Pick Your Poison: Columbia Scientists Create Open Access Database For Medical Venom Research

Scolopendra polymorpha
Columbia scientists have created an open-access database on all things venom, in order to better help researchers find potential medicinal uses. Above is one such venomous creature, the common desert centipede. Matt Reinbold, CC BY-SA 2.0

Ever wanted to know what scorpion venom’s good for? Well, now you can, thanks to two Columbia scientists.

This Tuesday in Scientific Data, Nicholas Tatonetti, an assistant professor of biomedical informatics at Columbia, and graduate student Joseph Romano announced the unveiling of their open-access database on all things venom, called VenomKB. Though venoms often get a bad rap for their less than friendly effects on strangers, scientists have long known about the potential benefits that they can offer humanity. Unfortunately, it’s a still widely untapped potential, so Tatonetti and Romano created the database as a means of bringing together the most up-to-date information on all known and possible medicinal uses for venoms.

“With this list we can take stock of what we know about venoms and their therapeutic effects” Tatonetti explained in a statement released by Columbia. “The question now is: How can we use this information with other databases to discover new compounds and therapies?”

Manually Curated

Devising VenomKB was by no means an easy task. The two researchers first delved into the ever-expansive MEDLINE, itself a publicly-accessible database of scientific articles on nearly all research related to biology and medicine — a database that contained over 22 million papers at the time.

With the aid of computer algorithms, they then slimmed down their selection to just over 5,000 studies on venom therapies, collectively detailing 42,723 unique effects of venoms on the human body. They then manually created a summary for the first 275 venom studies they came across (after the order was randomized to avoid bias), complete with links to the actual research.

In addition to the personally vetted aspect of VenomKB, they also created two additional automated functions that will allow the user to search for any particular physiological effect or venom compound they so desire. It’s hoped that over time, with the help of contributors, the algorithms that govern the automated database will become better refined so as to avoid false positives.

“VenomKB allows for users to ‘flag’ individual records for removal,” the two explained in their paper. “This method of ‘crowd sourcing’ the removal of erroneous records will continue to improve in its robustness as VenomKB gains content and new users.” The pair plan to offer their own future research to their database, studying dried black mamba venom as a means of finding treatments for chronic pain, diabetes and heart disease

Venoms are so illustrious in their therapeutic potential because they are comprised of a “complex cocktail of organic compounds” which are often peptide-based. One such example noted by Tatonetti and Romano is that of the cone snail’s (C. magus) venom, from which a powerful peptide painkiller called ziconotide was created. It’s estimated there are more than 10 million venomous species out in the world that we haven’t classified yet, dwarfing the 173,000 species we do know about. Owing to their biological nature, each venom is unique to their specific species.

Though the two are often synonymous (even in the headline!), venoms do differ from poisons in how they’ve delivered to their unfortunate victims, with poisons only being harmful if they’re ingested, whereas venoms are directly introduced via a bite or similarly purposeful method.

And as for that scorpion venom? Well, a peptide derived from it called butoxin just might offer some protection against radiation. Thanks, VenomKB!

Source: Tatonetti N, Romano J.VenomKB, a new knowledge base for facilitating the validation of putative venom therapies. Scientific Data. 2015.

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