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

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Cornelius)  
 
Cornelius)  
 
:11:00    Requirements brought in from OBO Foundry/Semweb (Alan)  
 
:11:00    Requirements brought in from OBO Foundry/Semweb (Alan)  
−
:11:15-11:30     The FMA and its ontological commitment(s) (Stefan)  
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:11:15    The FMA and its ontological commitment(s) (Stefan)  
  
 
'''Review and discussion of current approaches'''
 
'''Review and discussion of current approaches'''
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:3:15    Who's using FMA, and how? - Onard Mejino  
 
:3:15    Who's using FMA, and how? - Onard Mejino  
 
:3:45      Presentation of specific challenges - Onard Mejino  
 
:3:45      Presentation of specific challenges - Onard Mejino  
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Discussion sections addressing issues identified 
 
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above, focused on cardiovascular system as exemplar
 
 
:4:15      Single/Multiple inheritance and inferred hierarchies  
 
:4:15      Single/Multiple inheritance and inferred hierarchies  
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     Problem: Single inheritance hierarchy prohibits multi-supertype  
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     Problem: Single inheritance hierarchy prohibits multi-supertype assignments.  
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assignments.  
 
 
     Examples:  
 
     Examples:  
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         - primary incisor tooth can be a subtype of either incisor  
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         - primary incisor tooth can be a subtype of either incisor tooth or primary tooth  
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tooth or primary tooth  
+
         - right female breast can be a subtype of female breast or right breast  
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         - right female breast can be a subtype of female breast or  
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         - proximal phalanx of thumb can be a subtype of either phalanx of thumb or proximal phalanx of finger  
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right breast  
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         - question: can OWL automatically infer one of the supertypes in the inferred hierarchy  
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         - proximal phalanx of thumb can be a subtype of either  
 
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phalanx of thumb or proximal phalanx of finger  
 
−
         - question: can OWL automatically infer one of the supertypes  
 
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in the inferred hierarchy  
 
  
 
'''Friday, November 13'''
 
'''Friday, November 13'''
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             Biatrial part and biventricular part  
 
             Biatrial part and biventricular part  
 
             T7, T8, T9, T10 parts  
 
             T7, T8, T9, T10 parts  
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These are all valid regional parts but the slot has regional part can 
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    These are all valid regional parts  
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only accommodate one context, in the case of the FMA it’s the 
 
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classical anatomical representation and the rest are relegated to the 
 
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attributed slot attributed part because it would be inappropriate to 
 
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create has regional part 1, has regional part 2 and has regional part 
 
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3 slots
 
 
:9:45              Review of relations and their usage.  
 
:9:45              Review of relations and their usage.  
 
   - Axiomization  
 
   - Axiomization  
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:2:00 Technical methods to achieve interoperability and orthogonality:  
 
:2:00 Technical methods to achieve interoperability and orthogonality:  
 
:2:10 OWL Modularity – Uli Sattler   
 
:2:10 OWL Modularity – Uli Sattler   
−
:2:20 Ontology views – Todd Detwiler (10 min)
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:2:20 Ontology views – Todd Detwiler  
−
:2:30      Cross-references and semantic web linking methods – Alan  
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:2:30      Cross-references and semantic web linking methods – Alan Ruttenberg
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Ruttenberg
 
  
 
:3:00 Break  
 
:3:00 Break  
 
:3:30-5:00      Discussion, action items, and future plans – Jim Brinkley, Alan Ruttenberg, Olivier Bodenreider  
 
: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
 
:5:00    Closing remarks Cornelius Rosse, Mark Musen, Barry Smith

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
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