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VenomKB v2.0: A knowledge repository for computational toxinology

View ORCID ProfileJoseph D. Romano, Victor Nwankwo, View ORCID ProfileNicholas P. Tatonetti
doi: https://doi.org/10.1101/295204
Joseph D. Romano
1Department of Biomedical Informatics, Columbia University, New York, NY, 10032.
2Department of Systems Biology, Columbia University, New York, NY, 10032.
3Institute for Genomic Medicine, Columbia University, New York, NY, 10032.
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Victor Nwankwo
4Department of Medicine, Rush University Medical Center, Chicago, IL, 60612.
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Nicholas P. Tatonetti
1Department of Biomedical Informatics, Columbia University, New York, NY, 10032.
2Department of Systems Biology, Columbia University, New York, NY, 10032.
3Institute for Genomic Medicine, Columbia University, New York, NY, 10032.
5Department of Medicine, Columbia University, New York, NY, 10032.
6Data Science Institute, Columbia University, New York, NY, 10032.
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  • For correspondence: nick.tatonetti@columbia.edu
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Abstract

Motivation Venom peptides comprise one of the richest sources of bioactive compounds available for drug discovery. However, venom data and knowledge are fragmentary and poorly structured, and fail to capitalize on the important characteristics of venoms that make them so interesting to the biomedical community.

Results We present VenomKB v2.0, a new open-access resource for knowledge representation and retrieval of venom bioactivities, sequences, structures, and classifications. VenomKB provides a complete infrastructure for computational toxinology, with a focus on drug discovery and effects that venoms have on the human body. VenomKB is accompanied by a suite of tools for programmatic access, and, in this article, we highlight scenarios demonstrating its usefulness and novel contributions to toxinology, pharmacology, and informatics.

Availability VenomKB can be accessed online at http://venomkb.org/, and the code can be found at https://github.com/tatonetti-lab/venomkb/. All code and data are available under open-source and open-access licenses.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 06, 2018.
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VenomKB v2.0: A knowledge repository for computational toxinology
Joseph D. Romano, Victor Nwankwo, Nicholas P. Tatonetti
bioRxiv 295204; doi: https://doi.org/10.1101/295204
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VenomKB v2.0: A knowledge repository for computational toxinology
Joseph D. Romano, Victor Nwankwo, Nicholas P. Tatonetti
bioRxiv 295204; doi: https://doi.org/10.1101/295204

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