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Why we need the OBO Core

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Why we need the OBO Core Michael Ashburner, Suzanna Lewis and Barry Smith – PowerPoint PPT presentation

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Title: Why we need the OBO Core


1
Why we need the OBO Core
  • Michael Ashburner,
  • Suzanna Lewis and Barry Smith

2
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

5
Disease Ontology
  • Fitting and adjustment of wheelchair
  • is_a disease

6
Goal of the OBO Core project
  • To introduce some of the features of scientific
    peer review into biomedical ontology development

7
Some OBO ontologies are of high quality
  • Some not
  • How to avoid poisoning of the wells?

8
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

9
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

10
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

11
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

12
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)

13
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

14
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

15
OBO CORE EVALUATION CRITERIA
  • http//smi.stanford.edu/projects/cbio/mwiki-intern
    al/images/2/21/OBO-criteria-v7.doc

16
  • 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.

17
OBO Relation Ontology
Foundational is_apart_of
Spatial located_incontained_inadjacent_to
Temporal transformation_ofderives_frompreceded_by
Participation has_participanthas_agent
18
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.

19
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.

20
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.

21
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
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