The Future of the Foundational Model of Anatomy

Date: November 12-13, 2009

Venue: Stanford University

Organizers: Onard Mejino, Natasha Noy, Alan Ruttenberg

Agenda

Thursday, November 12

Preliminaries

8:30 Welcome - Mark Musen, Barry Smith, Cornelius Rosse

9:00 Short introductions by participants

9:15 Objectives of the FMA group for the meeting - Jim Brinkley

9:30 Presentation by FMA group explaining semantics, deficiencies in

current representation, questions and targets for OWL (Onard and Cornelius)

11:00 Requirements brought in from OBO Foundry/Semweb (Alan)

11:15 The FMA and its ontological commitment(s) (Stefan)

Review and discussion of current approaches

11:30 Current approaches to translation - Christine Golbreich

12:05 Current approaches to translation - Natasha Noy

12:40 Lunch

1:30 Current approaches to translation - Chris Mungall

2:10 Introduction to OWL 2 and its features - Uli Sattler

2:50 Break

Details

3:15 Who's using FMA, and how? - Onard Mejino

3:45 Presentation of specific challenges - Onard Mejino

Discussion sections addressing issues identified above, focused on cardiovascular system as exemplar

4:15 Single/Multiple inheritance and inferred hierarchies

    Problem: Single inheritance hierarchy prohibits multi-supertype assignments. 
    Examples: 
        - primary incisor tooth can be a subtype of either incisor tooth or primary tooth 
        - right female breast can be a subtype of female breast or right breast 
        - proximal phalanx of thumb can be a subtype of either phalanx of thumb or proximal phalanx of finger 
        - question: can OWL automatically infer one of the supertypes in the inferred hierarchy 

Friday, November 13

9:00

Representation of different contexts using the same relation.

    Examples: 
        - prostate can be regionally subdivided into different parts using different contexts; 
            a. classically into anterior lobe, median lobe, right lateral lobe, left lateral lobe and posterior lobe 
            b. histologically into peripheral zone, central zone, transition zone, and peri-urethral zone 
            c. surgically into right median lobe, left median lobe, right lateral lobe, left lateral lobe, right dorsal lobe and left dorsal lobe 
        - heart can subdivided into different contexts: 
            Right side and left side 
            Biatrial part and biventricular part 
            T7, T8, T9, T10 parts 
    These are all valid regional parts 

9:45 Review of relations and their usage.

  - Axiomization 
  - Use of Attributed/reified relationships 
     - Are they necessary? 
     - If necessary how to represent them in OWL 

10:30 Break

11:00 Post-Coordination

11:45 What can be inferred? Quality assurance - error and consistency checks

12:30 Lunch

Moving forward

1:30 Review of goals and outlines of possible solutions - Jim Brinkley

2:00 Technical methods to achieve interoperability and orthogonality:

2:10 OWL Modularity – Uli Sattler

2:20 Ontology views – Todd Detwiler

2:30 Cross-references and semantic web linking methods – Alan Ruttenberg

3:00 Break

3:30-5:00 Discussion, action items, and future plans – Jim Brinkley, Alan Ruttenberg, Olivier Bodenreider

5:00 Closing remarks Cornelius Rosse, Mark Musen, Barry Smith