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Main workshop topics

 

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) 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.

 

 

·         Collaborative Biocurator Assistant: 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.

 

·         CHEMDNER patents:  Identification of chemical compounds and of gene and protein mentions in medicinal chemistry patents

 

·         Chemical-disease relation: 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.

 

·         Extraction of causal network information in Biological Expression Language: 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.

 

·         Interactive Curation: Demonstration and evaluation of web-based systems addressing user-defined tasks, evaluated by curators on performance and usability.

 

·         Literature curation and biological databases: The importance and practical use of text mining and information extraction systems for the extraction of biological and biomedical annotations and integration to existing life sciences knowledgebases.

 

·         Crowdsourcing and text annotation for database curation: Demonstration of real world cases of crowdsourcing and community annotations for generating Gold Standard annotations for text mining and information extraction systems and database annotations

 

·         Disease Annotation and connections to the medical literature and clinical text mining: Use of text mining strategies to extract clinically relevant information from public data and clinical records, with a special focus on disease and symptoms related concepts.

Deadlines
Early Registration Closing
Tuesday, August 25, 2015
Abstract Submission Closing
Friday, September 4, 2015

Sponsored by
inab.org
www.cnio.es/ing/index.asp
https://www.cima.es/home
www.ncbi.nlm.nih.gov/
https://www.ncsu.edu/
www.fraunhofer.de/en.html
www.mitre.org/
www.nigms.nih.gov/
pir.georgetown.edu/
www.ciccartuja.es/en/home/
www.prb2.org/es/home
www.isciii.es/
Acknowledgments
USA Department of Energy Grant: DE-SC0010838
USA National Institute of General Medical Sciences Grant: R13-GM109648-01A1
Biomolecular and Bioinformatics Resources Platform of Institute of Health Carlos III Grant: PT13/0001/0001