Building Ontologies Best practices, pitfalls and positives Olivier Bodenreider Lister Hill National Center for Biomedical Communications Bethesda, Maryland - USA Cell Behavior Ontology Workshop National Institutes of Health Campus, Bethesda, MD May 4, 2009
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Building OntologiesBest practices, pitfalls and positives
Olivier Bodenreider
Lister Hill National Centerfor Biomedical Communications
Bethesda, Maryland - USA
Cell Behavior Ontology Workshop National Institutes of Health Campus, Bethesda, MD
May 4, 2009
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Outline
If ontology is the solution, what is the problem?Think use cases
Don’t try this at home!Ontologies for dummies hasn’t been written yet
Where to start?
If ontology is the solution,what is the problem?
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Uses of biomedical ontologies
Knowledge managementAnnotating data and resourcesAccessing biomedical informationMapping across biomedical ontologies
Data integration, exchange and semantic interoperabilityDecision support
Data selection and aggregationDecision supportNLP applicationsKnowledge discovery
[Bodenreider, YBMI 2008]
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Properties of biomedical ontologies
Knowledge managementAnnotating data and resourcesAccessing biomedical informationMapping across biomedical ontologies
Data integration, exchange and semantic interoperabilityDecision support
Data selection and aggregationDecision supportNLP applicationsKnowledge discovery
Controlledvocabularies
Ontologicalresources
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Ontology “spectrum”
http://www.mathiswebs.com/ontology.htm
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Instances, classes, collectives
“Lmo-2 interacts with Elf-2” One individual Lmo-2 molecule interacts with one individual Elf-2 molecule.A collective of Lmo-2 molecules interacts with one individual Elf-2 molecule.One individual Lmo-2 molecule interacts with a collective of Elf-2 molecules.A collective of Lmo-2 molecules interacts with a collective of Elf-2 molecules.[…]
[Schulz and Landsen, Applied ontology 2009]
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Top-level ontologies
Basic Formal Ontology (BFO)DOLCEBioTop
Ground domain ontologies into sound philosophical foundationsDifficult to understand for “folks form the trenches”
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A pyramid of ontologies
BioTop, http://www.imbi.uni-freiburg.de/biotop/
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Power tools for ontologies
Ontology editorsProtégéOBO-Edit
Semantic wikisIntermediate representationsCollaborative development
Too complexfor mostbiologists
Simplifiedrepresentations
Where to start?
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Collect entities from the universe of discourse
From expertsWorkshops
From textual corporaManuallyAutomatic term extraction
From existing terminologies and ontologies
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Shop around Ontology repositories
http://bioportal.bioontology.org/
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Link to/Borrow from existing ontologies
AdvantagesAvoid reinventing the wheelBenefit from the experience of specialists of a given subdomain
DisadvantagesBorrow ontological commitment from these ontologiesMight align (or not) with the ontological commitment in your ontology
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Decide on standards and tools
With the help of experienced ontologists
For knowledge representatione.g., OWL
For editing ontologiese.g., Protégé
For ontological commitmente.g., top-level ontology, relation ontology
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Guidelines for ontology development
OBO Foundry principlesOpennessCommon shared syntax (OBO or OWL)Unique identifier space within the OBO FoundryVersioning mechanismClearly specified and clearly delineated contentTextual definitions for all termsUse relations from the OBO Relation OntologyThe ontology is well documentedPlurality of independent usersCollaborative development with other OBO Foundry members [Smith et al., Nature Biotechnology 2007]
International Classification of Diseases (ICD11 revisions)Semantic wiki approach + Protégé backgroundhttp://www.who.int/classifications/icd/ICDRevision/en/index.html
Neuroscience Information Frameworkhttp://neuinfo.org/
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Additional references
Bodenreider O. Biomedical ontologies in practiceShort course at the University of Utah, Department of Biomedical Informatics, Salt Lake City, Utah, June 9-11, 2008.http://mor.nlm.nih.gov/pubs/pres/080609-11_bioontologies_in_practice.pdfSmith B. Introduction to Biomedical Ontologies – A training course in eight lectures (video)http://ontology.buffalo.edu/smith/Ontology_Course.html
International Conference on Biomedical OntologyUniversity at Buffalo, NY · July 24-26, 2009http://icbo.buffalo.edu/