CALL FOR PAPERS

Journal of Biomedical Informatics (Elsevier) - http://www.elsevier.com/locate/yjbin
Special Issue on Community-Driven Curation of Ontologies and Knowledge Bases in HealthCare and Life Sciences

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Important Dates
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* Submission deadline: October 1st, 2011
* Notification: December 2011
* Final Version due: January 2011
* Publication: Early 2012

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Submission Guidelines
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* Manuscript preparation - Instructions for Authors: http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/authorinstructions
* Manuscript submission: http://ees.elsevier.com/jbi/

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Aims and objectives
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We are inviting submissions for a special issue of the Journal of Biomedical Informatics devoted to the topic of community-driven curation of ontologies and knowledge bases in Health Care and Life Sciences. The use of formal systems to define biomedical concepts and to represent and store biomedical knowledge has never been more important. In the past decade, ontologies have become central to the construction of intelligent decision-support systems, simulation systems, information-retrieval systems, and natural language systems. With the adoption of ontologies, especially by the broad biomedical community, the further development of ontologies and knowledge bases evolved into a community-driven process. This resulted in an increased number of knowledge bases published openly on the Web. Ontologies and knowledge bases are now authored/curated by more domain and knowledge experts than ever before. To ensure a high quality of the community-generated content, a well-defined cura!
tion process has to become a prominent and integral part of the life cycle of biomedical knowledge artifacts.

Several large biomedical projects are trying to apply the "wisdom of the crowds" model for building and curating their knowledge content. This model is already familiar to most experts (c.f. Web 2.0) and has already been proven successful in large community projects in other domains. The emergence of different types of collaborative environments, such as, Wikis, content management systems, and collaborative ontology editors, enables novel ways of curating knowledge, hence transforming the workflow from being curator-centered to being community-driven. Such systems provide the means for communities of experts in different fields to collaboratively create, share and re-use knowledge. Their goal is to foster long term expansion and maximization of knowledge curation, extraction and reasoning, by creating live knowledge bases within their specific domains.

The collaborative aspect of curation raises a series of challenges ranging from specific initial design decisions to capturing and maintaining temporal and change elements of the knowledge content. The aim of this issue is to build upon and complement the research detailed in the Special Issue on Ontologies for Clinical and Translational Research (Vol. 44, Issue 1, 2011) by focusing on collaboration, its associated challenges and emerging methods for knowledge and ontology curation. The use of ontologies, as shared conceptualizations of a domain, has proved to provide support in diverse areas of biomedical informatics, such as the development of databases or biosample repositories. This issue intends to take a step back and analyze the foundational aspect of achieving and maintaining the shared (community-driven) agreement of the conceptualization (and of the resulting knowledge bases) by scrutinizing a series of intrinsic issues like design patterns, consistency or emerging!
knowledge discovery.

The issue is seeking, in particular, original methodological research papers, but will also consider survey papers, meant to provide a clear overview of the current state of the art in its specific themes of interest. Applications or system descriptions will be considered only as providing a context or use case for a detailed methodology, and not as individual (stand-alone) submissions. The topics of interest for the issue can be grouped into three main categories:

1. Challenges and experiences emerging from the collaborative aspects of knowledge capture in HealthCare and Life Sciences, including:
* design patterns
* workflows for knowledge capture or refinement
* managing change or revision of knowledge
* managing inconsistent knowledge
* hypotheses Ð representation, evaluation and validation
* using linked data to support knowledge capture
* user experience

2. Innovative methods for collaborative knowledge management, including:
* knowledge representation and reasoning
* knowledge discovery
* knowledge revision
* hypotheses management
* use of statistics in decision support systems
* intelligent knowledge-based retrieval
* knowledge integration from external sources

3. Evaluation methods and metrics for:
* the quality of the resulting curated knowledge
* collaborative knowledge acquisition
* collaborative knowledge discovery
* intelligent knowledge-based retrieval

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Guest Editors
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* Tudor Groza
School of ITEE, The University of Queensland, Australia

* Tania Tudorache
Stanford Center for Biomedical Informatics Research, Stanford University, USA

* Michel Dumontier
Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, Canada
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