Difference between revisions of "The Future of the Foundational Model of Anatomy"

Latest revision as of 09:20, 14 February 2012

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

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

@@ Line 1: / Line 1: @@
-FMA in OWL meeting agenda, an NCBO Dissemination Event
+'''Date:''' November 12-13, 2009
-November 12-13, 2009
-Organizers: Onard Mejino, Natasha Noy, Alan Ruttenberg
+'''Venue:''' Stanford University
-Venue: Stanford University (details)
-Attendees are kindly requested to have read the papers in the reading
+'''Organizers:''' Onard Mejino, Natasha Noy, Alan Ruttenberg
-list
-Thursday,
-November 12
+== '''Agenda''' ==
-Preliminaries
-:30-8:50       Welcome - Mark Musen, Barry Smith, Overview by Chair -
-Cornelius Rosse
+'''Thursday, November 12'''
-:50-9:00       Logistics - assign scribes, timekeepers, review protocol
-:00-9:15       Short introductions by participants
+'''Preliminaries'''
-:15-9:30       Objectives of the FMA group for the meeting - Jim Brinkley
+:8:30       Welcome - Mark Musen, Barry Smith, Cornelius Rosse
-:30-10:30
+:9:00 Short introductions by participants
-Coffee Break
+:9:15 Objectives of the FMA group for the meeting - Jim Brinkley
-:30-11:00
+:9:30  Presentation by FMA group explaining semantics, deficiencies in
-Presentation by FMA group explaining semantics, deficiencies in
 current representation, questions and targets for OWL (Onard and
 Cornelius)
-:00-11:15     Requirements brought in from OBO Foundry/Semweb (Alan)
+:11:00     Requirements brought in from OBO Foundry/Semweb (Alan)
-:15-11:30     The FMA and its ontological commitment(s) (Stefan)
+:11:15     The FMA and its ontological commitment(s) (Stefan)
-Review and discussion of current approaches
-:30-12:05     Current approaches to translation - Christine Golbreich
+'''Review and discussion of current approaches'''
-:05-12:40     Current approaches to translation - Natasha Noy
+:11:30     Current approaches to translation - Christine Golbreich
-:40-1:30      Lunch
+:12:05     Current approaches to translation - Natasha Noy
-:30-2:10       Current approaches to translation - Chris Mungall
+:12:40      Lunch
-:10-2:50       Introduction to OWL 2 and its features - Uli Sattler
+:1:30       Current approaches to translation - Chris Mungall
-:50-3:15       coffee break
+:2:10       Introduction to OWL 2 and its features - Uli Sattler
-Details
+:2:50 Break
-:15-3:45       Who's using FMA, and how? - Onard Mejino
-:45-4:15       Presentation of specific challenges - Onard Mejino
+'''Details'''
-Discussion sections (continuing friday) addressing issues identified
+:3:15    Who's using FMA, and how? - Onard Mejino
-above, focused on cardiovascular system as exemplar. Rotating
+:3:45       Presentation of specific challenges - Onard Mejino
-moderators.
+:4:15       Single/Multiple inheritance and inferred hierarchies
-:15-5:00       Single/Multiple inheritance and inferred hierarchies
+      Problem: Single inheritance hierarchy prohibits multi-supertype assignments.
-      Problem: Single inheritance hierarchy prohibits multi-supertype
-assignments.
       Examples:
-          - primary incisor tooth can be a subtype of either incisor
+          - primary incisor tooth can be a subtype of either incisor tooth or primary tooth
-tooth or primary tooth
+          - right female breast can be a subtype of female breast or right breast
-          - right female breast can be a subtype of female breast or
+          - proximal phalanx of thumb can be a subtype of either phalanx of thumb or proximal phalanx of finger
-right breast
+          - question: can OWL automatically infer one of the supertypes in the inferred hierarchy
-          - proximal phalanx of thumb can be a subtype of either
-phalanx of thumb or proximal phalanx of finger
+'''Friday, November 13'''
-          - question: can OWL automatically infer one of the supertypes
+:9:00
-in the inferred hierarchy
-Friday,
-November 13
-Discussion sections (continued from thursday) addressing issues
-identified above, focused on cardiovascular system as exemplar.
-Rotating moderators.
-:00-9:45
 Representation of different contexts using the same relation.
       Examples:
-          - prostate can be regionally subdivided into different parts
+          - prostate can be regionally subdivided into different parts using different contexts;
-using different contexts;
+              a. classically into anterior lobe, median lobe, right lateral lobe, left lateral lobe and posterior lobe
-              a. classically into anterior lobe, median lobe, right
+              b. histologically into peripheral zone, central zone, transition zone, and peri-urethral zone
-lateral lobe, left lateral lobe and posterior lobe
+              c. surgically into right median lobe, left median lobe, right lateral lobe, left lateral lobe, right dorsal lobe and left dorsal 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
+     These are all valid regional parts
-only accommodate one context, in the case of the FMA it’s the
+:9:45              Review of relations and their usage.
-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
-slots
-: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
-:30-11:00     Coffee
+:10:30 Break
-:00-11:45
+:11:00 Post-Coordination
-Post Coordination (see expanded discussion)
+:11:45      What can be inferred?  Quality assurance - error and consistency checks
-:45-12:30     What can be inferred? (see expanded discussion)
+:30 Lunch
-Quality assurance - error and consistency checks
-:30-1:30              Lunch
+'''Moving forward'''
-Moving forward
+:1:30 Review of goals and outlines of possible solutions - Jim Brinkley
-:30-2:00       Review of goals and outlines of possible solutions - Jim
+:2:00 Technical methods to achieve interoperability and orthogonality:
-Brinkley
+:2:10 OWL Modularity – Uli Sattler
-:00-3:00
+:2:20 Ontology views – Todd Detwiler
-Technical methods to achieve interoperability and orthogonality:
+:2:30       Cross-references and semantic web linking methods – Alan Ruttenberg
-       OWL Modularity – Uli Sattler (10 min)
-       Ontology views – Todd Detwiler (10 min)
+:3:00 Break
-       Cross-references and semantic web linking methods – Alan
+:3:30-5:00       Discussion, action items, and future plans – Jim Brinkley, Alan Ruttenberg, Olivier Bodenreider
-Ruttenberg (10 min)
+:5:00     Closing remarks Cornelius Rosse, Mark Musen, Barry Smith
-       Discussion (30 min)
-:00-3:30       Coffee
-:30-5:00       Discussion, action items, and future plans – Jim Brinkley,
-Alan Ruttenberg, Olivier Bodenreider
-:00
-Closing remarks Cornelius Rosse, Mark Musen, Barry Smith

Difference between revisions of "The Future of the Foundational Model of Anatomy"

Latest revision as of 09:20, 14 February 2012

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