Mapping OBO to OWL 1.1

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Mapping OBO to OWL 1.1

• Christine Golbreich Ian Horrocks

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OBO and OWL

• 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

• OWL
• W3C standard ontology language
• Large user community
• Many in life sciences
• Extensive library of ontologies
• High quality tools
• Formally specified syntax and semantics

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OWL and OBO

• OWL
• 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

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Term stanzas define terms (classes), e.g.
• Term id GO0001555name oocyte growthis_a
  GO0016049 ! cell growth relationship part_of
  GO0048601 ! oocyte morphogenesis
  intersection_of GO0040007 ! growth
  intersection_of has_central_participant
  CL0000023

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Typedef stanzas define relationships
  (properties), e.g.
• Typedef id propreois_described_by domain
  propreochemical_entity range __Description177

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Instance stanzas define instances (individuals),
  e.g.
• Instance id propreowater_molecule
  instance_of propreoinorganic_solvent_molecule
  property_value propreois_described_by
  propreoCHEBI_15377

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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.
  ...

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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 ...

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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

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Proposed Solution

• Formalise OBO semantics via mapping to OWL 1.1
• relationship R C minCardinality3
• a ObjectMinCardinality(3 R C)

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Proposed Solution

• Formalise OBO semantics via mapping to OWL 1.1
• Term id Aname Example Classis_a B
  relationship R C minCardinality3
• a SubClassOf(A B)SubClassOf(A ObjectMinCardinalit
  y(3 R C))EntityAnnotation(OWLClass(A)
  Label(Example Class))

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Advantages of Our Approach?

• Clarifies and disambiguates OBO syntax
• E.g., can a relationship have more than one
  range?
• typedef-stanza Typedef 'range'
  termOrReserved

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Advantages of Our Approach?

• Clarifies and disambiguates OBO semantics
• E.g., is cardinality qualified or not?
• relationship R C minCardinality3
• 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

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Advantages of Our Approach?

• Can capture almost all of OBO in OWL 1.1, e.g.
• Typedefid 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)

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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

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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

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Advantages of Our Approach?

• Could easily extend OBO infrastructure to handle
  OWL
• To exploit OWL reasoners
• To handle (some) OWL ontologies

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Advantages of Our Approach?

• Could easily extend OBO infrastructure to handle
  OWL
• To exploit OWL reasoners
• To handle (some) OWL ontologies

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Advantages of Our Approach?

• OWL reasoners can deal with (most) OBO ontologies

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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)

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Term stanzas define terms (classes), e.g.
• Term id GO0001555name oocyte growthis_a
  GO0016049 ! cell growth relationship part_of
  GO0048601 ! oocyte morphogenesis
  intersection_of GO0040007 ! growth
  intersection_of has_central_participant
  CL0000023 ! oocyte
• Defines GO0001555 (oocyte growth) as a subclass
  of GO0016049 (cell growth) with a part_of
  relationship to GO0048601 (oocyte
  morphogenesis), and also as equivalent to the
  intersection of GO0040007 (growth) and a
  relationship has_central_participant to
  CL0000023 (oocyte).

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Typedef stanzas define relationships
  (properties), e.g.
• Typedef id propreois_described_by domain
  propreochemical_entity range __Description177
• Defines propreois_described_by and states that
  it has domain propreochemical_entity and range
  __Description177.

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OBO at a Glance

• Ontology consists of a set of stanzas (frames)
• Instance stanzas define instances (individuals),
  e.g.
• Instance id propreowater_molecule
  instance_of propreoinorganic_solvent_molecule
  property_value propreois_described_by
  propreoCHEBI_15377
• Defines id propreowater_molecule as an instance
  of propreoinorganic_solvent_molecule with a
  propreois_described_by relationship to the
  instance propreoCHEBI_15377.