BioCreative - Call for Participation

Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BioCreative V

Call for Participation [2015-03-31]

BioCreative V Challenge and Workshop

September 9-11, 2015
Sevilla, Spain

BioCreative: Critical Assessment of Information Extraction in Biology is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. Built on the success of the previous BioCreative Challenge Evaluations and Workshops (BioCreative I, II, II.5, III, 2012 workshop, and IV) [1-6] the BioCreative Organizing Committee will host the BioCreative V Challenge in Sevilla, Spain on September 9-11, 2015. One key goal of BioCreative is the active involvement of the text mining user community in the design of the tracks, preparation of corpus and the testing of interactive systems. For BioCreative V, the selection of the tracks has been driven in part by suggestions from the biocuration community, by our goal of addressing interoperability -- a major barrier to adoption to text mining tools --, and via an open call for tasks of interest to both the bioNLP and user communities.

BioCreative V will consist of five tracks. Teams can participate in one or more of these tracks. Team registration will start on January 1, 2015 and will continue until final commitment is requested by the individual tracks.

To register a team go to http://www.biocreative.org/events/biocreative-v/biocreative-v-team/.

Funds are available for US participants to attend BioCreative 5. Information on how to apply will follow. Women, under-represented minorities, students, and post-doctoral fellows are encouraged to apply.

Track 1: Collaborative Biocurator Assistant Task (BioC) – Development of BioC-compatible modules which complement each other and an integrated system that assists BioGRID curators. A non-competitive, cooperative task in which participants work together to build a better system.
Organizers:Sun Kim, Donald Comeau, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri and W. John Wilbur
Important Dates
March 2015: Deadline for participation
Mar-May. 2015: Developing individual systems and iterative system integration
June 2015: Individual systems due date
June-July 2015: Overall system evaluation
August 2015: Manuscript deadline for meeting proceedings
URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/

Track 2: CHEMDNER patents - Identification of chemical compounds and of relevant biological context in patents.
Organizers:Martin Krallinger, Alfonso Valencia, Florian Leitner, Obdulia Rabal and Julien Oyarzabal
Important Dates
February 2015: Sample set release together with annotation guidelines
June 9th 2015: Training set release, guidelines and Markyt annotation interface (updated, Wed, 3 June 2015)
July 1st 2015: Development set release (updated, Wed, 3 June 2015)
August 14 2015: Test set release (updated, Wed, 3 June 2015)
August 21 2015: Test set prediction due (updated, Wed, 3 June 2015)
August 25 2015: The evaluated results returned to the participants (updated, Wed, 3 June 2015)
September 2 2015: The camera ready system description write ups (1-2 pages) (updated, Wed, 3 June 2015)
URL: http://www.biocreative.org/tasks/biocreative-v/track-2-chemdner/

Track 3: Chemical-disease relation (CDR) task - Automatic detection of chemical/drugs and diseases, and their relations in PubMed abstracts. In particular, the CDR task focuses on extracting the relationship of drug-induced diseases.
Organizers:Zhiyong Lu and Thomas Wiegers
Important Dates
February-March 2015: Release of training data
April-May 2015: Release of development data
July 2015: Release of test data
July-August 2015: Team submissions due
August-Early September, 2015: Team workshop paper due
URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/

Track 4: Extraction of causal network information in Biological Expression Language (BEL) - Text mining solutions to develop and test novel approaches for relation extraction in the context of pathway networks. The goal is to assess the utility of such tools for the automated annotation and network expansion, and their suitability as supporting tools for assisted curation.
Organizers:Fabio Rinaldi, Sam Ansari and Juliane Fluck
Important Dates
February 15, 2015: Release sample data
February 28, 2015: Release training data
June 14, 2015: Release test data
June 16, 2015: Submission of results deadline
July 10, 2015: Delivery of evaluation results
July 20, 2015: Paper submission
August 15, 2015: Camera-ready
Please note that all dates are indicative only and subject to change
URL: http://tinyurl.com/beltask
URL: http://www.biocreative.org/tasks/biocreative-v/track-4-bel-task/

Track 5: Interactive Curation (IAT): Demonstration and evaluation of web-based systems addressing user-defined tasks, evaluated by curators on performance and usability.
Organizers:Catalina Oana Tudor, Qinghua Wang and Cecilia Arighi
Important Dates
January 31, 2015: Submission of letter of intent by teams
March 31, 2015: Submission of system document by teams
April 10, 2015: Notification of accepted systems
April-May 2015: Systems development
Mid-June 2015: Individual systems ready for user testing
June-July 2015: Overall system evaluation by curators
August 2015: Manuscript deadline for meeting proceedings
URL: http://www.biocreative.org/tasks/biocreative-v/track-5-IAT/

BIOCREATIVE ORGANIZING COMMITTEE

Cecilia Arighi, University of Delaware, USA

Kevin Cohen, University of Colorado, USA

Donal Comeau, National Center for Biotechnology Information (NCBI), NIH, USA

Juliane Fluck, Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Germany

Rezarta Islamaj Dogan, National Center for Biotechnology Information (NCBI), NIH, USA

Lynette Hirschman, MITRE Corporation, USA

Sun Kim, National Center for Biotechnology Information (NCBI), NIH, USA

Martin Krallinger, Spanish National Cancer Centre, CNIO, Spain

Zhiyong Lu, National Center for Biotechnology Information (NCBI), NIH, USA

Fabio Rinaldi, Institute of Computational Linguistics, University of Zurich, Switzerland

Alfonso Valencia, Spanish National Cancer Centre, CNIO, Spain

Thomas Wiegers, North Carolina State University, USA

John Wilbur, National Center for Biotechnology Information (NCBI), NIH, USA

Cathy Wu, University of Delaware and Georgetown University, USA

BioCreative is partially funded by NIH/NIGMS R13-GM109648-01A1

REFERENCES

Hirschman, L., A. Yeh, C. Blaschke, and A. Valencia, Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics, 2005. 6 Suppl 1: p. S1. PMCID:PMC1869002
Krallinger, M., A. Morgan, L. Smith, F. Leitner, L. Tanabe, J. Wilbur, L. Hirschman, and A. Valencia, Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol, 2008. 9 Suppl 2: p. S1. PMCID:PMC2559980
Leitner, F., S.A. Mardis, M. Krallinger, G. Cesareni, L.A. Hirschman, and A. Valencia, An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform, 2010. 7(3): p. 385-99.
Arighi, C.N., Z. Lu, M. Krallinger, K.B. Cohen, J. Wilbur, A. Valencia, L. Hirschman, and C.H. Wu, Overview of the BioCreative III Workshop BMC Bioinformatics, 2011. 12 Suppl. 8: p. S1.
Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger Martin, Lu Z, Mattingly C, Valencia A, Wiegers TC, Wilbur WJ: Editorial: BioCreative-2012 Virtual Issue. Database (Oxford) 2012:bas049.PMC3514749.
Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z,Wilbur JW, Wiegers TC. BioCreative-IV virtual issue. Database (Oxford). 2014 May 22;2014. PMCID: PMC4030502.