[Elsnet-list] BioCreative II.5 - Call for Participation

Krallinger.Martin mkrallinger at cnio.es
Thu Feb 5 13:18:03 CET 2009

BioCreative II.5 Challenge (2009)


Can Information Extraction contribute to the creation of Structured
Digital Abstracts (SDAs)?

*) BioCreative II.5 builds on the FEBS Letters experiment for the
creation of SDAs.
*) BC II.5 will systematically assess the potential use of automated IE
in the curation of full-text articles.

See previous controversial articles:
* Ceol et al., Linking entries in protein interaction database to
structured text: The FEBS Letters experiment., FEBS Letters (2008) vol.
582 (8) pp. 1171-7
* Gerstein et al., Structured digital abstract makes text mining easy.,
Nature (2007) May 10;447(7141):142
* Hahn et al., Text mining: powering the database revolution., Nature
(2007) May 10;447(7141):142
* Leitner et al., A text-mining perspective on the requirements for
electronically annotated abstracts., FEBS Letters (2008) vol. 582 (8)
pp. 1178-81



The BioCreative challenge evaluation consists of a community-wide effort
for promoting the development and evaluation of text mining and
information extraction systems applied to the biological domain.
Previous BioCreative challenges attracted considerable interest not only
in the bio-text mining community but also in the bioinformatics and
biological database domain, resulting in two special journal issues and
useful data resources for the development of biomedical text mining

BioCreative II.5 will evaluate real-time text mining capabilities on
full text articles and explore future possibilities for author-assisted
annotations using information extraction tools.

Interesting new aspects of BioCreative II.5 relate to:

1) The use of an online MetaServer platform as basic evaluation
infrastructure, allowing direct comparison of multiple participating
2) Collaboration of article authors, publishers and expert human
annotators (for the preparation of task resources).
3) Use of full text articles in various formats including XML.
4) Alignment of various tasks on a common data collection.


1) INT - Interaction normalization task
(Given an article extract a set of biological entities, namely mentioned
interactor proteins)
2) IPT - Interaction pair task
(Extraction of biological relations, namely pairs of interacting proteins)
3) ACT - Article categorization task
(Binary classification of articles as relevant for extracting
interaction annotations)

For more information on the tasks, please visit the website at:


Evaluation will be based on direct comparison of automatically generated
predictions by participating systems against a Gold Standard of manually
generated annotations, so-called Structured Digital Abstracts (SDAs)
generated by the original article authors themselves as well we by
expert biological database annotators. In order to assure a more robust
evaluation setting and to be able to directly compare and visualize
different online predictions the BioCreative MetaServer (BCMS) platform
will be used.


The BioCreative II.5 challenge will result in high-impact publications
following the line of previous BioCreative publications, including
collaborative papers, evaluation articles and technical descriptions.

BioCreative I - BMC Bioinformatics
BioCreative II - Genome Biology


To join the BioCreative mailing list:

To obtain data (BioCreative data and workshop proceedings):

If you are interested in the BC II.5 challenge, register at:

(Note: Servers will be down on Sat., 7th Feb., from 900-1400 GMT for


- Registration Opening: now
- Training Phase/AS testing: Feb. 16th, 2009
- Registration Closing: Apr. 3rd, 2009
- Test Phase: Apr. 8th, 2009
- Evaluation Phase: Apr. 10th, 2009

We encourage you to visit the website and sign up for further information.


- BioCreative website (new!): [http://www.biocreative.org]
- BioCreative MetaServer (BCMS): [http://bcms.bioinfo.cnio.es]
- Author-based annotations (FEBS Letters SDAs):
* summary [http://www.febsletters.org/content/sda_summary],
* special issue
- BioCreative I: special issue
- BioCreative II: special issue [http://genomebiology.com/supplements/9/S2]

Thank you,

the BioCreative Organizers

Alfonso Valencia
Martin Krallinger
Florian Leitner
* CNIO - Spanish National Cancer Research Centre

Lynette Hirschman
Scott Mardis
* The MITRE Corporation

Gianni Cesareni
* MINT Database

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