Ontology description
(rdf:type owl:Ontology ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 ) | |
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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 |