Ontology Development for Animal Behaviour and Welfare Research

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Ontology Development for Animal Behaviour and
Welfare Research

• Joanna Bagniewska
• Supervisor Dr. David Shotton

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What and why?

• Not a typical research project Intellectual
  creative endeavour. Or simply tool development!
• Animal behaviour and welfare research mainly
  based on observations.
• Problems
• Time consuming
• Introducing bias
• Metadata difficult to store and recover
  hampering knowledge sharing!
• Need a program facilitating video analysis.
• Basis ONTOLOGY.

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What is an ontology?

• An ontology is a controlled vocabulary that
  describes objects and the relations between them
  in a formal way.

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Example of an ontology
parent class
child class
D.M. Shotton, Ontologies, images and databases,
Seminar presentation at MRC Harwell, 2006,
(http//www.weblearn.ox.ac.uk/site/mathsphys/biolo
gy/msc/).
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Background

• Previous research
• 2003 Oxford University Standard Animal
  Behaviour Ontology (SABO)
• 2004, 2005 Cornell University core Animal
  Behavior Ontology (ABOcore) ? basis of this
  project.
• 2006 MRC Harwell, Mammalian Genetics Lab
  Behavioural Assays Ontology
• Aim further development.

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Methodology

• Building blocks
• Language Web Ontology Language OWL DL
  (Description Logics)
• Software Protégé 3.2.1
• Storage Ontogenesis Network Wiki,
• http//ontogenesis.ontonet.org/moin/AnimalBehaviou
  rOntologyDevelopment
• Ontology development
• Term search
• Definition search
• Structure

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Limitations imposed on the project

• Limited to the is_a relation.
• Independent (not importing any other ontology).
• One parent class per term.
• Ideally a maximum of 4-5 nested levels.
• Time constraint.
• Keep it SMALL and SIMPLE (not a simple task)!

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Animal Behavior Ontology

• Scope as broad as possible.
• Volitional acts. What is volitional?
• Division between behavioral activities and
  behavioral functions defined by humans

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Animal Behavior Ontology

• Initial work semantic clean up the ABOcore ? ABO
  v1.0.
• E.g. class names changed into singular nouns,
  capitalizations removed.
• Follow the is_a relation
• Development
• Restructure
• Broaden currently 349 classes (initially 292)
• Add definitions from literature, communication,
  personal experience.

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ABO Dilemmas

• What is an activity, what is a function?
• How much detail is available?
• How much detail do we want to have?
• Who is the observer?
• Mice babies huddle in a nest. How to record this?
• Version 1. Act grouping, function huddling.
• Version 2. Act huddling, function temperature
  regulation.
• is_a relation requires broadened categories.
• territoriality is_a behavioral_function
• BUT
• patrolling_behavior is_a territoriality_aspect

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Animal Welfare Ontology

• Scope Animals under human husbandry.
• Ontology of VIOLATIONS of animal welfare.
• Definition sources
• Research papers
• Governmental publications
• Animal welfare organization websites

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Initial idea

• Structured around assay techniques
• Non-invasive
• Hands-on
• Invasive

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Harwell Ontology

• More relations is_a, but also others like
  tested_for or assayed_by

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AWO Current structure

• Idea
• term ? species ? assay ? result ? normal_range ?
  unit
• Currently, just dealing with terms.
• Three ontologies
• behavioral_indicator
• environmental_indicator
• physical_indicator
• 265 classes

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AWO Current structure
Introducing bias in wording
Dilemma trade-off between functionality and
logical correctness!
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Conclusions

• Tools for use in academia, farming, research,
  policy-making etc.
• Creating is different from using!
• Future research
• Developing the structure
• Adding more terms not complete currently!
• Publication online.

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Blog

• www.awontology.blogspot.com
• www.awontology.wordpress.com

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Thank you for your attention!
http//lsdis.cs.uga.edu/projects/glycomics/report/
Report2006.html