And now for something completely different. Typically we highlight software that’s nucleotide or amino acid sequence related in some way. But this software is on a whole ‘nother level. It looks at interactions between species. This week we highlight GloBI, the Global Biotic Interactions database.
Before you start thinking of Bambi and butterflies, though, consider the image shown right at the beginning of the slide presentation about this project (slide 2). It includes interactions such as lunch. Here’s where it started to get me thinking about the implications for genomics. There have been some papers talking about sequences from other species, which may or may not have been eaten, appearing in various samples. Are these contaminants, or are they real? If they are real, we might expect to see some of these “interactions” reflected in sequence repositories. So it struck me that knowledge of these might be helpful in sussing out some of those situations. In fact, from this project, I learned about a whole bunch of “diet” databases that were new to me (see slide 5, for example, Avian Diet Database).
But also, for ecological purposes, there’s a lot of value in this data. I loved this quip on their “about” page:
Now that folks have mapped the human genome, put a man on the moon, isn’t it time to provide easy access to how, when and where organisms interact with each other so that we can better understand and better preserve our ecosystems? Perhaps GloBI can become the OpenStreetMap of ecology: a global map that shows how organisms rely on each other . . .
Certainly that’s worthwhile. And I’m glad to see this effort to capture and share this information. And the structure of the data, using a number of ontologies including some that were new to me, looks very helpful. The GloBI data is subsequently used in the Encyclopedia of Life to connect people with information about food sources for species, too.
So this week’s video tip of the week is the intro video that the team has provided:
Interesting side note about the data that’s currently available to use–seems there’s a lot of proprietary data that’s been collected in this field, and they have created a “Dark GloBI” to allow people to access that restricted stuff within their framework (see the discussion in the paper below). How can that US government data not be public?? But they hope to entice a lot of this data to come out of the dark side and be publicly available.
So check out this resource for species interactions, and contribute data if you have it. There have been some classroom projects collecting information that might be great for people in teaching situations too. It looks very valuable on a number of levels.
Hat tip to Esther Martinez on G+ https://plus.google.com/u/0/+EstherMartinez/posts/fnSNdZyvzFs
Global Biotic Interactions: http://www.globalbioticinteractions.org/
Poelen, J., Simons, J., & Mungall, C. (2014). Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets Ecological Informatics, 24, 148-159 DOI: 10.1016/j.ecoinf.2014.08.005