P1- Text mining applications: literature curation and beyond

This panel will address 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 knowledge bases as well as in literature/publishing sources.

Chairs: Cecilia Arighi, and Zhiyong Lu

Jo McEntyre, EMBL-EBI
Thomas Lemberger, EMBO
Natalie Cattlet, Selventa
Shawn Polson, University of Delaware
Ioannis Xenarios, Swiss Bioinformatics Institute

Johanna McEntyre

Johanna McEntyre is Team Leader for Literature Services at the European Bioinformatics Institute (EMBL-EBI), where she is responsible for developing Europe PMC, the European database for full-text life science research articles (http://europepmc.org). Her primary focus is on the integration of the open access literature with open life sciences data, to develop new ways for researchers to access and discover useful information.

Thomas Lemberger

Thomas Lemberger is Chief Editor of the open access journal Molecular Systems Biology published by EMBO press and Deputy Head of Scientific Publications at EMBO. Trained as a molecular biologist, he joined EMBO in 2005 as scientific editor of The EMBO Journal and Molecular Systems Biology. He leads the SourceData project, which is developed in collaboration with the Swiss Institute of Bioinformatics, Wiley and HighWire Press, with support of the Robert Bosch Foundation.

Natalie Cattlet

Natalie Catlett is a Senior Computational Scientist at Selventa, where she works on OpenBEL (www.openbel.org), a platform for capture, share, and use of biological knowledge. Selventa developed the Biological Expression Language (BEL) to represent causal and correlative biological relationships from the scientific literature in a computable form.  At Selventa, she has co-authored several papers involving the use of BEL for building biological networks, interpreting transcriptomic data sets, and developing predictive biomarkers for response to targeted therapies. Natalie holds a Ph.D. in Biochemistry from the University of Iowa, and performed postdoctoral work in functional genomics at the Torrey Mesa Research Institute (Syngenta) and UC Berkeley.

Shawn Polson

University of Delaware
Shawn Polson is the Coordinator of the Bioinformatics Core Facility and faculty in the Departments of Computer and Information Sciences and Biological Sciences at University of Delaware. He is also the Associate Director of the Bioinformatics Network of Delaware providing Bioinformatics education, training, and research support to six institutions across the state. His research interests lie at the intersection of genomics and microbial ecology, examining the ways in which microorganisms and viruses affect and are affected by their environments. He is involved in multiple metagenomics-related projects involving both the development of bioinformatics resources to analyze and visualize metagenomics data, such as VIROME (Viral Informatics Resource for Metagenome Exploration), and MgOl (Metagenomes Online); and active research, e.g. on the role of microorganisms in health and disease of organisms such as humans, coral, and oysters, as well as their role in various environments including deep-sea hydrothermal vents, estuarine and oceanic water, and agricultural settings.

Ioannis Xenarios

Swiss Institute of Bioinformatics
Ioannis Xenarios is the Director of Vital-IT. He received a Ph.D in immunology at the Ludwig Institute of Cancer Research and the Institute of Biochemistry. He worked on the development of the Database of Interacting Proteins (DIP) under the supervision of Prof. David Eisenberg at the University of California Los Angeles. He then became the head of Translational Bioinformatics at Serono (now Merck Serono) where his group developed computational methodologies in the area of proteomics, microarray and genetics. He is one of the Principal investigators of the ENFIN project aiming at providing methods in dynamical systems modeling. Ioannis Xenarios is UNIL full Professor ad personam, affiliated with the CIG, since August 2010.

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

Sponsored by
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