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Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. + Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. diff --git a/README.md b/README.md index 4fb8362..c885c65 100644 --- a/README.md +++ b/README.md @@ -170,5 +170,5 @@ has a likelihood of 0.1 and position 2 has a likelihood of 0.9. License ------- -[![Creative Commons License](http://i.creativecommons.org/l/by/3.0/88x31.png)](http://creativecommons.org/licenses/by/3.0/) This work is licensed under a [Creative Commons Attribution 3.0 Unported License](http://creativecommons.org/licenses/by/3.0/). +[![Creative Commons License](http://creativecommons.org/images/deed/nolaw.png)](http://creativecommons.org/publicdomain/zero/1.0/) This work is licensed under a [Creative Commons Zero 1.0 Public Domain Dedication](http://creativecommons.org/publicdomain/zero/1.0/). diff --git a/faldo.ttl b/faldo.ttl index 65a0c74..e4a2164 100644 --- a/faldo.ttl +++ b/faldo.ttl @@ -9,21 +9,23 @@ rdf:type owl:Ontology ; - spin:imports , , ; + + ; + spin:imports , , ; owl:versionInfo "Created with TopBraid Composer"^^xsd:string . :BagOfRegions rdf:type owl:Class ; rdfs:comment "Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file."^^xsd:string ; rdfs:seeAlso ; - rdfs:subClassOf rdf:Bag , :CollectionOfRegions . + rdfs:subClassOf :CollectionOfRegions , rdf:Bag . :BothStrandsPosition rdf:type owl:Class ; rdfs:comment "The 'both strands position' indicates a region that is best described as being on 'both' strands of a double-stranded sequence, rather than one or the other."^^xsd:string ; rdfs:label "Both strands"^^xsd:string ; rdfs:subClassOf :StrandedPosition ; - owl:disjointWith :ForwardStrandPosition , :ReverseStrandPosition . + owl:disjointWith :ReverseStrandPosition , :ForwardStrandPosition . :CollectionOfRegions rdf:type owl:Class ; @@ -48,14 +50,14 @@ owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty :position ] ; - owl:disjointWith :InBetweenPosition , :InRangePosition , :OneOfPosition . + owl:disjointWith :OneOfPosition , :InRangePosition , :InBetweenPosition . :ForwardStrandPosition rdf:type owl:Class ; rdfs:comment "The position is on the forward (positive, 5' to 3') strand. Shown as a '+' in GFF3 and GTF."^^xsd:string ; rdfs:label "Positive strand"^^xsd:string ; rdfs:subClassOf :StrandedPosition ; - owl:disjointWith :BothStrandsPosition , :ReverseStrandPosition . + owl:disjointWith :ReverseStrandPosition , :BothStrandsPosition . :FuzzyPosition rdf:type owl:Class ; @@ -82,7 +84,7 @@ "1"^^xsd:nonNegativeInteger ]) ] ; - owl:disjointWith :ExactPosition , :OneOfPosition , :InRangePosition . + owl:disjointWith :InRangePosition , :OneOfPosition , :ExactPosition . :InRangePosition rdf:type owl:Class ; @@ -103,20 +105,20 @@ owl:onProperty :end ]) ] ; - owl:disjointWith :OneOfPosition , :StrandedPosition , :ExactPosition , :InBetweenPosition . + owl:disjointWith :InBetweenPosition , :ExactPosition , :StrandedPosition , :OneOfPosition . :ListOfRegions rdf:type owl:Class ; - rdfs:comment "Should be used when the location of a region is defined by an ordered list of Regions. However, try to avoid using these types in favor of using more explicit semantics about why the order is important."^^xsd:string , "As an ordered list of regions (but the list might not be complete)."^^xsd:string ; + rdfs:comment "As an ordered list of regions (but the list might not be complete)."^^xsd:string , "Should be used when the location of a region is defined by an ordered list of Regions. However, try to avoid using these types in favor of using more explicit semantics about why the order is important."^^xsd:string ; rdfs:seeAlso ; - rdfs:subClassOf rdf:Seq , :CollectionOfRegions . + rdfs:subClassOf :CollectionOfRegions , rdf:Seq . :OneOfPosition rdf:type owl:Class ; rdfs:comment "The position is known to be one of the more detailed positions listed by the location predicate."^^xsd:string ; rdfs:label "One of positions"^^xsd:string ; rdfs:subClassOf :FuzzyPosition ; - owl:disjointWith :InBetweenPosition , :InRangePosition , :ExactPosition . + owl:disjointWith :ExactPosition , :InRangePosition , :InBetweenPosition . :Position rdf:type owl:Class ; @@ -154,7 +156,7 @@ rdfs:comment "The position is on the reverse (complement, 3' to 5') strand of the sequence. Shown as '-' in GTF and GFF3."^^xsd:string ; rdfs:label "Negative strand"^^xsd:string ; rdfs:subClassOf :StrandedPosition ; - owl:disjointWith :ForwardStrandPosition , :BothStrandsPosition . + owl:disjointWith :BothStrandsPosition , :ForwardStrandPosition . :StrandedPosition rdf:type owl:Class ; @@ -207,7 +209,7 @@ :position rdf:type owl:DatatypeProperty ; - rdfs:comment "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is."^^xsd:string , "Denoted in 1-based closed coordinates, i.e. the position on the first amino acid or nucleotide of a sequence has the value 1."^^xsd:string ; + rdfs:comment "Denoted in 1-based closed coordinates, i.e. the position on the first amino acid or nucleotide of a sequence has the value 1."^^xsd:string , "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is."^^xsd:string ; rdfs:domain :ExactPosition ; rdfs:range [ rdf:type rdfs:Datatype ;