Appel: Second International Workshop on Definitions in Ontologies (DO 2014)

Thierry Hamon hamon at LIMSI.FR
Wed May 21 07:56:38 UTC 2014

Date: Sun, 18 May 2014 23:17:00 +0200
From: Nathalie Aussenac <nathalie.aussenac-gilles at>
Message-ID: <5379234C.1090405 at>

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Second International Workshop on Definitions in Ontologies (DO 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, excluding references,
formatted using the JBS templates at­-
main-manuscript, and submitted via EasyChair


Workshop paper submission: July 15, 2014

Notification of paper acceptance: August 15, 2014

Camera-ready copies for the proceedings: September 15, 2014

Workshops: October 6-­-7, 2014


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


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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