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Mapping OBO to OWL 1.1

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Defines GO:0001555 (oocyte growth) as a subclass of GO:0016049 (cell growth) ... Defines id: propreo:water_molecule as an instance of propreo: ... – PowerPoint PPT presentation

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Title: Mapping OBO to OWL 1.1


1
Mapping OBO to OWL 1.1
  • Christine Golbreich Ian Horrocks

2
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

3
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

4
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

5
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

6
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

7
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.
    ...

8
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 ...

9
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

10
Proposed Solution
  • Formalise OBO semantics via mapping to OWL 1.1
  • relationship R C minCardinality3
  • a ObjectMinCardinality(3 R C)

11
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))

12
Advantages of Our Approach?
  • Clarifies and disambiguates OBO syntax
  • E.g., can a relationship have more than one
    range?
  • typedef-stanza Typedef 'range'
    termOrReserved

13
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

14
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)

15
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

16
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

17
Advantages of Our Approach?
  • Could easily extend OBO infrastructure to handle
    OWL
  • To exploit OWL reasoners
  • To handle (some) OWL ontologies

18
Advantages of Our Approach?
  • Could easily extend OBO infrastructure to handle
    OWL
  • To exploit OWL reasoners
  • To handle (some) OWL ontologies

19
Advantages of Our Approach?
  • OWL reasoners can deal with (most) OBO ontologies

20
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)

21
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).

22
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.

23
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.
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