[Fwd: BioCreative II.5 Call for Participation]

attached mail follows:

BioCreative II.5 - Call for Participation

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BioCreative II.5 Challenge (2009)



[http://www.biocreative.org]





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

[http://linkinghub.elsevier.com/retrieve/pii/S0014-5793(08)00196-8

<http://linkinghub.elsevier.com/retrieve/pii/S0014-5793%2808%2900196-8>]

* Gerstein et al., Structured digital abstract makes text mining easy.,

Nature (2007) May 10;447(7141):142

[http://www.nature.com/nature/journal/v447/n7141/full/447142a.html]

* Hahn et al., Text mining: powering the database revolution., Nature

(2007) May 10;447(7141):142

[http://www.nature.com/nature/journal/v448/n7150/full/448130b.html]

* Leitner et al., A text-mining perspective on the requirements for

electronically annotated abstracts., FEBS Letters (2008) vol. 582 (8)

pp. 1178-81

[http://linkinghub.elsevier.com/retrieve/pii/S0014-5793(08)00195-6

<http://linkinghub.elsevier.com/retrieve/pii/S0014-5793%2808%2900195-6>]





CALL FOR PARTICIPATION



OVERVIEW



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

systems.

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.



TASKS



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:

[http://www.biocreative.org/events/biocreative-ii5/biocreative-ii5/]



EVALUATION



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.



PUBLICATIONS



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

[http://www.biomedcentral.com/1471-2105/6?issue=S1&page=1

<http://www.biomedcentral.com/1471-2105/6?issue=S1&page=1>]

BioCreative II - Genome Biology

[http://genomebiology.com/supplements/9/S2]



MAILING LIST / REGISTRATION



To join the BioCreative mailing list:

[http://lists.sourceforge.net/mailman/listinfo/biocreative-participant]



To obtain data (BioCreative data and workshop proceedings):

[http://www.biocreative.org/accounts/register/]



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

[http://www.biocreative.org/team/create/]



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

maintenance.)



DATES



- 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.



REFERENCES AND LINKS



- 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

<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