Nodes, Paths and Steps, are the three core parts of any VG graph in RDF.
A Node in the VG RDF corresponds directly to the Node concept in the VG protobuf serialization.
Paths are a number of Steps that represent a sequence of Node visits that generate a linear biological sequence.
Each Step connects a Node into a Path
Path are annotations on the graph, some paths represent a reference genome, others are the genome of a patient. Yet some represent a gene, regulatory element or any other feature that we can annotate on any biological sequence.
For example lets say we have a small VG graph:
node:100 a vg:Node ; vg:linksForwardToForward node:101 ; rdf:value "ACT" .
node:101 a vg:Node ; vg:linksForwardToForward node:102 : rdf:value "TGAAGT" .
node:102 a vg:Node ; vg:linksForwardToForward node:103 ; rdf:value "A" .
node:103 a vg:Node ; vg:linksForwardToForward node:104 ; rdf:value "TGA" .
alternative_node:103 a vg:Node ; vg:linksForwardToForward node:104 ; rdf:value "A" .
node:102 a vg:Node ; vg:linksForwardToForward alternative_node:103 .
In this example node:101 to node:104 are on the reference genome path. They are also annotated to be a gene coding region.
@prefix ex:<an example ontology, could be SO> .
my_example:some_gene a ex:Gene, SO:Gene, vg:Path .
my_example:some_gene_step_1 a vg:Step ; vg:rank 1;vg:node node:101 .
my_example:some_gene_step_2 a vg:Step ; vg:rank 2;vg:node node:102 .
my_example:some_gene_step_3 a vg:Step ; vg:rank 3;vg:node node:103 .
my_example:some_gene_step_4 a vg:Step ; vg:rank 4;vg:node node:104 .
me:example:some_gene rdfs:seeAlso ENSEMBL:ESG00000XXXX . #and then pick up the annotation from the ENSEMBL gene build.2 ecoli genomes, with ensembl and uniprot annotation
At this moment VG RDF wants a fully embedded variation graph. e.g. all positions in vg json have a single edit which covers a whole node. This is to enable easy SPARQL queries where substring operations are rarely used.
On top of VG RDF, we can describe the same path information on Pantograph format as well.
<vg/zoom10> a vg:ZoomLevel ;
vg:components <vg/zoom10/component1>, <vg/zoom10/component2> ;
vg:zoomFactor 10 .
<vg/zoom1000> a vg:ZoomLevel ;
vg:components <vg/zoom1000/component1>, <vg/zoom1000/component2> ;
vg:zoomFactor 1000 . // zoomFactor is binWidth here.
<vg/zoom1000/component1> a vg:Component ;
vg:componentRank 1 ; # The order of component is inferred by rank.
vg:forwardComponentEdge <vg/zoom1000/component2> ;
vg:bins <vg/zoom1000/component1/bin1>, <vg/zoom1000/component1/bin2> .
<vg/zoom1000/component1/bin1> a vg:Bin ;
vg:forwardBinEdge <vg/zoom1000/component2/bin2> ;
vg:binRank 1 ;
vg:cells <vg/zoom1000/component1/bin1/cell1>, <vg/zoom1000/component1/bin1/cell2> .
<vg/zoom1000/component2/bin2> a vg:Bin ;
vg:reverseBinEdge <vg/zoom1000/component2/bin3> ;
vg:forwardBinEdge <vg/zoom1000/component2/bin3> ;
vg:binRank 2 ;
vg:cells <vg/zoom1000/component1/bin2/cell1>, <vg/zoom1000/component1/bin2/cell2> .
<vg/zoom1000/component1/bin1/cell1> a vg:Cell ;
vg:positionPercent 0.04 ;
vg:inversionPercent 0.98 ;
vg:cellRegion <path1/region/6-100> . # To infer firstNucleotide and last Nucleotide. faldo:begin of stepRegion is the first position. faldo:end of cellRegion is the last position.
<vg/zoom1000/link1> a vg:Link ; # This is a non-linear connection between Bins.
vg:arrival <vg/zoom1000/component1/bin1> ;
vg:departure <vg/zoom1000/component2/bin2> ;
vg:forwardLinkEdge <vg/zoom1000/link2> ;
vg:linkRank 1 ;
vg:linkPaths <path1> <path2> ; # Participants of the link
vg:linkZoomLevel <vg/zoom10> .
<path1/region/6-100> a faldo:Region ;
faldo:begin <path1/position/6> ;
faldo:end <path1/position/100> .