2005-08-05 BioPAX-Boston Meeting

Boston BioPAX 5 August 2005 - Joanne's notes (so far)

Attendees: Frank Schacherer, Jeremy Brown, Jeremy Zucker, Jonathan Rees, Dan Corwin, Alan Ruttenberg, Joanne Luciano, Nada Hashmi (random order)

Agenda:

• Go over Alan's ontology ideas; critique and help solve problems

• Discuss implications of radical changes for backward compatibility

• Ideas on setting up an executive committee for BioPAX

Directions to Stata: https://www.csail.mit.edu/contact/contact.html

Map showing Stata: http://whereis.mit.edu/map-jpg?selection=32&Buildings=go

Map showing room 397: www.csail.mit.edu/resources/maps/3/397.gif

Ontology Ideas:

• How to import other ontologies

• How to do inference

• "Instance of" = GO "Part-of" E.g. Look for all things in a membrane

• Who is responsible for a-box reasoning? The client?

• Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan Rector, Cornelius Rosse, “Relations in Biomedical Ontologies”, Genome Biology, 2005, 6 (5), R46.)

  • http://genomebiology.com/2005/6/5/R46

• Example of something you can't do in OWL DL - ask it the sum of the

  • weight of a molecule is the same on both sides of an equation

• Uses of BioPAX that distinguish it from top level BioPAX

• Provide reference standards - to add under refinements to BioPAX

• Can it be made modular?

• Examples of all issues

• Reasoning over chemcical structures

• Define reasoning capabilities desired first

• "Prove it or state it" philosophy

• OWL-Nothing, Blank nodes with IDs

• Can know what you don't know

• generics

• The Description Logic Handbook: Theory, Implementation and Applications. Cambridge University Press, 2002. ISBN 0521781760. Edited by F. Baader, D. Calvanese, D. McGuinness, D. Nardi, P. F. Patel-Schneider. Contributors: D. Nardi, R.J. Brachman, F. Baader, W. Nutt, F.M. Donini, U. Sattler, D. Calvanese, R. Molitor, G. De Giacomo, R. Kuesters, F. Wolter, D.L. McGuinness, P.F. Patel-Schneider, R. Moeller, V. Haarslev, I. Horrocks, A. Borgida, C. Welty, A. Rector, E. Franconi, M. Lenzerini, R. Rosati.

  • http://www.cambridge.org/uk/catalogue/catalogue.asp?ISBN=0521781760

  • [Joanne: see http://www.inf.unibz.it/~franconi/dl/course/ for good stuff on DLs]

Backward Compatibility:

• The quality of the ontology moving forward should not be hindered by backward compatiblity issues.

• BioPAX is still in early development and formats change (Some of you will remember Protege OWL Alpha and Beta?)

• Provide converters

Executive Committee:

• Discussed the function of an executive committe and how membership should be determined

• Discussed steering committee functions

• Discussed meeting agendas and organizing committee functions