Why we need the OBO Core

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Why we need the OBO Core

• Michael Ashburner,
• Suzanna Lewis and Barry Smith

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DO

• Accident to powered aircraft, other and
  unspecified, injuring occupant of military
  aircraft, any rank
• Other accidental submersion or drowning in water
  transport accident injuring occupant of other
  watercraft crew

3
DO

• Fall on stairs or ladders in water transport
  injuring occupant of small boat, unpowered
• Railway accident involving collision with
  rolling stock and injuring pedal cyclist
• Non-traffic accident involving motor-driven snow
  vehicle injuring pedestrian

4
DO

• Fitting and adjustment of wheelchair

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Disease Ontology

• Fitting and adjustment of wheelchair
• is_a disease

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Goal of the OBO Core project

• To introduce some of the features of scientific
  peer review into biomedical ontology development

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Some OBO ontologies are of high quality

• Some not
• How to avoid poisoning of the wells?

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Further arguments

• Some OBO ontologies are already designated as OBO
  Core ontologies
• The community wanted it so we need to publish
  the criteria
• Several groups within the Center want to do this
• Several new groups without the Center want us to
  do this (preNCIT, FuGO, ...)
• It is entirely voluntary

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NCI Thesaurus

• http//www.cbd-net.com/index.php/search/show/9384
  64
• Review of NCI Thesaurus and Development of
  Plan to Achieve OBO Compliance

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Further arguments

• The idea is part of what we agreed to do in the
  BISTI proposal
• We will take steps to forge a common set of
  principles (best practices) and a common
  methodology for those active in ontology building
  in the life sciences
• Core 6 needs an explicit statement of methodology
  and criteria in order to do its work

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Further arguments

• It is an exciting and original alternative to the
  wiki/democracy/schemaweb based approaches à la
  CBioC
• It will provide a small reward for those doing
  good work in science-based ontology
• It will provide a step towards the day when
  interoperability through controlled vocabularies
  can be enforced through agreements with
  biological research groups, clinical guidelines
  bodies, and scientific journals

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Further arguments

• No objections have been made to the actual
  criteria proposed, except ...
• Orthogonality ontology groups who choose to be
  part of the OBO Core thereby commit themselves to
  collaborating to resolve disagreements which
  arise where their respective domains overlap
• (They commit themselves to conceiving ontology as
  a science, not as a hobby)

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How to achieve orthogonality

1. Good ontologies (FMA) can incorporate alternative
   views or partitions of the same domain (regional
   partition, structural partition ...)
2. Some ontologies (NCIT) will be Application
   Ontologies, which commit to maintaining
   compatibility with Reference Ontologies covering
   overlapping domains

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Some OBO ontologies are of high quality

• Some are not
• Compare a scientific journal which publishes
  both high-quality peer-reviewed articles, and
  some other stuff, ...
• but does not distinguish between them

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OBO CORE EVALUATION CRITERIA

• http//smi.stanford.edu/projects/cbio/mwiki-intern
  al/images/2/21/OBO-criteria-v7.doc

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• The ontologies are developed in collaboration
  with other OBO core ontologies. When
  disagreements arise the rationale for these
  disagreements should be documented, and efforts
  will be undertaken, for example, within the
  framework of the Centers Dissemination
  Workshops, in order to resolve these
  disagreements.
• The ontology is open and available to be used by
  all
• The ontology is in, or can be instantiated in, a
  common shared syntax. See http//obo.sf.net/
• The ontology possesses a unique identifier space.
• The ontology provider has procedures for
  identifying distinct successive versions.
• The ontology is well-documented.
• The ontology has a plurality of independent
  users.
• The ontology has clearly specified and clearly
  delineated content.
• The ontology includes textual definitions for all
  terms.
• The ontology uses relations which are
  unambiguously defined following the pattern of
  definitions laid down in the OBO Relation
  Ontology.

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OBO Relation Ontology
Foundational is_apart_of
Spatial located_incontained_inadjacent_to
Temporal transformation_ofderives_frompreceded_by
Participation has_participanthas_agent
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How to use the OBO Relation Ontology

• Tell curators to keep in mind that when they
  make e.g. an
• A is_a B
• assertion in an ontology, they need to remember
  that this is a statement about As to the effect
  that each A is a B.

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OBO CORE EVALUATION CRITERIA

• Further criteria will be added over time in
  order to bring about a gradual improvement in the
  quality of ontologies included in the OBO core.

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Reference Ontology vs. Application Ontology

• A reference ontology is analogous to a scientific
  theory it seeks to optimize descriptive or
  representational adequacy to its subject matter
  to the maximal degree that is compatible with the
  constraints of computational usefulness.
• An application ontology is comparable to an
  engineering artifact such as a software tool. It
  is constructed for specific practical purposes.

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Reference Ontology vs. Application Ontology

• Application ontologies often built afresh for
  each new task commonly introducing not only
  idiosyncrasies of format or logic, but also
  simplifications or distortions of their
  subject-matters.
• To solve this problem OBO Core proposes a
  methodology according to which application
  ontology development shoud take place always
  against the background of a formally robust
  reference ontology framework