbol (string-trim-both (field GeneList_rn33 geneSymbol))) (set gnt:chromosome (field GeneList_rn33 chromosome)) (set gnt:tx_start (annotate-field diff --git a/examples/generif.scm b/examples/generif.scm index dca59b6..3b794fa 100755 --- a/examples/generif.scm +++ b/examples/generif.scm @@ -47,7 +47,7 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") '(("'" . "\\'")))))) (set rdf:type 'gnc:gn_wiki_entry) (set gnt:symbol (field GeneRIF symbol)) - (set gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) (set dct:created (string->symbol (format #f "~s^^xsd:datetime " @@ -119,7 +119,7 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") (string-append (format #f "gnc:ncbi_wiki_entry ;\n") (format #f "\trdfs:label ~a ;\n" comment) - (format #f "\tgnt:belongs_to_species ~a ;\n" species) + (format #f "\tgnt:has_species ~a ;\n" species) (format #f "\tgnt:symbol ~s ;\n" symbol) (format #f "\tgnt:has_gene_id generif:~a ;\n" gene-id) (match taxon-id diff --git a/examples/genotype.scm b/examples/genotype.scm index ac170be..e2ac782 100755 --- a/examples/genotype.scm +++ b/examples/genotype.scm @@ -63,7 +63,7 @@ (set gnt:has_alt_source_name (field ("IF((Source2 = Source), NULL, Source2)" Source2))) - (set gnt:belongs_to_species + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)) #:separator "_" #:proc string-downcase)) diff --git a/examples/strains.scm b/examples/strains.scm index 1619876..cc98d71 100755 --- a/examples/strains.scm +++ b/examples/strains.scm @@ -67,7 +67,7 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used. (field Strain Name) #:separator "_") (set rdf:type 'gnc:strain) - (set gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) ;; Name, and maybe a second name (set rdfs:label (sanitize-rdf-string (field Strain Name))) (set skos:altLabel (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2)))) |