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[bioontology-support] [bioportal-announce] 2nd International Workshop on Definitions in Ontologies (IWOOD 2014, ex-DO 2014) - EXTENDED DEADLINE: August 15, 2014

seljamar seljamar at
Tue Jul 29 12:05:46 PDT 2014

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Second International Workshop on Definitions in Ontologies (IWOOD 2014) 
at the International Conference on Biomedical Ontologies (ICBO 2014)

October 6-7, 2014
Houston, USA


This workshop is a follow-up to the workshop on Definitions in 
Ontologies (DO 2013) held last year in Montreal in conjunction with ICBO 
2013. The focus of this second workshop is on definition practices in 
either human or machine-assisted ontology development.

A current problem in ontology development is constructing the needed 
definitions of terms either logical or in natural language. For example, 
ontologies built using OBO Foundry principles are advised to include 
both logical and natural language definitions, but ontology developers 
too often focus on only one of these, or they pay insufficient attention 
to whether they are equivalent.

Explicit definitions of terms in ontologies serve a number of purposes. 
Logical definitions allow reasoners to create inferred hierarchies, 
lessening the burden of asserting and checking the validity of 
subsumptions. Natural language definitions help to ameliorate the 
pervasive problem of low inter-annotator agreement. In specialized 
domains, experts will know their own field well, but may only have 
limited knowledge of adjacent disciplines. Good definitions make it 
possible for non-experts to understand unfamiliar terms and thereby make 
it possible for more confident reuse of terms by external ontologies, 
which in turn facilitates data integration.

The goal of this workshop is to bring together interested researchers 
and developers to explore these issues by presenting case studies in a 
biomedical domain discussing the difficulties that arise when 
constructing definitions with a view to sharing strategies in the 
future. Even in the seemingly narrow domain of definition construction, 
cross-fertilization from related disciplines should yield benefits in 
quality and help to identify novel approaches.

Papers submitted should include one or more case studies and raise 
specific questions related to definitions with a link to a biomedical 
domain. Reports on successful or unsuccessful methods are both 

-experiences in formulating definitions
-tools that assist in definition editing, including collaborative 
-coordination of logical and textual definitions
-validation and quality control of definitions, e.g., checking that 
definitions comply with the all/some form
-methods for constructing definitions from multiple sources
-use of controlled languages such as Rabbit or ACE for more 
user-friendly logical definition creation
-use of templates to systematize definition creation

This will be a half-day workshop with a selected mix of presentations 
based on accepted papers. In order to promote discussion, each 
presentation will be followed by a short response by a participant of 
the workshop to be arranged in advance of the workshop.

This workshop will document findings on the workshop’s website 
( We expect 
accepted papers to be published in the Journal of Biomedical Semantics 

-ontologists, tool developers, and domain experts whose work encounters 
issues regarding definitions
-tool developers building definition- or ontology-authoring tools
-philosophers and logicians
-biomedical researchers working on definitions in nomenclatures such as 
-computer scientists addressing these issues in languages like OWL
-NLP researchers working on definition extraction, generation, or 
-NLP/IR researchers reusing definitions produced for ontologies

All papers should include one or more case studies and raise specific 
questions related to definitions with a link to a biomedical domain.
Papers should be between 5 and 10 pages long (rendered), excluding 
references, formatted using the JBS templates at, 
and submitted via EasyChair 

Workshop paper submission: August 15, 2014
Notification of paper acceptance: September 1, 2014
Camera-ready copies for the proceedings: September 15, 2014
Workshops: October 6-7, 2014

Selja Seppälä (University at Buffalo, USA)
Patrick Ray (University at Buffalo, USA)
Alan Ruttenberg (University at Buffalo, USA)

Nathalie Aussenac-Gilles (National Center for Scientific Research 
(CNRS), France)
Mélanie Courtot (MBB Department Simon Fraser University and BC Public 
Health Microbiology & Reference Laboratory, Canada)
Natalia Grabar (Université de Lille 3, France)
Janna Hastings (European Bioinformatics Institute, Cambridge, UK)
James Malone (European Bioinformatics Institute, Cambridge, UK)
Alexis Nasr (Aix Marseille Université, France)
Richard Power (The Open University, UK)
Allan Third (The Open University, UK)

The Swiss National Science Foundation (SNSF)
The State University of New York at Buffalo

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