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[bioontology-support] [bioportal-announce] DO 2014 - EXTENDED DEADLINE: July 25, 2014
selja.seppala.unige at gmail.com
Mon Jul 14 12:33:04 PDT 2014
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EXTENDED DEADLINE: July 25, 2014
Second International Workshop on Definitions in Ontologies (DO 2014) at the International Conference on Biomedical Ontologies (ICBO 2014)
October 6-7, 2014
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 appropriate.
-experiences in formulating definitions
-tools that assist in definition editing, including collaborative systems
-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
FORMAT AND OUTCOMES
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 (https://sites.google.com/site/definitionsinontologies/). We expect accepted papers to be published in the Journal of Biomedical Semantics (JBS).
-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 SNOMED
-computer scientists addressing these issues in languages like OWL
-NLP researchers working on definition extraction, generation, or checking
-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 http://www.jbiomedsem.com/authors/instructions/research#preparing-main-manuscript, and submitted via EasyChair (https://www.easychair.org/conferences/?conf=do2014).
Workshop paper submission EXTENDED DEADLINE: July 25, 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)
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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