AnimalBehaviourOntologyDevelopment

Animal Behaviour Ontology Development

This is a start page within the Ontogenesis Network wiki for collecting notes concerning development of an ontology for animal behaviours. Additional pages may be created and linked from this page. See http://ontogenesis.ontonet.org/moin/AccessingThisWiki for information about using this wiki.

Contents:

1. Background Documents
2. Behavioural Acts Ontology Module, Revised January 2007
3. Behavioural Functions Ontology Module, Revised January 2007
4. Material for Further Ontology Modules
5. Joanna Bagniewska's Ontology Development
   1. Project plan
   2. Tutorials
   3. Ontology versions
      1. ABO core
      2. ABO v0.1
      3. Drafts
   4. Cleaned up versions
   5. Ontology Thesis
   6. Presentation
   7. Additional work
6. Final Ontologies
   1. Useful links

1. Background Documents

• Cornell Second Animal Behavior Metadata Meeting Report attachment:SecondMeetingAgenda.doc

• Cornell Metadata II information attachment:info.pdf

• Oxford Proposal for Cornell Metadata II attachment:oxford_propsal.pdf

• Second Animal Behavior Metadata Workshop Report attachment:workshop_report.doc

• Protege 4 alpha 25 attachment:Protege4Alpha25.zip

• The draft Behavioural Acts and Functions ontology from the Second Animal Behavior Workshop is available at http://ethodata.org.

• Harwell Behavioural Assays Ontology, openable using OBO Edit attachment:firstASSAY1a.ontology

• Harwell Behavioural Assays Ontology, openable using NotePad or similar text editor attachment:firstASSAY1a_ontology_DAGEdit_format.txt

• OBO Edit installation file attachment:setup_oboedit_1_002_win.exe

2. Behavioural Acts Ontology Module, Revised January 2007

3. Behavioural Functions Ontology Module, Revised January 2007

4. Material for Further Ontology Modules

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5. Joanna Bagniewska's Ontology Development

5.1. Project plan

• Project plan attachment:ProjectProposalv2.doc

• Write-up attachment:Write-up.doc

5.2. Tutorials

• ProtegeOWL Tutorial by Matt Horridge: http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf. Learn how to build pizzas.

• Ontology 101 by Noy and McGuinness: http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html. Learn how to classify wines.

• There are many other excellent materials from the Manchester group at http://www.co-ode.org/resources/tutorials/.

5.3. Ontology versions

5.3.1. ABO core

• Original ABO from Cornell in .owl format attachment:ABOcore0.1.owl. Can be obtained from www.ethodata.org

5.3.2. ABO v0.1

• This is the edited version of the Cornell ontology attachment:ABOv0.1.owl

• The changes took into account the comments of Barry Smith posted in the Projects Forum http://mlsource.ornith.cornell.edu/forum/viewtopic.php?t=21&sid=72d1a178676206814f874c5db4698332

• Additional comments:

1. American spelling was maintained throughout the ontology (and will also be used for its future versions). Although the initial idea was to anglicize it, the American version should prove more universal.

2. The terms were modified to describe actions rather than their results. (E.g. "kicking" rather than "kick").

3. The categories themselves were not changed, except for the cases where two concepts were placed in the same class, separated by "/", "and", "or". These were separated into two classes where appropriate.

• Changes made on 25 Jan 2007 by Joanna Bagniewska

5.3.3. Drafts

• Attempts to create the Animal Welfare Ontology attachment:AWO29jan2007.owl

• Most recent version of ABO. I put XXX next to very dubious sections, although there's still a lot of work to be done on it. The behavioral_phenomenon section is just a stub. attachment:3ABO1feb2007.owl

ABO: attachment:6ABO7feb2007.owl

AWO: attachment:13AWO16mar2007.owl

AWO: attachment:14AWO19mar2007.owl

5.4. Cleaned up versions

ABO: attachment:ABOclean.owl

AWO: attachment:AWOclean.owl

5.5. Ontology Thesis

Thesis: attachment:ThesisOntologies.pdf

5.6. Presentation

Presentation: attachment:OntologyPresentation.ppt

5.7. Additional work

There needs to be some general definitions: Keeper/caregiver - referred to throughout the whole text. I added "Characteristic" to a lot of the terms to make them comply with the "is_a" format. Where the definitions appeared self-explanatory, I left them as they were in the term name.

What still needs to be done:

1. Overall commentary

• putting in all the general definitions (caregiver/keeper/etc)

• stating that different species (wild, domesticated, semi-domesticated) have diffrent needs. Also if they are social/solitary, aquatic/terrestrial etc.

• different contexts for animal keeping (zoos, farms, labs, companion animals) require different approaches

2. Be consistent with terminology - e.g. if there are synonyms (provision = availability) use just one form.

3. Make the reference links uniform (in brackets, as a separate comment, etc. Could also put a context in which the term was found, plus a link to a video or a photo).

4. Check the relations with Pellet. Make them disjoint etc.

5. Get rid of placeholders. On the 19march version it's just the ontology itself, no animal keeping context. Also "types of enclosure" is gotten rid of in the march20 version.

6. Final Ontologies

ABO v1.0: attachment:ABOfinal.owl

AWO v1.0: attachment:AWOfinal.owl

6.1. Useful links

• Criticisms of relations in biomedical ontologies http://genomebiology.com/2005/6/5/R46

• Manual http://www.ifomis.uni-saarland.de/bfo/manual/manual.pdf

• A very informative website with rat behaviors: http://www.ratbehavior.org/Glossary.htm#Brux

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-- GrahamKlyne 2005-09-26 12:41:35