| VG RDF: RDF properies and classes used to describe genomic variant graphs

Ontology description
Classes ( 16 ) |
Properties ( 30 )
Object properties ( 23 ) |
Datatype properties ( 7 ) |
Instance data ( 0 ) |

## Ontology description

(rdf:type owl:Ontology )
dcterms:license | http://creativecommons.org/publicdomain/zero/1.0/
spin:imports | http://topbraid.org/spin/owlrl-all
spin:imports | http://topbraid.org/spin/rdfsplus
spin:imports | http://topbraid.org/spin/spinowl
owl:versionInfo | "Created at the DBCLS RDF Summit 2, Sendai Japan and COVID-19 Virtual Biohackathon" xsd:string

## 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 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:linkZoomLevel (rdf:type owl:ObjectProperty )
rdfs:comment | "A link is related to each zoom level." xsd:string
rdfs:domain | vg:Link
rdfs:label | "linkZoomLevel" xsd:string
rdfs:range | vg:ZoomLevel

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