Re: Towards ontology metrics to guide the development and assessment of "good" ontologies

Hey Michel,


> 1 - What metrics should we use to assess ontology quality and determine  
> whether an ontology is "good".


Ben Good took a stab at this with the OntoLoki project (see chapter in  
Ben's thesis starting on page 61  
http://circle.ubc.ca/bitstream/handle/2429/7115/ubc_2009_spring_good_benjamin.pdf)...  
Ben, Chris Mungall, Soroush Samadian and I have been discussing perhaps  
resurrecting the project and working together on finishing it... though  
we're questioning whether it is really useful for evaluating an ontology,  
versus bootstrapping the DL-ification of OBO-style ontologies.


> 2 - Can we re-factor existing, and well used terminologies (SNOMED-CT,  
> NCI-T, ICD) into "good" ontologies for health care and the life sciences?


OntoLoki speaks to this issue also (see link above), and as soon as  
Soroush finishes his PhD candidacy exam in 2 weeks, we'll be writing and  
submitting a paper on how we have re-factored the cardiovascular part of  
GALEN - we can send you a draft of that as soon as it is ready.  The  
re-factoring was done manually in this case, but we plan to use  
OntoLoki-style pattern-discovery in the future to see if we can at least  
partically automate the process.  Part of soroush's thesis project is to  
connect OntoLoki to the iCAPTURER (an Elisa-style Q&A interface) to see if  
we can combine pattern discovery with human-expert validation  
simultaneously to allow end-users to create their own DL ontologies.

if any of this is helpful let me know and I'll send you whatever we have  
:-)

Mark



--
Mark Wilkinson
Assistant Professor, Medical Genetics
PI Bioinformatics, Heart + Lung Institute @ St. Paul's Hospital
University of British Columbia
Vancouver, BC
Canada