Video Tip of the Week: PaleoBioDB, for your paleobiology searches

Yeah, I know, it’s not genomics–but it’s the history of life on this planet–right?  The Paleobiology Database has been keeping records of this ancient biology for a while now, and they have some really nice tools to explore the fossil records and resources that have become available. It’s also interesting to me to see the informatics needs of this type of project. It has a lot of overlap with databases of more recent biology, like the GOLD one–they need taxonomy for the organisms, they need literature links–but they have other needs to capture both geographical regions and the layers of time as well.

There are a couple of ways to access the data. When you arrive at the main landing page, you have the choice to “Launch PBDB”, or “Launch Navigator”. PBDB is a “classic” interface, with typical search boxes and query results. Since this is the internet, I used that “quick search” and looked for paleo cats, and found a lot of Felis in there. But that’s not the only way to look around. They have a newer graphical access mechanism that’s called the Navigator. You can use the navigator to search the world, filter for specific items or time periods–but my favorite thing is you can reset the planet to be what it looked like eons ago. This is covered in their intro video that is this week’s Tip of the Week:

They have other videos as well, you can see that they have both this Navigator interface and help with the classic style. Their “apps” offer other types of searches too. You can even search for insect size. Another way to access information is via R. I began to look around at this because David Bapst on Google+ pointed to their new publication announcement (linked below), offering their R package for accessing their underlying data.

According to their publications page, this resource supports a wide range (and copious amount) of research in this field. It was really neat to have a look at a rather different scale of bioinformatics across the time horizon. Check out the Paleobiology Database resources for your fossil needs.

Quick link:

Paleobiology DB:

Varela S., González-Hernández J., Sgarbi L., Marshall C., Uhen M., Peters S. & McClennen M. (2014). paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database, Ecography, DOI: 10.1111/ecog.01154