NetworkMeeting5

Network Meeting 5: Experiment in Collaborative Normalisation of the Cell Type Ontology

The aim of the meeting is to do collaborative normalisation of the CTO (Cell type Ontology).

We will be using the version at:

http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo

It is all asserted multiple inheritance.

Our goal is to normalise (on paper) and then Mikel will write the OPPL script (description later) to transform the CTO to a normal form.

Contents:

1. Meeting Details
   1. Dates/Time
   2. Meeting Location
   3. Accommodation
   4. Costs
2. Programme of speakers and presentations
3. Outcome
4. References
5. Organisers

1. Meeting Details

1.1. Dates/Time

June 25 and 26

1.2. Meeting Location

Wolfson College, University of Oxford

1.3. Accommodation

Accommodation is at the Linton Lodge Hotel, Linton Road, Oxford ( http://www.lintonlodge.com/), 400 metres up the road from Wolfson College. The rate is £75 per person per night bead and breakfast. People wanting rooms should have booked these individually for one or both nights, by phoning the hotel on 01865-553 461 using their own credit cards before May 30th, quoting reference number UNI2406. The hotel reservation manager is Karen Musto. Car parking is available both at the hotel and the college.

1.4. Costs

The Ontogenesis Network will cover the costs of both workshop days, one nights accommodation and reasonable travel for Ontogenesis Network Members and speakers.

2. Programme of speakers and presentations

In the both days we hope to:

1. Inspect CTO 2. Determine current axes of classification 3. Decide upon primary axis of classification 4. Create annotations describing activities etc. 5. Identify or create supporting ontologies (e.g., PETO) 6. Identify restrictions to place upon cells in primary axis 7. Formulate plan of transformation; and 8. have a little demo of what we're doing in Protege

The primary aim is "do it"!

We will aim to use some of the principles of OntoClean [3, 4] to help us identify appropriate axes for primary classification. We'll provide an OWL version of CTO. Reading the CTO paper [5] and looking at the ontology would be a good idea. For those of you who need a revision of normalisation, the paper is at the end of this note. Please note that the upcoming NetworkMeeting7 will specialize on collaborative ontology engineering using Collaborative Protege.

3. Outcome

The wiki page we used to collect minutes of the meeting: http://imageweb.zoo.ox.ac.uk/wiki/index.php/Collaborative_Ontology_Normalization

The page where we get the excell files to work with: http://www.cs.man.ac.uk/~sjupp/cto_experiment/

The guidelines for filling the excel files: http://sindominio.net/~pik/CTO_guideline.txt

The resulting ontology (result of last execution, more executions in the future - richer ontologies): http://sindominio.net/~pik/owl.tar.gz

4. References

[1] Alan L. Rector: Modularisation of domain ontologies implemented in description logics and related formalisms including OWL. K-CAP 2003: 121-128. http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf.

[2] Alan L. Rector, Chris Wroe, Jeremy Rogers, Angus Roberts: Untangling taxonomies and relationships: personal and practical problems in loosely coupled development of large ontologies. K-CAP 2001: 139-146. http://www.cs.man.ac.uk/~rector/papers/rector-k-cap-untangling-taxonomies-web.pdf.

[3] Christopher A. Welty: An Overview of OntoClean. Handbook on Ontologies 2004: 151-172. http://www.ontoclean.org/; http://www.research.ibm.com/people/w/welty/presentations/index.html; http://www.ontoclean.org/ontoclean.html.

[4] Nicola Guarino, Christopher A. Welty: Evaluating ontological decisions with OntoClean. Commun. ACM 45 (2): 61-65 (2002). http://portal.acm.org/citation.cfm?doid=503124.503150.

[5] An ontology for cell types Jonathan Bard, Seung Y Rhee and Michael Ashburner Genome Biology 2005 Volume 6, Issue 2. http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=551541&blobtype=pdf

5. Organisers

Robert Stevens ( robert.stevens@manchester.ac.uk) and George Moulton ( georgina.moulton@manchester.ac.uk)

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-- GeorginaMoulton 2006-10-18 16:27:51

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