[Elsnet-list] CHEMDNER CFP and training data release

Martin Krallinger krallinger.martin at gmail.com
Thu Aug 1 16:54:20 CEST 2013


CALL FOR PARTICIPATION: CHEMDNER task: Chemical compound and drug name
recognition task (see
http://www.biocreative.org/tasks/biocreative-iv/chemdner)

(1) The CHEMDNER task (part of The BioCreative IV competition) is a
community challenge on named entity recognition of chemical compounds. The
goal of this task is to promote the implementation of systems that are able
to detect mentions in text of chemical compounds and drugs.

(2) The datasets relevant to the CHEMDNER tasks will all be listed under
the following link:

http://www.biocreative.org/resources/corpora/bc-iv-chemdner-corpus

The CHEMDER training set is now online, together with an updated version of
the annotation guidelines. They are available at:

http://www.biocreative.org/media/store/files/2013/CHEMDNER_TRAIN_V01.zip

 (3) Dates: Please notice the following CHEMDNER schedule, in particular
the test set prediction due.

*25th June: sample data collection, detailed task description, annotation
and evaluation script
31st July: training data collection, annotations and updated guidelines
16th August : development data annotations
3nd September: test set release
12th September: test set prediction due
17th September: invite teams for workshop presentation talks
19th September: CHEMDNER workshop proceedings paper due (2-4 pages)
7th-9th October: BioCreative IV workshop
<http://www.biocreative.org/events/biocreative-iv/workshop/>
*

(4) Frequently asked questions (FAQ). Considering the numerous questions we
have got from various teams (many of them related to the CDI subtask
ranking). We have placed online a FAQ document at:

http://www.biocreative.org/media/store/files/2013/chemdner_faq.pdf

(5) Evaluation workshop. The evaluation results will be presented at this
workshop and in the corresponding workshop proceedings evaluation paper.
This is in line with other community challenges such as Critical Assessment
of protein Structure Prediction (CASP) experiments. There will be a session
devoted to the CHEMDNER task during the workshop as well as a poster
session and selected talks from participating teams. The link of the
workshop as well as additional details and registration is online at:

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

(6) Workshop proceedings. The second volume of the BioCreative workshop
proceedings will be devoted entirely to the CHEMDER task. The proceedings
papers for the CHEMDER task should be 2-4 pages long, describing your
system and results obtained for the training or development set (or both).
Please refer to the following URL for more information. For more details
refer to:

http://www.biocreative.org/events/biocreative-iv/workshop/#proceedings

(7) CHEMDER special issue publications

There will be a journal issue devoted to BioCreative IV and also one for
the CHEMDER task. This is in line with previous BioCreative challenges were
special issues were published in BMC Bioinformatics, Genome Biology and the
journal Database. We will announce more details on the selection process
and the target journal after the workshop.




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Martin Krallinger

Structural Computational Biology Group

Structural Biology and BioComputing Programme

Spanish National Cancer Research Centre (CNIO)

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