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CFP: Journal of Biomedical Informatics - Special Issue on Community-Driven Curation of Ontologies and Knowledge Bases in HealthCare and Life Sciences

From: Tudor Groza <tudor.groza@gmail.com>
Date: Thu, 7 Jul 2011 20:01:27 +1000
Message-ID: <CACqucCyEOiJtk_vgVgBEnguihrMd_THPPOniu+hWDaHAJNw33w@mail.gmail.com>
To: public-semweb-lifesci <public-semweb-lifesci@w3.org>
[Apologies for cross-posting]
===================================================

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
===================================================

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

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Submission Guidelines
===================================================

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

===================================================
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 curation 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 – 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
Received on Friday, 8 July 2011 13:40:29 GMT

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