Building biological networks with BEL open source language

Meetup Synopsis

One major challenge in fully utilizing the vast public databases of biomedical literature is representing biological relationships in a standardized, computable format. The Biological Expression Language (BEL) [http://openBEL.org (http://openbel.org/)] is an emerging standard to capture and compile causal relationships while maintaining relevant contextual information as metadata. This presentation will provide an overview of the Biological Expression Language (BEL) format and how it has been applied in combination with the Cytoscape visualization software to construct a large array of biological networks. We will also highlight unique features of BEL that distinguish it from other prominent languages commonly utilized for network building.

The second part of the presentation will highlight the series of biological networks available as part of the ongoing Network Verification Challenge (NVC), a collaborative online project aimed at crowd-sourcing the improvement of biological network models for use by the global scientific community. We will review the foundation of language architecture using specific examples derived from the NVC project, as well as highlight the large array of visualization styles possible for language representation within networks. This tutorial will familiarize users with language semantics and demonstrate its broad applicability to scientific knowledge representation within the analytics community.

Speaker Bios

R. Brett Fields – Associate Scientist at Selventa

Brett has been a team member at Selventa since June 2012, during which time he served an instrumental role in constructing the series of human biological networks being reviewed during the Network Verification Challenge. Brett received his Bachelor of Science (B.S.) degree in Biochemistry from The Georgia Institute of Technology in Atlanta, GA and received a Master of Science (M.S.) degree in Cellular Biology from The Scripps Research Institute in La Jolla, CA.

Jennifer S. Park, Ph.D – Associate Director of Research at Selventa

Jennifer has been a scientist at Selventa since 2008, during which time she built numerous molecular models for a variety of inflammatory diseases, cancer and metabolic diseases. She was the scientific lead for building the tissue repair and angiogenesis networks that will be reviewed during the Network Verification Challenge, and was heavily involved with construction of the other NVC networks. Jennifer received her Bachelor of Science degree in Bioengineering from Cornell University in Ithaca, NY and received a Ph.D. in Bioengineering from University of California, Berkeley in Berkeley, CA.

Sponsor:

Hack/Reduce (http://hackreduce.org/) for Venue

Selventa (http://selventa.com/) for Food/Raffle

[ See you all at Analytics.Club ]