Classes

faldo: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:label "Bag of regions" xsd:string
rdfs:seeAlso http://www.insdc.org/files/feature_table.html
rdfs:subClassOf faldo:CollectionOfRegions
rdfs:subClassOf rdf:Bag
faldo: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 position" xsd:string
rdfs:subClassOf faldo:StrandedPosition
owl:disjointWith faldo:ForwardStrandPosition
owl:disjointWith faldo:ReverseStrandPosition
faldo:CollectionOfRegions (rdf:type owl:Class )
rdfs:comment "Sometimes a location of a feature is defined by a collection of regions e.g. join() and order() in INSDC records. One should always try to model the semantics more accurately than this, these are fallback options to encode legacy data." xsd:string
rdfs:label "Collection of regions" xsd:string
rdfs:subClassOf owl:Thing
rdfs:subClassOf Restrict rdfs:member
faldo:ExactPosition (rdf:type owl:Class )
rdfs:comment "A position that is exactly known." xsd:string
rdfs:label "Exact position" xsd:string
rdfs:subClassOf faldo:Position
rdfs:subClassOf Restrict faldo:position to owl:cardinality 1
owl:disjointWith faldo:InBetweenPosition
owl:disjointWith faldo:InRangePosition
owl:disjointWith faldo:OneOfPosition
owl:hasKey owl:hasKey consisting of (
faldo:position
and
faldo:reference
)
faldo:N-TerminalPosition (rdf:type owl:Class )
rdfs:comment "The position of the starting amino-acid a protein or polypeptide terminated by an amino acid with a free amine group (-NH2). The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus. Instances of this class are often used when the reference sequence is not complete " xsd:string
rdfs:seeAlso http://en.wikipedia.org/wiki/N-terminus
rdfs:subClassOf faldo:ExactPosition
owl:disjointWith faldo:C-TerminalPosition
faldo:C-TerminalPosition (rdf:type owl:Class )
rdfs:comment "The C-terminus is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH)." xsd:string
rdfs:label "C-Terminal position" xsd:string
rdfs:seeAlso http://en.wikipedia.org/wiki/C-terminus
rdfs:subClassOf faldo:ExactPosition
owl:disjointWith faldo:N-TerminalPosition
faldo: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 "Forward/positive strand position" xsd:string
rdfs:subClassOf faldo:StrandedPosition
owl:disjointWith faldo:BothStrandsPosition
owl:disjointWith faldo:ReverseStrandPosition
faldo:FuzzyPosition (rdf:type owl:Class )
rdfs:comment "A position that lacks exact data." xsd:string
rdfs:label "Fuzzy position" xsd:string
rdfs:subClassOf faldo:Position
faldo:InBetweenPosition (rdf:type owl:Class )
rdfs:comment "This indicates that a feature is between two other positions that are both known exactly and that are next to each other. An example is a restriction enzyme cutting site. The cut is after one position and before the other position (hence, in between)." xsd:string
rdfs:label "In between positions" xsd:string
rdfs:subClassOf faldo:Position
rdfs:subClassOf owl:intersectionOf (
Restrict faldo:before owl:onClass faldo:ExactPosition
and
Restrict faldo:after owl:onClass faldo:ExactPosition
)
owl:disjointWith faldo:ExactPosition
owl:disjointWith faldo:InRangePosition
owl:disjointWith faldo:OneOfPosition
faldo:InRangePosition (rdf:type owl:Class )
rdfs:comment "Use when you have an idea of the range in which you can find the position, but you cannot be sure about the exact position." xsd:string
rdfs:label "Indeterminate position within a range" xsd:string
rdfs:subClassOf faldo:FuzzyPosition
rdfs:subClassOf owl:intersectionOf (
Restrict faldo:begin owl:onClass faldo:Position to owl:maxQualifiedCardinality 1
and
Restrict faldo:end owl:onClass faldo:Position to owl:maxQualifiedCardinality 1
)
owl:disjointWith faldo:ExactPosition
owl:disjointWith faldo:InBetweenPosition
owl:disjointWith faldo:OneOfPosition
owl:disjointWith faldo:StrandedPosition
faldo:ListOfRegions (rdf:type owl:Class )
rdfs:comment "As an ordered list of regions (but the list might not be complete)." xsd:string
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
rdfs:label "List of regions" xsd:string
rdfs:seeAlso http://www.insdc.org/files/feature_table.html
rdfs:subClassOf faldo:CollectionOfRegions
rdfs:subClassOf rdf:Seq
faldo: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 faldo:FuzzyPosition
owl:disjointWith faldo:ExactPosition
owl:disjointWith faldo:InBetweenPosition
owl:disjointWith faldo:InRangePosition
faldo:Position (rdf:type owl:Class )
rdfs:comment "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate." xsd:string
rdfs:label "Position" xsd:string
rdfs:subClassOf owl:Thing
rdfs:subClassOf Restrict faldo:reference to owl:cardinality 1
faldo:Region (rdf:type owl:Class )
rdfs:comment "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene." xsd:string
rdfs:label "Region" xsd:string
rdfs:subClassOf owl:Thing
rdfs:subClassOf owl:intersectionOf (
Restrict faldo:begin owl:onClass faldo:Position
and
Restrict faldo:end owl:onClass faldo:Position
)
owl:hasKey owl:hasKey consisting of (
faldo:begin
and
faldo:end
)
faldo:ReverseStrandPosition (rdf:type owl:Class )
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/reverse strand position" xsd:string
rdfs:subClassOf faldo:StrandedPosition
owl:disjointWith faldo:BothStrandsPosition
owl:disjointWith faldo:ForwardStrandPosition
faldo:StrandedPosition (rdf:type owl:Class )
rdfs:comment "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'." xsd:string
rdfs:label "Stranded position" xsd:string
rdfs:subClassOf faldo:Position

Properties

Object properties

faldo:after (rdf:type owl:ObjectProperty )
rdfs:comment "This predicate is used when you want to describe a non-inclusive range. Only used in the InBetweenPosition to say it is after a nucleotide, but before the next one." xsd:string
rdfs:domain faldo:InBetweenPosition
rdfs:label "after" xsd:string
rdfs:range faldo:ExactPosition
faldo:before (rdf:type owl:ObjectProperty )
rdfs:comment "This predicate is used to indicate that the feature is found before the exact position. Use to indicate, for example, a cleavage site. The cleavage happens between two amino acids before one and after the other." xsd:string
rdfs:domain faldo:InBetweenPosition
rdfs:label "before" xsd:string
rdfs:range faldo:ExactPosition
faldo:begin (rdf:type owl:ObjectProperty )
rdfs:comment "The inclusive beginning of a position. Also known as start." xsd:string
rdfs:domain owl:unionOf (
faldo:Region
or
faldo:InRangePosition
)
rdfs:label "begin" xsd:string
rdfs:range faldo:Position
owl:inverseOf faldo:beginOf
faldo:beginOf (rdf:type owl:ObjectProperty )
rdfs:comment "This is the inverse of the begin:property. It is included to make it easier to write a number of OWL axioms. You should rarely use this in your raw data." xsd:string
rdfs:label "beginOf" xsd:string
owl:inverseOf faldo:begin
faldo:end (rdf:type owl:ObjectProperty )
rdfs:comment "The inclusive end of the position." xsd:string
rdfs:label "end" xsd:string
rdfs:range faldo:Position
owl:inverseOf faldo:endOf
faldo:endOf (rdf:type owl:ObjectProperty )
rdfs:comment "This is the inverse of the begin:end. It is included to make it easier to write a number of OWL axioms. You should rarely use this in your raw data." xsd:string
rdfs:label "endOf" xsd:string
owl:inverseOf faldo:end
faldo:location (rdf:type owl:ObjectProperty )
rdfs:comment "This is the link between the concept whose location you are annotating and its range or position. For example, when annotating the region that describes an exon, the exon would be the subject and the region would be the object of the triple or: 'active site' 'location' [is] 'position 3'." xsd:string
rdfs:label "location" xsd:string
rdfs:range owl:unionOf (
faldo:CollectionOfRegions
or
faldo:Region
or
faldo:Position
)
faldo:reference (rdf:type owl:ObjectProperty )
rdfs:comment "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly." xsd:string
rdfs:label "reference" xsd:string

Datatype properties

faldo:position (rdf:type owl:DatatypeProperty )
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. For nucleotide sequences we count from the 5'end of the sequence, while for Aminoacid sequences we start counting from the N-Terminus." xsd:string
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
rdfs:domain faldo:ExactPosition
rdfs:label "position" xsd:string
rdfs:range Restrict owl:onDatatype to xsd:integer with a value of at least 1