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[Computational-biology] BioCreative II.5 - Call for Participation

Martin Krallinger via comp-bio%40net.bio.net (by mkrallinger from cnio.es)
Thu Feb 5 08:38:19 EST 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 systems.

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  
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  


- 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 
[http://www.sciencedirect.com/science/issue/4938-2008-994179991-684107 ]
- BioCreative I: special issue 
[http://www.biomedcentral.com/1471-2105/6?issue=S1&page=1 ]
- 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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