CALL FOR PARTICIPATION: Fifth BioCreative Challenge workshop

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 ****************************************************************
**************************************************************** Fifth
BioCreative Challenge workshop, Seville, Spain



Home page: http://www.biocreative2015.org

Challenge tasks: http://www.biocreative.org/events/biocreative-v/CFP

Workshop date: 9-11th Sept 2015



Workshop format: Keynote speech, paper presentations, poster and group
discussions.


****************************************************************
****************************************************************



[Apologies for multiple postings]


***********

*1. **SCOPE*
***********

BioCreative: Critical Assessment of Information Extraction in Biology is a
community-wide effort for evaluating text mining and information extraction
systems applied to the biological domain.



Built on the success of the previous BioCreative Challenge Evaluations and
Workshops (BioCreative I, II, II.5, III, 2012 workshop, and IV), the
BioCreative Organizing Committee will host the BioCreative V Challenge in
Sevilla, Spain on September 9-11, 2015.




***********

*2. TOPICS*
***********

This workshop invites proceedings papers and posters of teams participating
in the BioCreative V tracks. Additionally we invite also posters on other
topics related to biomedical text mining, information retrieval and natural
language processing. Topics of interest include:



*  Development and integration of BioC compatible modules that assist
interaction database curation

 * Named entity recognition of chemical compounds and gene/protein mentions
in patents

*** Automatic detection of chemical/drugs and diseases, and their relations
in PubMed abstracts

 *  Text mining solutions to develop and test novel approaches for relation
extraction in the context of pathway networks

 * Demonstration and evaluation of web-based systems addressing
user-defined tasks, evaluated by curators on performance and usability

 * Demonstration of tools to extract metagenomics metadata, including
environment and habitat metadata

 * The importance and practical use of text mining and information
extraction systems for the extraction of biological and biomedical
annotations and integration to existing life sciences knowledgebases

* Demonstration of real world cases of crowdsourcing and community
annotations for generating Gold Standard annotations for text mining and
database annotations

* Use of text mining strategies to extract clinically relevant information
from public data and clinical records, with a special focus on disease and
symptom related concepts.



Authors can submit short proceedings papers and posters describing systems
participating in BioCreative V tracks. Additionally we invite also posters
on other topics related to biomedical text mining, information retrieval
and natural language processing.  Proceedings authors will be invited to
submit full papers for a special journal issue. Previous special issues:

http://www.biocreative.org/resources/publications


***********

*3. DATES *
***********
Submission deadline: August 15th 2015 (check task timelines:
http://www.biocreative.org/events/biocreative-v/CFP)
Workshop date: 9-11th September 2015




***********

*4. **BIOCREATIVE ORGANIZING COMMITTEE*
***********

Cecilia Arighi, University of Delaware, USA

Kevin Cohen, University of Colorado, USA

Donald Comeau, National Center for Biotechnology Information (NCBI), NIH,
USA

Juliane Fluck, Fraunhofer Institute for Algorithms and Scientific Computing
SCAI, Germany

Rezarta Islamaj Dogan, National Center for Biotechnology Information
(NCBI), NIH, USA

Lynette Hirschman, MITRE Corporation, USA

Sun Kim, National Center for Biotechnology Information (NCBI), NIH, USA

Martin Krallinger, Spanish National Cancer Centre, CNIO, Spain

Zhiyong Lu, National Center for Biotechnology Information (NCBI), NIH, USA

Fabio Rinaldi, Institute of Computational Linguistics, University of
Zurich, Switzerland

Alfonso Valencia, Spanish National Cancer Centre, CNIO, Spain

Thomas Wiegers, North Carolina State University, USA

John Wilbur, National Center for Biotechnology Information (NCBI), NIH, USA

Cathy Wu, University of Delaware and Georgetown University, USA





Martin Krallinger,

On behalf of the BioCreative organizing committee

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<h2 style=3D"margin:0.1pt 0cm"><span style=3D"font-size:11pt;color:windowte=
xt;font-weight:normal">Fifth
BioCreative Challenge workshop, Seville, Spain</span></h2>

<pre style=3D"margin:0.1pt 0cm"><span style=3D"font-size:11pt;font-family:C=
alibri">=C2=A0</span></pre><pre style=3D"margin:0.1pt 0cm"><span style=3D"f=
ont-size:11pt;font-family:Calibri">Home page: <a href=3D"http://www.biocrea=
tive2015.org">http://www.biocreative2015.org</a><br>
Challenge tasks: <a href=3D"http://www.biocreative.org/events/biocreative-v=
/CFP">http://www.biocreative.org/events/biocreative-v/CFP</a><br>
Workshop date: 9-11th Sept 2015</span></pre>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">W=
orkshop format: Keynote speech, paper presentations,
poster and group discussions.</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">**************************************************=
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ight:normal"></span></h2>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style>[<span class=3D"">Apologies</span>
for multiple postings]</span><span style=3D"font-size:11pt;font-family:Cali=
bri"></span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><b style><span style=3D"font-size:11pt;font-family:C=
alibri">1. </span></b><b style><span style=3D"font-size:11pt;font-family:Ca=
libri" lang=3D"ES-TRAD">SCOPE</span></b><b style><span style=3D"font-size:1=
1pt;font-family:Calibri"></span></b></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">B=
ioCreative: Critical Assessment of Information
Extraction in Biology is a community-wide effort for evaluating text mining=
 and
information extraction systems applied to the biological domain. </span></p=
>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">B=
uilt on the success of the previous BioCreative
Challenge Evaluations and Workshops (BioCreative I, II, II.5, III, 2012
workshop, and IV), the BioCreative Organizing Committee will host the
BioCreative V Challenge in Sevilla, Spain on September 9-11, 2015. </span><=
/p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><b style><span style=3D"font-size:11pt;font-family:C=
alibri">2. TOPICS</span></b></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">T=
his workshop invites proceedings papers and posters
of teams participating in the BioCreative V tracks. Additionally we invite =
also
posters on other topics related to biomedical text mining, information
retrieval and natural language processing. Topics of interest include:</spa=
n></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">*=
 <span style>=C2=A0</span></span><span style=3D"font-size:11pt;font-family:=
Calibri">Development and integration of BioC compatible modules
that assist interaction database curation</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0<span style>*</span>
Named entity recognition of chemical compounds and gene/protein mentions in
patents</span></p>

<p class=3D"MsoNormal"><i><span style=3D"font-size:11pt;font-family:Calibri=
">*</span></i><span style=3D"font-size:11pt;font-family:Calibri"> Automatic=
 detection of chemical/drugs and
diseases, and their relations in PubMed abstracts</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0*<span style>=C2=A0
</span>Text mining solutions to develop and test novel approaches for relat=
ion
extraction in the context of pathway networks</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0* Demonstration and evaluation of web-based
systems addressing user-defined tasks,<span class=3D""><ins cite=3D"mailto:=
mkrallinger" datetime=3D"2015-06-24T14:19"> </ins></span>evaluated
by curators on performance and usability<span class=3D""><ins cite=3D"mailt=
o:Hirschman,%20Lynette" datetime=3D"2015-06-23T14:57"></ins></span></span><=
/p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0* Demonstration of tools to extract metagenomics
metadata, including environment and habitat metadata</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0* The importance and practical use of text
mining and information extraction systems for the extraction of biological =
and
biomedical annotations and integration to existing life sciences knowledgeb=
ases</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">*=
 Demonstration of real world cases of crowdsourcing
and community annotations for generating Gold Standard annotations for text
mining and database annotations</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">*=
=C2=A0Use of text mining strategies to extract
clinically relevant information from public data and clinical records, with=
 a
special focus on disease and symptom related concepts.</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri" l=
ang=3D"ES-TRAD">Authors can submit short proceedings papers and posters des=
cribing
systems participating in BioCreative V tracks. </span><span style=3D"font-s=
ize:11pt;font-family:Calibri">Additionally we
invite also posters on other topics related to biomedical text mining,
information retrieval and natural language processing.<span style>=C2=A0 </=
span>Proceedings authors will be invited to
submit full papers for a special journal issue. Previous special issues:</s=
pan><a name=3D"_GoBack"></a><span style=3D"font-size:11pt;font-family:Calib=
ri" lang=3D"ES-TRAD"></span></p>

<p class=3D"MsoNormal"><span lang=3D"ES-TRAD"><a href=3D"http://www.biocrea=
tive.org/resources/publications"><span style=3D"font-size:11pt;font-family:=
Calibri" lang=3D"EN-US">http://www.biocreative.org/resources/publications</=
span></a></span><span style=3D"font-size:11pt;font-family:Calibri" lang=3D"=
ES-TRAD"> </span><span style=3D"font-size:11pt;font-family:Calibri"></span>=
</p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><b style><span style=3D"font-size:11pt;font-family:C=
alibri" lang=3D"ES-TRAD">3. DATES </span></b></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span><span style=3D"font-size:11pt;co=
lor:windowtext;font-weight:normal" lang=3D"ES-TRAD"><br>
Submission deadline: August 15th 2015 (check task timelines: <a href=3D"htt=
p://www.biocreative.org/events/biocreative-v/CFP">http://www.biocreative.or=
g/events/biocreative-v/CFP</a>)<br>
Workshop date: 9-11th September 2015</span><span style=3D"color:windowtext;=
font-weight:normal" lang=3D"ES-TRAD"></span></h2>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

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normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><b style><span style=3D"font-size:11pt;font-family:C=
alibri" lang=3D"ES-TRAD">4. </span></b><b style><span style=3D"font-size:11=
pt;font-family:Calibri">BIOCREATIVE ORGANIZING COMMITTEE</span></b></p>

<h2 style=3D"margin:0.1pt 0cm"><span style=3D"color:windowtext;font-weight:=
normal" lang=3D"ES-TRAD">***********</span></h2>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">C=
ecilia Arighi, University of Delaware, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">K=
evin Cohen, University of Colorado, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">D=
onald Comeau, National Center for Biotechnology
Information (NCBI), NIH, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">J=
uliane Fluck, Fraunhofer Institute for Algorithms and
Scientific Computing SCAI, Germany</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">R=
ezarta Islamaj Dogan, National Center for
Biotechnology Information (NCBI), NIH, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">L=
ynette Hirschman, MITRE Corporation, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">S=
un Kim, National Center for Biotechnology Information
(NCBI), NIH, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">M=
artin Krallinger, Spanish National Cancer Centre,
CNIO, Spain</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">Z=
hiyong Lu, National Center for Biotechnology
Information (NCBI), NIH, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">F=
abio Rinaldi, Institute of Computational Linguistics,
University of Zurich, Switzerland</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">A=
lfonso Valencia, Spanish National Cancer Centre,
CNIO, Spain</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">T=
homas Wiegers, North Carolina State University, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">J=
ohn Wilbur, National Center for Biotechnology
Information (NCBI), NIH, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">C=
athy Wu, University of Delaware and Georgetown
University, USA</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">M=
artin Krallinger,</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">O=
n behalf of the BioCreative organizing committee</span></p>

<p class=3D"MsoNormal"><span style=3D"font-size:11pt;font-family:Calibri">=
=C2=A0</span></p>





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