[BiO BB] CALL FOR PARTICIPATION: CHEMDNER task: Chemical compound and drug name recognition task

[Martin Krallinger]

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



(1) TASK GOAL AND MOTIVATION

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. The
recognition of chemical entities is also crucial for other subsequent text
processing strategies, such as detection of drug-protein interactions,
adverse effects of chemical compounds or the extraction of pathway and
metabolic reaction relations. A range of methods have been explored to the
recognition of chemical compound mentions, including machine learning
techniques, rule-bases approaches and different dictionary-lookup
strategies.



We foresee a considerable interest in the result of this task by the
NLP/text mining community on one side, as well as by the bioinformatics,
drug discovery/biomedicine and chemoinformatics communities on the other
side. As has been the case in previous BioCreative efforts (resulting in
high impact papers in the field), we expect that successful participants
will have the opportunity to publish their system descriptions in a journal
article.



(2) CHEMDNER TRACK DESCRIPTION

The CHEMDNER is one of the tracks posed at the BioCreative IV community
challenge (http://www.biocreative.org).



We invite participants to submit results for the CHEMDNER task providing
predictions for one or both of the following subtasks:



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 sub-task]



b) Provide for a given document the start and end indices corresponding to
all the chemical entities mentioned in this document [Chemical entity
mention recognition sub-task].



For these two tasks the organizers will release training and test data
collections. The task organizers will provide details on the used
annotation guidelines; define a list of criteria for relevant chemical
compound entity types as well as selection of documents for annotation.



(3) REGISTRATION

Teams can participate in the CHEMDNER task by registering for track 2 of
BioCreative IV. You can register additionally for other tracks too. To
register your team, go to the following page that provides more detailed
instructions: http://www.biocreative.org/news/biocreative-iv/team/



Mailing list and contact information:

You can post questions related to the CHEMDNER task to the BioCreative
mailing list. To register for the BioCreative mailing list, please visit
the following page: http://biocreative.sourceforge.net/mailing.html



(4) WORKSHOP

CHEMDNER is part of the BioCreative evaluation effort. The BioCreative
Organizing Committee will host the BioCreative IV Challenge evaluation
workshop (http://www.biocreative.org/events/biocreative-iv/CFP/) at NCBI,
National Institutes of

Health, Bethesda, Maryland, on October 7-9, 2013



(5) CHEMDNER TASK ORGANIZERS

Martin Krallinger, Spanish National Cancer Research Center (CNIO)

Obdulia Rabal, University of Navarra, Spain

Julen Oyarzabal, University of Navarra, Spain

Alfonso Valencia, Spanish National Cancer Research Center (CNIO)



(6) REFERENCES

- Vazquez, M., Krallinger, M., Leitner, F., & Valencia, A. (2011). Text
Mining for Drugs and Chemical Compounds: Methods, Tools and Applications.
Molecular Informatics, 30(6‐7), 506-519.

- Krallinger M, et al. The Protein-Protein Interaction tasks of BioCreative
III: classification/ranking of articles and linking bio-ontology concepts
to full text. BMC Bioinformatics. 2011;12 Suppl 8:S3

- Corbett, P., Batchelor, C., & Teufel, S. (2007). Annotation of chemical
named entities. BioNLP 2007: Biological, translational, and clinical
language processing, 57-64.

- Klinger, R., Kolářik, C., Fluck, J., Hofmann-Apitius, M., & Friedrich, C.
M. (2008). Detection of IUPAC and IUPAC-like chemical names.
Bioinformatics, 24(13), i268-i276.

- Hettne, K. M., Stierum, R. H., Schuemie, M. J., Hendriksen, P. J.,
Schijvenaars, B. J., Mulligen, E. M. V., ... & Kors, J. A. (2009). A
dictionary to identify small molecules and drugs in free text.
Bioinformatics, 25(22), 2983-2991.

- Yeh, A., Morgan, A., Colosimo, M., & Hirschman, L. (2005). BioCreAtIvE
task 1A: gene mention finding evaluation. BMC bioinformatics, 6(Suppl 1),
S2.

- Smith, L., Tanabe, L. K., Ando, R. J., Kuo, C. J., Chung, I. F., Hsu, C.
N., ... & Wilbur, W. J. (2008). Overview of BioCreative II gene mention
recognition. Genome Biology, 9(Suppl 2), S2.