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Mapping OBO to OWL 1.1
Christine Golbreich & Ian Horrocks
OWL and OBOOWL:
• W3C standard ontology language
• Large user community
– Many in life sciences
• Extensive library of ontologies
• High quality tools
• Formally specified syntax and semantics
OBO:
• De facto standard ontology language
• Large user community
– Mainly in life sciences
• Extensive library of ontologies
• High quality tools
• Informally specified syntax and semantics
OBO at a Glance• Ontology consists of a set of stanzas (frames)
• Term stanzas define terms (classes), e.g.
[Term] id: GO:0001555name: oocyte growthis_a: GO:0016049 ! cell growth relationship: part_of GO:0048601 ! oocyte morphogenesis intersection_of: GO:0040007 ! growth intersection_of: has_central_participant CL:0000023
OBO at a Glance• Ontology consists of a set of stanzas (frames)
• Typedef stanzas define relationships (properties), e.g.
[Typedef] id: propreo:is_described_by domain: propreo:chemical_entity range: __Description177
OBO at a Glance• Ontology consists of a set of stanzas (frames)
• Instance stanzas define instances (individuals), e.g.
[Instance] id: propreo:water_molecule instance_of: propreo:inorganic_solvent_molecule property_value: propreo:is_described_by propreo:CHEBI_15377
OBO and OWL• OBO $ OWL interoperability would be useful
– Sharing ontologies
– Extending tool sets
• Establishing exact relationship is not easy
– OBO syntax not formally specified, e.g.:
The intersection_of tag “indicates that this term represents the intersection of several other terms. The value is either a term id, or a relationship type id, a space, and a term id. [...]”
OBO and OWL• OBO $ OWL interoperability would be useful
– Sharing ontologies
– Extending tool sets
• Establishing exact relationship is not easy
– OBO semantics not formally specified, e.g.:
The relationship tag “describes a typed relationship between this term and another term. [...] cardinality constraints specify the number of relationships of a given type that may be defined for instances of this term [...]”
Proposed Solution• Formalise OBO syntax using BNF grammar, e.g.:
The intersection_of tag “indicates that this term represents the intersection of several other terms. The value is either a term id, or a relationship type id, a space, and a term id. [...]”
a intersection := intersection of: termOrRestr termOrRestr := term-id | restriction restriction := relationship-id term-id
Proposed Solution• Formalise OBO semantics via mapping to OWL 1.1
relationship: R C minCardinality=3
a ObjectMinCardinality(3 R C)
Proposed Solution• Formalise OBO semantics via mapping to OWL 1.1
[Term] id: Aname: Example Classis_a: B relationship: R C minCardinality=3
a SubClassOf(A B)SubClassOf(A ObjectMinCardinality(3 R C))EntityAnnotation(OWLClass(A) Label(“Example Class”))
Advantages of Our Approach?• Clarifies and disambiguates OBO syntax
– E.g., can a relationship have more than one range?
typedef-stanza :=‘[Typedef]’…[ 'range:' termOrReserved ]…
Advantages of Our Approach?• Clarifies and disambiguates OBO semantics
– E.g., is cardinality qualified or not?
relationship: R C minCardinality=3
a ObjectMinCardinality(3 R C)
– and what is the precise semantics?
(ObjectMinCardinality(3 R C))I =
{ x | #{ y | ( x, y ) ∈ RI and y ∈ CI } ≥ 3 }
Advantages of Our Approach?• Can capture almost all of OBO in OWL 1.1, e.g.:
[Typedef]id: locationtransitive_over: part_of
a SubObjectPropertyOf( SubObjectPropertyChain(location part_of) location))
• Only fails to capture
– “cyclic” relations (semantics?)
– negative assertions about relations (e.g., not transitive)
Advantages of Our Approach?• Can easily extend OWL infrastructure to handle OBO
– OWL API extended with OBO parser and serialiser
– All tools built on top of API can now read/write OBO
Advantages of Our Approach?• Can easily extend OWL infrastructure to handle OBO
– OWL API extended with OBO parser and serialiser
– All tools built on top of API can now read/write OBO
Advantages of Our Approach?• Could easily extend OBO infrastructure to handle OWL
– To exploit OWL reasoners
– To handle (some) OWL ontologies
Advantages of Our Approach?• Could easily extend OBO infrastructure to handle OWL
– To exploit OWL reasoners
– To handle (some) OWL ontologies
Advantages of Our Approach?• OWL reasoners can deal with (most) OBO ontologies
Summary• OBO $ OWL interoperability would be useful
• Proposed solution is
– Formalise OBO syntax using BNF grammar
– Formalise OBO semantics via mapping to OWL 1.1
• Benefits include
– Sharing of tools and ontologies
• OWL community gets access to OBO ontologies(and major ongoing development effort)
• OBO community gets access to OWL tools(and major ongoing development effort)
