Merge pull request #217 from JervenBolleman/ontology

#109 Start with making public stable URIs for the VG graph RDF concepts

ontology/README.md

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+# VG in RDF
+
+## Conceptual model
+
+Nodes, Paths and Steps, are the three core parts of any VG graph in RDF.
+Node in the VG RDF corersponds directly to the Node concept in the VG protobuf serialization.
+Paths are a series of steps that represent a sequence of Node visits that are conceptually a 
+biological sequence.
+Steps are a way to easily find out the 
+
+
+
+## Annotations on a VG
+
+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:
+
+```turtle
+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.
+
+```turtle
+@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.
+
+
+```
+
+
+## Linking a Genomic VG to a Protein VG
+
+