BioLINK SIG: Linking Literature, Information and Knowledge for Biology

BioLINK SIG 2013: Roles for text mining in biomedical knowledge discovery and translational medicine

The Annual Meeting of the ISMB BioLINK Special Interest Group

In Association with ISMB/ECCB 2013, Berlin, Germany

July 20, 2013

The SIG meeting is now over! Thank you for your interest and participation.

Please note: The ISMB/ECCB 2013 USB Flash drive provided at the conference inadvertently left out the full proceedings volume for the SIG. It is available here.

Congratulations to the F1000 Research Poster Prize winners:

David Campos, Sérgio Matos and José Luís Oliveira.

Neji: a tool for heterogeneous biomedical concept identification

David Campos, Poster Prize Winner

Mariana Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz and Ulf Leser.

Text mining for characterizing cells and tissues.

Mariana Neves, Poster Award

Phoebe Roberts.

A quantitative analysis of causal and associative events involving genes and proteins.

The winners have won a free one-year subscription to F1000Prime and a free submission to F1000Research.

Some more photos of the poster session:

Florian Leitner, Lars Jensen, Mariana Neves
Jin-Dong Kim, Florian Leitner
Karin reading out Poster Prize winners

Workshop Theme

With the increasing availability of text data related to biology and medicine in the scientific literature, database annotations, the electronic health record, clinical trials data, and health information online, exciting opportunities arise to provide access to pertinent biomedical information and to advance biomedical knowledge. An evolving research direction is the integration of information from diverse data sources, including textual data, to support deeper understanding of biological systems, the genomic basis of disease, and genotype-phenotype relationships.

This year we propose to focus the BioLINK SIG Workshop on text-based applications which link between biological and clinical information. We will build on the topic of the well-attended previous special session on data integration, but shift the focus towards the use of text mining in applications that aim to further biological or medical understanding. We will solicit submissions from researchers working on all aspects of mining text in the biological, medical and clinical domains.

The BioLINK SIG meeting has been regularly held in association with the ISMB conference since 2001, focusing on the development and application of resources and tools for biomedical text mining. The SIG is interdisciplinary in nature focusing on the community of users, including biomedical experimentalists, researchers and database curators, who are interested in using text mining methods as part of their tools. The meeting includes invited talks, reports from recent evaluations and workshops, as well as a poster session. We will encourage posters with short abstracts presenting new/preliminary work, and dedicate some time to discussing them.

We anticipate a productive workshop that will facilitate discussion and exchange of ideas by bringing together multiple communities: the users of text mining tools, including curators of biological databases, bench scientists and bioinformaticians; and the researchers applying natural language processing, ontologies, text mining, image analysis, information extraction and retrieval to problems in the biomedical domain.