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<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">=============================</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">FINAL CALL
FOR PARTICIPATION </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">BioCreative
IV CHEMDNER Task: Chemical compound and drug name recognition task</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">Task webpage:
<a href="http://www.biocreative.org/tasks/biocreative-iv/chemdner/">http://www.biocreative.org/tasks/biocreative-iv/chemdner/</a></span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">=============================</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">We are pleased
to announce that the CHEMDNER task development data set has been released.</span></p>
<p class="" style="text-autospace:none"><font class="Apple-style-span" color="#1a1a1a" face="Arial"><span class="Apple-style-span" style="font-size:17px"><br></span></font></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">CHEMDNER
OVERVIEW</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">There is an
increasing interest to facilitate more efficient access to information on
chemical compounds and drugs (chemical entities) described in repositories
of scientific articles and abstracts.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">The goal of
this task is to promote the implementation of systems that are able to detect
mentions of chemical compounds and drugs, in particular those chemical entity
mentions that can be subsequently linked to a chemical structure, rather
than other macromolecules like genes and proteins that had been already
addressed in previous BioCreative efforts.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">We invite
participants to submit results for the CHEMDNER task providing predictions for:</span><span class="Apple-style-span" style="color:rgb(26,26,26);font-family:Arial;font-size:17px"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">a) Given a
set of documents, return for each of them a ranked list of chemical entities
described within each of these documents [Chemical document indexing (CDI)
sub-task]</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">b) Provide
for a given document the start and end indices corresponding to all the
chemical entities mentioned in this document [Chemical entity mention (CEM)
recognition sub-task].</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">For these two
tasks the organizers released both a training and a development data set, each consisting
in 3500 PubMed abstracts exhaustively annotated manually by chemical domain
experts following carefully developed annotation guidelines.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">CHEMDNER TASK
RESOURCES</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Training
set: 3500 manually annotated PubMed abstracts for chemical
entity mentions.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Development
set: 3500 manually annotated PubMed abstracts for chemical entity mentions.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Test set:
will consist in 3000 manually
annotated PubMed abstracts for chemical entity mentions.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Evaluation
scripts: scripts that can be used to evaluate performance of automated systems.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Annotation
guidelines: detailed document describing the used manual annotation criteria.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Frequently
asked question (FAQ): list of questions posed by registered teams.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*Useful
resource collection: compendium of useful software and lexical resources/data
for the task.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">Based on the
participating systems performance a selected number of teams will be invited to
submit</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">a manuscript
for a special journal issue on the CHEMDNER task.</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">IMPORTANT
DATES</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*25th June:
sample data collection, detailed task
description, annotation and evaluation script </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*31st July:
training data collection, annotations
and updated guidelines </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*16th August
: development data annotations</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*3rd
September: test set release </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*12th
September: test set prediction due </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*17th September:
invite teams for workshop presentation talks </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*19th
September: CHEMDNER workshop proceedings paper due (2-4 pages) </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">*7th-9th
October: BioCreative IV workshop: National Institutes of Health (NIH), in
Washington DC </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> <span style> </span><span style> </span><span style> </span><span style> </span> (see
<a href="http://www.biocreative.org/events/biocreative-iv/workshop/">http://www.biocreative.org/events/biocreative-iv/workshop/</a>)</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">TASK
ORGANIZERS</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">* Martin
Krallinger, Spanish National Cancer Research Center (CNIO)</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">* Obdulia
Rabal, University of Navarra, Spain</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">* Julen
Oyarzabal, University of Navarra, Spain</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">* Alfonso Valencia,
Spanish National Cancer Research Center (CNIO)</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"> </span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">INQUERIES</span></p>
<p class="" style="text-autospace:none"><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)">For further
information, please contact the task organizer at</span></p>
<p class=""><span style="font-size:13pt;font-family:Arial;color:rgb(26,26,26)"><a href="mailto:mkrallinger@cnio.es">mkrallinger@cnio.es</a></span><span style></span></p>
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