[Corpora-List] BioCreative II.5 Workshop: Call for Participation

Tue Sep 8 09:28:42 UTC 2009

Call for Participation

BioCreative II.5 Workshop on Digital Annotations

October 7th-9th, 2009
Madrid, Spain

http://www.biocreative.org/events/biocreative-ii5/biocreative-ii5-workshop/

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Preliminary Program

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Wed, Oct 7th, 2009

09:00-09:30 Registration I

09:30-11:00 Special Session on Digital Annotations I

11:30-13:00 Special Session on Digital Annotations II

13:00-14:15 Registration II

14:15-14:30 Workshop Opening (Alfonso Valencia)
14:30-15:30 Keynote A (invited speaker)
15:30-16:00 BC II.5 Overview (Martin Krallinger)

16:30-17:00 The BioCreative Meta-Server (Florian Leitner)
17:00-17:30 Participant System 1
17:30-18:00 Participant System 2

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Thu, Oct 8th, 2009

08:30-9:00 Registration III

09:00-10:00 Keynote B (invited speaker)
10:00-10:30 Participant System 3

11:00-11:30 Inter-Annotator Agreement (Lynette Hirschman)
11:30-12:00 Participant System 4
12:00-12:30 Participant System 5

14:30-15:30 Keynote C (invited speaker)
15:30-16:00 Participant System 6

16:30-17:00 BC II.5 Results and Evaluation (Scott A. Mardis)
17:00-18:00 Discussion

Conference Dinner

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Fri, Oct 9th, 2009

09:00-10:00 Keynote D (invited speaker)
10:00-10:30 SDAs & the FEBS Experiment (Gianni Cesareni)

11:00-11:30 Participant System 7
11:30-12:00 BC III, Future & Closing (TBA)

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Confirmed Speakers for Special Session:
  • Udo Hahn (Uni Jena)
  • Ian Harrow (Pfizer UK)
  • Adriaan Klinkenberg (Elsevier)
  • database representative (pending)

Confirmed Speakers for Workshop:
  • Judith Blake (JAX)
  • Dietrich Rebholz-Schuhmann (EBI)
  • Larry Hunter (UCHSC)
  • Anna Taramontano (Uni Roma)

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Registration Information

Any workshop participant can submit poster abstracts via the
registration page.
Participant System talks will be chosen according to their performance
in the challenge.
ALL ABSTRACTS SUBMITTED VIA THE REGISTRATION PAGE ARE FOR POSTER
ABSTRACTS ONLY!

Registration fee: € 120,-
Registration page: https://www.cnio.es/eventos/index.asp?ev=3

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Workshop Description

The workshop on BioCreative II.5 will be held in Madrid at the CNIO
during October 7th and 9th, 2009. It will focus on the tasks created
for the challenge, specifically the extraction of protein-protein
interactions (PPIs), with the background of creating structured
annotations (SDAs, structured digital abstracts) for full-text papers.
These PPIs were generated by the paper authors themselves and MINT
database curators (a PPI DB). There will be four invited speakers
discussing various topics relevant to Information Extraction in Text
Mining and the topic of digital annotations and meta-services in
Bioinformatics.

The workshop will begin after a possible special session in the
morning and will cover presentations from seven to nine participant
systems from the challenge, the result evaluation, an inter-annotator-
and curator to author-agreement study, the SDAs and the FEBS Letters
Experiments, and a talk about the BioCreative Meta-Server, as well as
some plans on the future of BioCreative (BC III). This means we will
continue in the tradition of former BioCreative challenges and - much
like the CASP challenges in Structural Biology - present the final
results of the participants during the workshop.

Given the topic of the SDAs and online digital annotation, we are also
having a special session on this topic the morning before the actual
workshop. This "round table" should cover the topic of electronic/
structured annotations on publications from the viewpoints of the most
important stakeholders: the academic world, (pharma) industry, the
publishers, and the databases. We intend to have at least one
prominent speaker from each of these areas followed by a discourse
about how all stakeholders can cooperate to overcome issues and
achieve the necessary requirements for creating and maintaining an
infrastructure to promote digital annotations.

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Scientific Committee (preliminary)

  • Sophia Ananiadou
  • Mons Barend
  • Christian Blaschke
  • Nigel Collier
  • Henning Hermjakob
  • Eivind Hovig
  • Lars Juhl Jensen
  • Jin-Dong Kim
  • Michael Krauthammer
  • Ryan McDonald
  • Claire Nédellec
  • Goran Nenadic
  • Jong C. Park
  • Sampo Pyysalo
  • Dietrich Rebholz-Schuhmannnever
  • Patrick Ruch
  • Andrey Rzhetsky
  • Vijay Shanker
  • Hagit Shatkay
  • Neil Smalheiser
  • Ashish Tendulkar
  • Junichi Tsujii
  • Karin Verspoor
  • W. John Wilbur

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Organizers

FEBS/MINT:
  • Gianni Cesareni

MITRE:
  • Scott A. Mardis
  • Lynette Hirschman

CNIO:
  • Belén Bañeres
  • Martin Krallinger
  • Florian Leitner
  • Alfonso Valencia

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Sponsors

ENFIN Network - http://www.enfin.org/
EMBRACE Grid Network - http://www.embracegrid.info/

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Contacts

Belén Bañeres <bbaneres at cnio.es>
Florian Leitner <fleitner at cnio.es>

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