The Future of the Foundational Model of Anatomy
FMA in OWL meeting agenda, an NCBO Dissemination Event November 12-13, 2009 Organizers: Onard Mejino, Natasha Noy, Alan Ruttenberg Venue: Stanford University (details) Attendees are kindly requested to have read the papers in the reading list Thursday, November 12 Preliminaries 8:30-8:50 Welcome - Mark Musen, Barry Smith, Overview by Chair - Cornelius Rosse 8:50-9:00 Logistics - assign scribes, timekeepers, review protocol 9:00-9:15 Short introductions by participants 9:15-9:30 Objectives of the FMA group for the meeting - Jim Brinkley 9:30-10:30 Coffee Break 10:30-11:00 Presentation by FMA group explaining semantics, deficiencies in current representation, questions and targets for OWL (Onard and Cornelius) 11:00-11:15 Requirements brought in from OBO Foundry/Semweb (Alan) 11:15-11:30 The FMA and its ontological commitment(s) (Stefan) Review and discussion of current approaches 11:30-12:05 Current approaches to translation - Christine Golbreich 12:05-12:40 Current approaches to translation - Natasha Noy 12:40-1:30 Lunch 1:30-2:10 Current approaches to translation - Chris Mungall 2:10-2:50 Introduction to OWL 2 and its features - Uli Sattler 2:50-3:15 coffee break Details 3:15-3:45 Who's using FMA, and how? - Onard Mejino 3:45-4:15 Presentation of specific challenges - Onard Mejino Discussion sections (continuing friday) addressing issues identified above, focused on cardiovascular system as exemplar. Rotating moderators. 4:15-5:00 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 Discussion sections (continued from thursday) addressing issues identified above, focused on cardiovascular system as exemplar. Rotating moderators. 9:00-9:45 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 but the slot has regional part can only accommodate one context, in the case of the FMA it’s the classical anatomical representation and the rest are relegated to the attributed slot attributed part because it would be inappropriate to create has regional part 1, has regional part 2 and has regional part 3 slots 9:45-10:30 Review of relations and their usage.
- Axiomization
- Use of Attributed/reified relationships
- Are they necessary?
- If necessary how to represent them in OWL
10:30-11:00 Coffee 11:00-11:45 Post Coordination (see expanded discussion) 11:45-12:30 What can be inferred? (see expanded discussion) Quality assurance - error and consistency checks 12:30-1:30 Lunch Moving forward 1:30-2:00 Review of goals and outlines of possible solutions - Jim Brinkley 2:00-3:00 Technical methods to achieve interoperability and orthogonality:
OWL Modularity – Uli Sattler (10 min)
Ontology views – Todd Detwiler (10 min)
Cross-references and semantic web linking methods – Alan
Ruttenberg (10 min)
Discussion (30 min)
3:00-3:30 Coffee 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