Classes

vg:Bin (rdf:type owl:Class )
rdfs:comment "A bin in the output of odgi bin, representing a sequence section." xsd:string
rdfs:label "Bin" xsd:string
rdfs:subClassOf owl:Thing
vg:Cell (rdf:type owl:Class )
rdfs:comment "A cell along a path of a specific group (component) of a specific zoom. A cell to a :Component and a :Path with supplemental informations." xsd:string
rdfs:label "Cell" xsd:string
rdfs:subClassOf owl:Thing
vg:Component (rdf:type owl:Class )
rdfs:comment "A region between Links structuring all bins and their present individuals into one component." xsd:string
rdfs:label "Component" xsd:string
rdfs:subClassOf owl:Thing
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/libvgio/master/deps/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/libvgio/master/deps/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/libvgio/master/deps/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/libvgio/master/deps/vg.proto
rdfs:label GCSA2
vg:Link (rdf:type owl:Class )
rdfs:comment "A link marks a graph traversal along a nonlinear connection." xsd:string
rdfs:label "Link" xsd:string
rdfs:subClassOf owl:Thing
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 graph." 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/libvgio/master/deps/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/libvgio/master/deps/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 Consists of nodes, edges, and paths. Nodes each have a unique ID and a DNA sequence, edges consist of two node sides (so the graph is bidirected), and paths are a sequence of nodes and orientations. Paths also have names.
rdfs:isDefinedBy https://raw.githubusercontent.com/vgteam/libvgio/master/deps/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/libvgio/master/deps/vg.proto
rdfs:label XG
rdfs:seeAlso vg:VG_Format
vg:ZoomLevel (rdf:type owl:Class )
rdfs:comment "A zoom level of Pangenome." xsd:string
rdfs:label "ZoomLevel" xsd:string
rdfs:subClassOf owl:Thing

Properties

Object properties

vg:arrival (rdf:type owl:ObjectProperty )
rdfs:comment "An end bin of nonlinear link. Incoming edge of the bin." xsd:string
rdfs:domain vg:Link
rdfs:label "arrival" xsd:string
rdfs:range vg:Bin
owl:inverseOf vg:departure
vg:bins (rdf:type owl:ObjectProperty )
rdfs:comment "A Component has one or more Bins." xsd:string
rdfs:domain vg:Component
rdfs:label "bins" xsd:string
rdfs:range vg:Bin
vg:cellRegions (rdf:type owl:ObjectProperty )
rdfs:comment "A cell is composed of the specific subsequence of paths." xsd:string
rdfs:domain vg:Cell
rdfs:label "cellRegions" xsd:string
rdfs:range http://biohackathon.org/resource/faldo#Region
vg:cells (rdf:type owl:ObjectProperty )
rdfs:comment "A Bin has one or more paths of a specific group (component) of a specific zoom. That is represented as cells on the matrix." xsd:string
rdfs:domain vg:Bin
rdfs:label "cells" xsd:string
rdfs:range vg:Cell
vg:components (rdf:type owl:ObjectProperty )
rdfs:comment "A zoom level has one or more components." xsd:string
rdfs:domain vg:ZoomLevel
rdfs:label "components" xsd:string
rdfs:range vg:Component
vg:departure (rdf:type owl:ObjectProperty )
rdfs:comment "A start bin of nonlinear link. Outgoing edge of the bin." xsd:string
rdfs:domain vg:Link
rdfs:label "departure" xsd:string
rdfs:range vg:Bin
owl:inverseOf vg:arrival
vg:forwardBinEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two bins are linked in forward orientation on the pangenome sequence." xsd:string
rdfs:domain vg:Bin
rdfs:label "forwardBinEdge" xsd:string
owl:inverseOf vg:reverseBinEdge
vg:forwardComponentEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two components are linked in forward orientation on the pangenome sequence." xsd:string
rdfs:domain vg:Component
rdfs:label "forwardComponentEdge" xsd:string
rdfs:range vg:Component
vg:forwardLinkEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two links are linked in forward orientation on the link column." xsd:string
rdfs:domain vg:Link
rdfs:label "forwardLinkEdge" xsd:string
rdfs:range vg:Link
vg:linkPaths (rdf:type owl:ObjectProperty )
rdfs:comment "A list of paths that follow the same non-linear link between two bins." xsd:string
rdfs:domain vg:Link
rdfs:label "linkPaths" xsd:string
rdfs:range vg:Path
vg:links (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two nodes are linked and does not allow one to infer which side to side it goes" xsd:string
rdfs:domain vg:Node
rdfs:label "links" xsd:string
rdfs:range vg:Node
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
rdfs:subPropertyOf vg:links
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
rdfs:subPropertyOf vg:links
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
rdfs:subPropertyOf vg:links
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
rdfs:subPropertyOf vg:links
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:path (rdf:type owl:ObjectProperty )
rdfs:comment "This means that this step occurs on the path that is the object of this statment" xsd:string
rdfs:domain vg:Step
rdfs:label "path" xsd:string
rdfs:range vg:Path
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:reverseBinEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two bins are linked in reverse orientation on the pangenome sequence." xsd:string
rdfs:domain vg:Bin
rdfs:label "reverseBinEdge" xsd:string
owl:inverseOf vg:forwardBinEdge
vg:reverseComponentEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two components are linked in reverse orientation on the pangenome sequence." xsd:string
rdfs:domain vg:Component
rdfs:label "reverseComponentEdge" xsd:string
owl:inverseOf vg:forwardComponentEdge
vg:reverseLinkEdge (rdf:type owl:ObjectProperty )
rdfs:comment "The super property that says two links are linked in reverse orientation on the link column." xsd:string
rdfs:domain vg:Link
rdfs:label "reverseLinkEdge" xsd:string
owl:inverseOf vg:forwardLinkEdge
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:binRank (rdf:type owl:DatatypeProperty )
rdfs:comment "The rank records that step place along its pangenome sequence." xsd:string
rdfs:domain vg:Bin
rdfs:label "binRank" xsd:string
rdfs:range xsd:positiveInteger
vg:componentRank (rdf:type owl:DatatypeProperty )
rdfs:comment "The rank records that step place along its pangenome sequence." xsd:string
rdfs:domain vg:Component
rdfs:label "componentRank" xsd:string
rdfs:range xsd:positiveInteger
vg:inversionPercent (rdf:type owl:DatatypeProperty )
rdfs:comment "The inversion percent of the path in the component." xsd:string
rdfs:domain vg:Cell
rdfs:label "inversionPercent" xsd:string
rdfs:range xsd:float
vg:linkRank (rdf:type owl:DatatypeProperty )
rdfs:comment "The rank records that step place along a link column." xsd:string
rdfs:domain vg:Link
rdfs:label "linkRank" xsd:string
rdfs:range xsd:positiveInteger
vg:positionPercent (rdf:type owl:DatatypeProperty )
rdfs:comment "The position coverage percent of the path in the component." xsd:string
rdfs:domain vg:Cell
rdfs:label "positionPercent" xsd:string
rdfs:range xsd:float
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
vg:zoomFactor (rdf:type owl:DatatypeProperty )
rdfs:comment "The zoom factor of pangenome, which is defined as bin width, generally." xsd:string
rdfs:domain vg:ZoomLevel
rdfs:label "zoomFactor" xsd:string
rdfs:range xsd:positiveInteger