Ontologies for Knowledge Sharing in Neuroanatomy

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Ontologies for Knowledge Sharingin Neuroanatomy

• John Gennari
• Informatics in Biology Medicine
• Information Computer Science Department
• University of California, Irvine

This work developed in collaboration with the UCI
Transdisciplinary Tobacco Use Research Center
(TTURC)
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The TTURC project

• At UCI, a Transdisciplinary Tobacco Use Research
  Center (an NIH project)
• Researchers from
• Cognitive Science
• Neuroanatomy
• Pharmacology
• Psychiatry
• Computer Science (informatics)

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The big picture

• Transdisciplinary scientific research
• Holistic science
• Cross-field fertilization of scientific ideas
• Transdisciplinary knowledge sharing and
  ontologies
• Abstraction
• Visualization
• Modeling
• Terminology management
• Easier access to experimental results

Gruber Ontologies for knowledge sharing --
Ontologies as a social contract for communication
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The long-term objectives

• Use Protégé-2000 for TTURC knowledge
  representation and sharing
• Protégé-2000 research question Are our tools
  effective and useful?
• TTURC research question Can transdisciplinary
  work accelerate or facilitate research in tobacco
  use?

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A knowledge sharing problem

• 1. Researchers in animal studies (rat) are
  measuring brain activity via CFOS staining
• 2. Social science researchers are studying
  tobacco use among (human) adolescents
• 3. Researchers in psychiatry are measuring brain
  activity (human) via MRI and PET scans

Challenge How can we combine research results?
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Knowledge combining scenario

• If we had
• Knowledge about correspondences between rat brain
  regions and human brain regions
• Knowledge about the function of brain regions
• Knowledge about the connectivity of brain regions
• Then we could
• Test theories about the effect of nicotine on
  cognitive function in rats and humans

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Knowledge requirements

• Ontologies ( knowledge bases) for
• Definitions of brain regions Neuroanatomy
• Brain region cross-species correspondences
• Brain region functionality
• Brain region connectivity

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Roadblocks (or challenges)

• The boundaries and definitions of brain regions
  are (sometimes) approximate
• The topology of brain regions is complex
• Terminologies conflict, even within species
• Functional knowledge is very limited
• Knowledge about brain region connectivity is not
  complete

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Ontologies(?) for neuroanatomy

• The USC Brain Project and the Human Brain Project
  consortium (NIH)
• NeuroScholar (USC)
• BrainMap (U Texas, San Antonio)
• Digital Anatomist (U Washington)
• NeuroNames (U Washington)

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Project status

• Strategy bottom up, from experimental data
• Built ontology for rat brain regions where CFOS
  expression is measured
• Developed tool for describing brain region
  connectivity
• Next steps
• Adding human brain regions and PET scan data
• Building tools for describing cross-species
  correspondences
• Storing functional knowledge for brain regions

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Rat brain region ontology
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Brain region connectivity diagram
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Acknowledgements

• The Protégé team
• Monica Crubezy
• Ray Fergerson
• William Grosso
• John Gennari
• Some TTURC investigators
• Francis Leslie
• James Beluzzi
• Rodham Shankle

Mark Musen Natasha Noy Samson Tu plus students
others
James Fallon Larry Jamner Carol Whalen
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