BioCreative II.5 - Bioinformática

Siguiendo la nueva tendencia en las competiciones bianuales en áreas de la Bioinformática, comenzada por CASP6.5 y continuada en CASP7.5, BioCreative, la competición relacionada con el área de text-mining, va a celebrar su propia edición fraccional (BioCreative II.5). Esta edición está principalmente pensada para participantes, debido a que las fechas proporcionadas por el comunicado oficial de la organización apuntan a los distintos plazos que tienen para entrenar sus herramientas, probarlas y evaluarlas.

Ya está abierto el plazo de inscripción, y se cerrará el próximo 3 de Abril. Aunque todavía no hay datos sobre el lugar de celebración ni las fechas de las reuniones que se suelen celebrar al final de estas competiciones, la página web de BioCreative II.5 va a ir actualizándose con información adicional. Además, hay una lista de correo electrónico dedicada a la competición: http://lists.sourceforge.net/mailman/listinfo/biocreative-participant

El anuncio completo original del evento viene a continuación:

BioCreative II.5 Challenge (2009)

Can Information Extraction contribute to the creation of StructuredDigital 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 IEin 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%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 forelectronically annotated abstracts., FEBS Letters (2008) vol. 582 (8)pp. 1178-81
http://linkinghub.elsevier.com/retrieve/pii/S0014-5793(08)00195-6

CALL FOR PARTICIPATION

OVERVIEW

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

BioCreative II.5 will evaluate real-time text mining capabilities onfull text articles and explore future possibilities for author-assistedannotations using information extraction tools.

Interesting new aspects of BioCreative II.5 relate to:

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

TASKS

INT – Interaction normalization task
(Given an article extract a set of biological entities, namely mentionedinteractor proteins)
IPT – Interaction pair task
(Extraction of biological relations, namely pairs of interacting proteins)
ACT – Article categorization task
(Binary classification of articles as relevant for extractinginteraction 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 manuallygenerated annotations, so-called Structured Digital Abstracts (SDAs)generated by the original article authors themselves as well we byexpert biological database annotators. In order to assure a more robustevaluation setting and to be able to directly compare and visualizedifferent online predictions the BioCreative MetaServer (BCMS) platformwill be used.

PUBLICATIONS

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

BioCreative I – BMC Bioinformatics
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 visit: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 9:00-14:00 GMT formaintenance.)

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]
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