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README-owlmapping.md

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This document defines the mapping between OWL and OBOGraphs. We use the more compact YAML form to specify the mapping.

For the reference implemetation, see the FromOwl class.

URIs and Context objects

Every identifier in an OBO Graph is iterpreted as a URI. At the JSON/YAML level, these may be compacted URIs. The expansion to a full URI is specified via a JSON-LD context object. Context objects may be at the level of the graph document or an individual graph.

Nodes

All nodes go in a nodes array object, placed immediately under the graph object

Class: C
  Annotations: rdfs:label N

==>

nodes:
 - id: C
   lbl: N
   type: "CLASS"

Analogous rules apply to individuals and properties

Edges

Two edge types:

Class: C
  SubClassOf: D

==>

edges:
 - subj: C
   pred: is_a
   obj: D

Class: C
  SubClassOf: P some D

==>

edges:
 - subj: C
   pred: P
   obj: D

Note that universal restrictions are not added into the main graph

Value restrictions are treated in an analogous fashion to existentials (this pattern should be rare for most bio-ontologies):

Class: C
  SubClassOf: P value J

==>

edges:
 - subj: C
   pred: P
   obj: J

STATUS: UNIMPLEMETED

See #7 (comment)

Handling of universal (all values from) axioms

These do not pollute the main edges list

Class: C
  SubCLassOf: P only D

allValuesFromEdges:
 - sub: C
   pred: P
   obj: D

LogicalDefinitionAxioms

All logical definitions go in a logicalDefinitionAxioms array object, placed immediately under the meta object

Given:

Class: C
EquivalentTo: G1 and ... and Gn and (P1 some D1) and ... and (Pm some Dm)

Where all variables refer to named entities (C, Gi and Di are classes, Pi are Object Properties)

We translate to:

  - definedClassId: C
    genusIds: [G1, ..., Gn]
    restrictions:
    - propertyId: P1 
      fillerId: D1
    - ...
    - propertyId: Pm 
      fillerId: Dm

RBox Axioms

SubPropertyOf Axioms

These treated as graph edges

ObjectProperty: P
  SubPropertyOf: Q

==>

edges:
 - subj: P
   pred: subPropertyOf
   obj: Q

InversePropertyOf Axioms

These treated as graph edges

ObjectProperty: P
  InverseOf: Q

==>

edges:
 - subj: P
   pred: inverseOf
   obj: Q

Property Chain Axioms

ObjectProperty: P
  SubPropertyChain: P1 o P2  

==>

propertyChainAxioms:
 - predicateId: P
   chainPredicateIds: [P1, P2]

Domain and Range Axioms

ObjectProperty: P
  Domain: D
  Range: R

==>

domainRangeAxioms:
 - predicateId: P
   domainClassIds: [D]
   rangeClassIds: [R]

ABox Axioms

For examples, see abox.owl and its translation abox.json

ObjectPropertyAssertion Axioms (Facts)

These treated as graph edges

Individual: I
  Facts: P J

==>

edges:
 - subj: I
   pred: P
   obj: J

TODO: Negative ObjectPropertyAssertions

ClassAssertion Axioms (type axioms)

When the class expression is a named class, these are also treated as graph edges

Individual: I
  Types: C

==>

edges:
 - subj: I
   pred: type
   obj: C

When the class expression is a simple existential restriction, this is also treated as a graph edge

Individual: I
  Types: P some D

==>

edges:
 - subj: I
   pred: P
   obj: D

STATUS: UNIMPLEMETED

See #7 (comment)

Meta objects

Meta objects can be placed at multiple levels:

  1. GraphDocument
  2. Graph
  3. Node
  4. Edge
  5. Axiom

Each element Meta object corresponds to an Annotation in OWL

Note for the final two, the Meta object corresponds to reification in RDF/OWL

The meta object looks like:

meta:
  definition: DEFINITION
  subsets: SUBSET-LIST
  xrefs: XREF-LIST
  synonyms: SYN-LIST
  comments: COMMENT-LIST
  basicPropertyValues: BPV-LIST

See the OBO-Syntax spec for details

If the meta object is at the level of a Graph (Ontology) then it may optionally have a version field, correspondig to the owl versionIRI

Synonym Meta objects

Example:

      synonyms:
      - pred: "hasExactSynonym"
        val: "intracellular membrane-enclosed organelle"
        xrefs: []

All synonyms go in a synonyms array object, placed immediately under the meta object

We specify the mapping in terms of OBO syntax as this is more compact

Given:

id: C
synonym: "VAL" SCOPE [XREF1, ..., XREFn]

We translate to:

      synonyms:
      - pred: "PRED"
        val: "VAL"
        xrefs: [XREF1, ..., XREFn]

where the mapping between SCOPE (e.g. EXACT, NARROW, ...) and PRED is defined by the OBO to OWL annotation vocabulary translation