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[ontolog-forum] CFP: JBI Special Issue on Community-Driven Curation of O

To: ontolog-forum@xxxxxxxxxxxxxxxx
From: Tania Tudorache <tudorache@xxxxxxxxxxxx>
Date: Wed, 06 Jul 2011 14:42:39 -0700
Message-id: <4E14D6CF.5000500@xxxxxxxxxxxx>
[Apologies for cross-posting]
===================================================    (01)


Journal of Biomedical Informatics (Elsevier) 
Special Issue on Community-Driven Curation of Ontologies and Knowledge Bases in 
HealthCare and Life Sciences    (03)

Important Dates
===================================================    (04)

* Submission deadline:    October 1st, 2011
* Notification:           December 2011
* Final Version due:      January 2011
* Publication:            Early 2012    (05)

Submission Guidelines
===================================================    (06)

* Manuscript preparation - Instructions for 
* Manuscript submission:http://ees.elsevier.com/jbi/    (07)

Aims and objectives
===================================================    (08)

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 curat
ion process has to become a prominent and integral part of the life cycle of 
biomedical knowledge artifacts.    (09)

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.    (010)

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.    (011)

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:    (012)

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    (013)

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    (014)

3. Evaluation methods and metrics for:
* the quality of the resulting curated knowledge
* collaborative knowledge acquisition
* collaborative knowledge discovery
* intelligent knowledge-based retrieval    (015)

Guest Editors
===================================================    (016)

* Tudor Groza
   School of ITEE, The University of Queensland, Australia    (017)

* Tania Tudorache
   Stanford Center for Biomedical Informatics Research, Stanford University, USA    (018)

* Michel Dumontier
   Department of Biology, Institute of Biochemistry and School of Computer 
Science, Carleton University, Canada    (019)

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