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[Gofriends] Bio-Ontologies SIG at ISMB 2010 - CFP (deadline at end of the week)

Nigam Shah nigam at
Tue Apr 13 21:22:29 PDT 2010

Apologies for cross-posting .. deadline at end of the week

*** NEW and Noteworthy

Recognizing the increasing synergy in medical and biological ontology
research and development, biomedical Knowledge Representation Working Group
(KR-WG) of the American Medical Informatics Association (AMIA) has chosen
the Bio-Ontologies SIG as the venue of the KR-WG's biannual knowledge
representation in medicine meetings (KR-MED, Bio-Ontologies
2010 will serve as host to KR-MED 2010 in the biannual meeting series. In
order to attend the biannual KR-MED meeting, please register for the
Bio-Ontology SIG.

*** Call for paper and posters

We invite submissions for Bio-Ontologies 2010: Semantic Applications in Life
Sciences at the 18th annual conference on Intelligent Systems for Molecular
Biology (ISMB) 2010, July 9-13, Boston, MA (

*** Key Dates

 - Submissions Due: April 16th (Friday)
 - Notifications: May 7th (Friday)
 - Final Version Due: May 14th (Friday)
 - Workshop: July 9th-10th (Friday and Saturday)

*** Selected papers from Bio-Ontologies 2009 will be out soon in Journal of
Biomedical Semantics. See table of contents below:

   1. Phillip Lord: *An evolutionary approach to function.*
   2. Clement Jonquet, Mark A. Musen and Nigam H. Shah: *Building a
   Biomedical Ontology Recommender Web Service.*
   3. The OBI Consortium: *Modeling biomedical experimental processes with
   4. David Shotton: *CiTO, the Citation Typing Ontology, and its use for
   annotation of reference lists and visualization of citation networks.*
   5. Allyson Lister, Phillip Lord, Matthew Pocock and Anil Wipat: *Annotation
   of SBML Models Through Rule-Based Semantic Integration.*
   6. Jose Cruz-Toledo, Michel Dumontier, Marc Parisien and Francois Major:
   *RKB: A Semantic Web Knowledge Base for RNA.*
   7. Matthias Samwald and Holger Stenzhorn: *Simple, Ontology-Based
   Representation of Biomedical Statements through Fine-Granular Entity Tagging
   and New Web Standards.*

URL: coming soon ...

*** Introduction

Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the
latest and most cutting-edge research in ontologies and more generally the
organisation, presentation and dissemination of knowledge in biology and
life sciences. It has existed as a SIG at ISMB (
for 12 years.

We are interested in approachs to organising, presenting and disseminating
knowledge in life sciences.

We invite papers and poster submissions in traditional areas, such as the
biological and medical applications of ontologies, newly developed
biomedical ontologies, and the use of ontologies in data sharing standards.
In addition, We invite submissions on a wide range of topics including, but
not limited to:

 - Semantic and/or Scientific Wikis.
 - Collaborative curation platforms
 - Collaborative ontology authoring and peer-review mechanisms
 - Automated ontology learning
 - Ontology design patterns and guidelines
 - Ontology evaluation
 - Mapping between ontologies
 - Biological and medical applications of ontologies
 - "Flash updates" on newly developed or existing ontologies
 - Use of ontologies in data standards
 - Semantic Web enabled applications (such as for enhanced publishing and
for capturing scientific discourse)
 - Research in ontology languages and its effect on biomedical ontologies

*** Instructions to Authors

We are inviting three types of submissions.

 - Short papers, up to 4 pages.
 - Poster abstracts, up to 1 page.
 - Flash updates, up to 1 page

Following review, successful papers will be presented at the meeting.
Posters will be exhibited
during the 2 days for at least one poster session. Flash updates are for
short talks (5 min)
giving the salient new developments on existing public ontologies (e.g. the
Foundational Model of Anatomy).
Posters authors can also indicate a desire to provide a flash update.

Unsuccessful papers will automatically be considered for poster
there is no need to submit both on the same topic.

*** Submissions

Submissions are now open and can be submitted through easychair

** Programme

The SIG will run for two days this year. On each day, the morning session
will have an invited keynote and selected papers; while the afternoon
session will have a panel session and selected talks. One of the talks
session will have "flash updates" from groups developing bio-ontologies as
part of large international, collaborative consortia and from selected
poster presenters.

09:00-10:00 Keynote

10:00-12:00 Research Talks (with coffee break)

12:00-13:30 Lunch and Poster Session

13:30-16:00 Research Talks (with coffee break)

16:00-17:30 Panel Session
17:30-close and Poster Session

This year's keynote speakers will by Andrew Rzhetsky (July 10th) and Tim
Clark (July 9th)

*** Organisers

Nigam Shah, Stanford University
Larisa Soldatova, University of Wales, Aberystwyth
Susanna-Assunta Sansone, EBI
Susie Stephens, Johnson & Johnson

*** Templates

Submission templates are available from the website

*** Programme Committee

The programme committee is confirmed. See:
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