[BioNLP] BioNLP Shared Task 2013 - Open Call for Supporting Analyses

Pontus Stenetorp pontus at stenetorp.se
Fri Dec 7 03:15:05 EST 2012


Summary: For the BioNLP 2013 Shared Task we are issuing an open call for
automated analyses from existing Natural Language Processing systems to ease
the burden on shared task participants and increase visibility of research
efforts that could benefit state-of-the-art Information Extraction systems.

We are issuing an open call to the Natural Language Processing to
provide supporting analyses of the texts that have been manually
annotated for the BioNLP 2013 Shared Task (http://2013.bionlp-st.org/)
on information extraction. As for the previous tasks in 2009 and 2011,
we aim to provide supporting analyses to the participants in order to
ease the workload required to participate in the shared task.
Syntactic analyses have been and continue to be a key component of the
state-of-the-art methods for the shared task [1,2] and semantic
analyses have been used to improve upon the performance existing
methods [3]. If you and/or your group has designed an NLP system which
you think could assist the extraction targets for the 2013 task, we ask you
to consider providing these supporting analyses for the benefit of the
shared task participants and the community at large and increase the
visibility of your tool among your fellow researchers. Researchers who
provide supporting analyses will be acknowledged with mention and
references on the shared task homepage and in related shared task
publications.

The procedure to participate is as follows:

1.) Send a statement of interest to the shared task organisers. We ask
those interested to notify us by December 19th 2012 (Wednesday).
Please send your messages to <bionlp-st-adm at googlegroups.com>.

2.) The raw text for the respective tasks will be made publicly available one
week prior to the release of the training and development sets in early
January 2013. Those that want to submit supporting analyses are expected to
run their tools within this week and send the resulting analyses to the shared
task organisers for inclusion in the public release of the annotations.
Sample data for all the tasks is already available from the shared task
homepage (http://2013.bionlp-st.org/tasks).

3.) The same proceduce take place for the test set releases, each supporting
analyses provider will once again have a full week to run their tools and
submit their analyses prior to the test set releases.

Tentative schedule:

* 8th of January 2013: Release of the training/development set texts
* 15th of January 2013: Public release of the training/development data sets
* 22nd of February 2013: Release of the test set texts (Tentative)
* 1st of March 2013: Public Release of the test data sets (Tentative)

In order to allow for the shared task participants to replicate and
apply the tools used to produced the automated analyses for purposes
other than the shared task, the following are emphasised (but not
strictly required) for reproducibility purposes:

* Availability of the tool and tool source-code for research purposes

* Support for well-established formats (if the tool uses its own
format, conversions to for example PTB for constituency output is
encouraged to be included along with the native format)

* Availability of scientific and technical documentation

When sending your statement of interest to the organisers, please
include the following information:

1.) Contact details for the members of your group that seek to participate
2.) Describe, briefly, how you think the tool could be used by the
shared task participants and ease their workload
3.) Homepage of the tool (if any)
4.) Relevant publications for the tool (if any) to be referenced in
the shared task publications and homepage
5.) Status of availability (source code, web service, binary,
non-public and so forth)

We warmly welcome your contributions towards advancing the
state-of-the-art in information extraction and we look forward to your
automated analyses.

On behalf of the BioNLP 2013 Shared Task organisers,
    Pontus Stenetorp

[1]: "Fast and Robust Joint Models for Biomedical Event Extraction", Riedel
and McCallum (2011)
[2]: "Generalizing Biomedical Event Extraction", Björne and Salakoski (2011)
[3]: "Bridging the Gap Between Scope-based and Event-based
Negation/Speculation Annotations: A Bridge Not Too Far", Stenetorp et
al. (2012)




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