OBI: Ontology for Biomedical Investigations

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OBI Ontology for Biomedical Investigations

• James Malone

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Overview

• The OBI Consortium
• Three rules of OBI Infrastructure,
  infrastructure, infrastructure
• Delegating the workload
• Progress to date
• Get Involved (also known as work is its own
  reward ? )

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The OBI Consortium

• OBI bring together a range of skills and
  backgrounds from around the globe

Computer Scientists
Statisticians
Biochemists
Philosophers
Biologists
Ontologists
MDs
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OBI Consortium Structure
Developers Working Group
Coordinating Committee
The Developers Working Group consists of all
developers within the communities collaborating
in the development of OBI, at the discretion of
current OBI Consortium members.

• Community Representatives

The representives of the communities
participating in the development of OBI.
Core Developers
Advisory Group
Core Developers are considered key to the
evolution of the ontology, but may or may not be
members of any single community.
The Advisors Group consists of individuals
invited by the Coordination Committee to provide
expert advice in areas such as ontology best
practices and technical implementation issues.
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Scope of OBI

• To develop an integrated ontology for the
  description of biological and medical experiments
  and investigations
• Set of 'universal' terms, that are applicable
  across various biological and technological
  domains, and domain-specific terms relevant only
  to a given domain.
• Support consistent annotation of biomedical
  investigations, regardless of the particular
  field of study.
• Unambiguous description of how the investigation
  was performed
• The ontology will model the design of an
  investigation, the protocols and instrumentation
  used, the material used, the data generated and
  the type analysis performed on it
• OBO Foundry member

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Infrastructure, infrastructre, infrastructure

• Design principle was to use an upper ontology to
  aid with interoperability
• Use of Barry Smiths Basic Formal Ontology (BFO)
• SOP for dealing with submitted terms
• Accession ID for every term, with range for
  each branch
• Transparent Evaluation Strategy

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Infrastructure Roles, Qualities and Function

• Role something which an entity can play but that
  is not essential to it
• e.g. a technique can play various roles depending
  upon context, classification
• e.g. role of a chemical compound in an experiment
• Qualities something inherent and intrinsic to
  the entity
• e.g. colour of a tomato
• e.g. atomic mass of an atom
• Function the end directed activity of an entity
  in virtue of that specific entity and the context
  it is made for
• e.g. function of the heart in the body to pump
  blood

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Delegating the Workload OBI Branch Work
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Coordinating the Workload

• Weekly branch calls
• Weekly developers call (all branches)
• Monthly coordinators call
• Biannual face to face workshop (next to be held
  in Jan 08 in Vancouver, then EBI Cambridge
  Summer 08)
• SVN (sourceforge) to track changes to owl files

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Progress to Date
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Progress to Date

• Currently OBI incorporates over 500 terms
• Mappings planned with several other ontologies
  including Software Ontology, PATO, ChEBI, GO.
• Key is orthogonal coverage, reuse of existing
  resources and shared frameworks and wide-scale
  community participation

OBI
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Wrestling with the Issues

• Role vs function vs quality
• Single vs multiple inheritance
• Representing time e.g. modelling a protocol
• Granularity e.g. instrument flow cytometer vs
  flow cytometer model xyz, serial number 12345
• Evaluation OBI has large scope and many
  evaluation models not well devloped
• Funding such a project!

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Get Involved

• There are numerous ways to get involved with OBI
• Join the development team
• Submit community terms
• Submit use cases to ensure we are covering your
  needs
• Subscribe to mailing lists (beware of the
  traffic!)
• Development Wiki https//wiki.cbil.upenn.edu/obiw
  iki/index.php?titleHomePage
• SVN files including all .owl required
  http//obi.svn.sourceforge.net/
• Submit use cases via email to malone_at_ebi.ac.uk
• Mailing lists http//obi.sourceforge.net/resource
  s/index.php

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OBI Consortium Credits

• Core Developers
• Melanie Courtot
• Allyson Lister
• Alan Ruttenberg
• Daniel Schober
• James Malone
• Community Representatives
• Jeff Grethe
• Daniel Rubin
• Bill Bug
• Stefan Wiemann  
• Jennifer Fostel
• Richard Bruskiewich
• Frank Gibson
• Ryan Brinkman
• Dawn Field
• Tanya Gray
• Richard Scheuermann
• Bjoern Peters

• Daniel Schober
• Bill Bug
• Philippe Rocca-Serra
• Tina Hernandez-Boussard
• Luisa Montecchi
• Chris Taylor    
• Trish Whetzel  
• Philippe Rocca-Serra
• Chris Stoeckert
• Gilberto Fragoso
• Joe White      
• Helen Parkinson
• Mervi Heiskanen      
• Liju Fan
• Helen Causton
• Elisabetta Manduchi
• Advisory Group
• Frank Hartel
• Suzi Lewis