Classes

vg:GAMP_Format (rdf:type owl:Class )
rdfs:comment Contains a DAG of subalignments to different paths through the reference graph
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label MultipathAlignment
vg:GAM_Format (rdf:type owl:Class )
rdfs:comment Contains an alignment to a graph
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label Alignment
rdfs:subClassOf http://edamontology.org/format_2055
vg:GBWT_Format (rdf:type owl:Class )
rdfs:comment Graph Burrows-Wheeler Transform, a succinct collection of paths through a genome graph, published by Jouni Siren. Usually represents haplotypes.
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label GBWT
vg:GCSA2_Format (rdf:type owl:Class )
rdfs:comment Generalized compressed suffix array 2, an exact match index published by Jouni Siren
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label GCSA2
vg:Node (rdf:type owl:Class )
rdfs:comment "A node in the variant graph, representing a sequence section." xsd:string
rdfs:label "Node" xsd:string
rdfs:subClassOf owl:Thing
vg:Path (rdf:type owl:Class )
rdfs:comment "A Path is a collection of steps from path to path that represent an asserdfs:labelmbled sequence integrated into the variant grap." xsd:string
rdfs:label "Path" xsd:string
rdfs:subClassOf owl:Thing
vg:Snarl_Format (rdf:type owl:Class )
rdfs:comment A series of Snarl objects, each of which contain: The boundaries of a snarl (a bubble-like motif in a graph), the snarl (if any) that contains this one, classifications of the snarl based on the reachability of the two boundary nodes from each other and the cyclic-ness of the subcomponent.
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label Snarl
vg:Snarl_Traversal_Format (rdf:type owl:Class )
rdfs:comment A series of SnarlTraversal objects, each of which contain: A walk in the graph through a Snarl, and optionally a name.
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label SnarlTraversal
vg:Step (rdf:type owl:Class )
rdfs:comment "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)." xsd:string
rdfs:label "Step" xsd:string
rdfs:subClassOf owl:Thing
vg:VG_Format (rdf:type owl:Class )
rdfs:comment Nodes, Edges, Paths. Nodes have ID and sequence, Edges consist of two node sides (so the graph is bidirected), Paths are a sequence of Nodes and orientations. Paths also have names
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label Graph
rdfs:subClassOf http://edamontology.org/format_2055
rdfs:subClassOf http://edamontology.org/format_2921
vg:XG_Format (rdf:type owl:Class )
rdfs:comment An immutable, succinct representation of a graph. Contains the same info as the .vg.
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto
rdfs:label XG
rdfs:seeAlso vg:VG_Format

Properties

Object properties

vg:linksForwardToForward (rdf:type owl:ObjectProperty )
rdfs:comment "This links a node from the forward (5' to 3') strand on the subject node to the forward (5' to 3') strand on the predicate node." xsd:string
rdfs:domain vg:Node
rdfs:label "++" xsd:string
rdfs:label "linksForwardToForward" xsd:string
rdfs:range vg:Node
vg:linksForwardToReverse (rdf:type owl:ObjectProperty )
rdfs:comment "This links a node from the forward (5' to 3') strand on the subject node to the reverse (3' to 5') strand on the predicate node." xsd:string
rdfs:domain vg:Node
rdfs:label "+-" xsd:string
rdfs:label "linksForwardToReverse" xsd:string
rdfs:range vg:Node
vg:linksReverseToForward (rdf:type owl:ObjectProperty )
rdfs:comment "This links a node from the reverse (3' to 5') strand on the subject node to the forward (5' to 3') strand on the predicate node." xsd:string
rdfs:domain vg:Node
rdfs:label "-+" xsd:string
rdfs:label "linksReverseToForward" xsd:string
rdfs:range vg:Node
vg:linksReverseToReverse (rdf:type owl:ObjectProperty )
rdfs:comment "This links a node from the reverse (3' to 5') strand on the subject node to the reverse (3' to 5') strand on the predicate node." xsd:string
rdfs:domain vg:Node
rdfs:label "--" xsd:string
rdfs:label "linksReverseToReverse" xsd:string
rdfs:range vg:Node
vg:node (rdf:type owl:ObjectProperty )
rdfs:comment "This means that this step occurs on the forward strand of the sequence attaced to the node (i.e. it is on the explicit encoded forward (5' to 3') strand) of the predicate node." xsd:string
rdfs:domain vg:Step
rdfs:label "node" xsd:string
rdfs:range vg:Node
vg:position (rdf:type owl:ObjectProperty )
rdfs:comment "This is the position on the reference path at which this step starts." xsd:string
rdfs:domain vg:Step
rdfs:label "position" xsd:string
rdfs:range xsd:positiveInteger
vg:reverseOfNode (rdf:type owl:ObjectProperty )
rdfs:comment "This means this step occurs on the revese complement of the sequence attaced to the node (i.e. it is on the implicit reverse (3' to 5') strand) of the predicate node." xsd:string
rdfs:domain vg:Step
rdfs:label "reverseOfNode" xsd:string
rdfs:range vg:Node

Datatype properties

vg:rank (rdf:type owl:DatatypeProperty )
rdfs:comment "The rank records the step place along its path." xsd:string
rdfs:domain vg:Step
rdfs:label "rank" xsd:string
rdfs:range xsd:positiveInteger