Tag Archives: species

otter_lunch

Video Tip of the Week: Global Biotic Interactions database, GloBI

otter_lunchAnd 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:

Global Biotic Interactions Introduction (2 Minutes, March 2014) from Jorrit Poelen on Vimeo.

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

Quick link:

Global Biotic Interactions: http://www.globalbioticinteractions.org/

Reference: 

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

Video Tip of the Week: Integrative Multi-species Prediction (IMP) Network Analysis Resource

A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips:

RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials for IMP are available from: http://t.co/zvlVmoph

This week I have claimed Mary’s “collected” tip idea & will be featuring one of their videos as this week’s quick tip.

The Integrative Multi-species Prediction (IMP) web server is a gene-gene network analysis resource. There are several such resources (Cytoscape, IntAct, MINT, STRING, VisANT, and one of my personal favorites GeneMania) that OpenHelix has tutorials on (see our Pathway catalog listing). The IMP developers provide a nice amount of help for their users – not only do they have multiple YouTube videos (as do we on the OpenHelix YouTube channel), but they also offer two interactive tutorials that allow users to be guided through an example usage of IMP.

For today’s tip I am featuring the third YouTube video that they list on their tutorial page, because I thought it had the best sound and image quality. The other videos are also informative & are worth a viewing – enjoy!

Reference:
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, & Troyanskaya OG (2012). IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research, 40 DOI: 10.1093/nar/gks458

VegBank

vegbankWe do mainly genomics and molecular biology resources around here, but I thought I’d mention this database I learned about at the Special Libraries Association conference this week. The database is “VegBank” and is a repository of plot data of species numbers and types from across the US and Canada. A great resource, I am told, if you do ecological studies.

So, it’s not specifically genomics nor molecular, but it is biological and a database so it might be of use to one of our readers!

This is one of the nice benefits of attending these conferences, we get to learn a lot about resources and databases we might not have heard about otherwise. There are so many out there, no directory or google search is going to find them all. From VegBank, Continue reading

Tip of the Week: Adopt-a-Species

eoltipEver wanted to adopt a pet? Perhaps you’ve thought of donating to a zoo by “adopting” a zoo animal, well, you can do even more. The Encyclopedia of Life (which I’ve written about before) needs someone to adopt a species as an ‘authenticator/curator’. The EOL has a lot of potential, but it’s going to require some volunteer work. This week’s tip introduces the EOL, what kind of data is there in the ‘model’ pages and shows you how to sign up!

Encyclopedic Tree of Life

Tree of Life image In 1993 I remember discovering the web. It wasn’t much longer after that I discovered the “Tree of Life (ToL).” I was studying for my Ph.D. in evolutionary biology and heard about it by word of mouth. Sometime in 1996 I found it on the web and was intrigued. It has grown since then, though still has a way to go. It’s goal? “… to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct.

Today saw the unveiling of the “Encyclopedia of Life (EOL),” which is “an ambitious… project to organize and make available via Encylopedia tree of lifethe Internet virtually all information about life present on Earth.” Carl Zimmer reports on the EOL on his blog and in a NYTimes article.

Those goals overlap a lot it would seem. So I did some checking of the ToL and the EOL for two things that are most interesting to me: genomic information and evolutionary information. A short critique below (with the caveat that EOL is VERY slow today because of the launch):

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Monday Fun: Species Names

It’s the beginning of the week and just revving up the blogging head, so I thought I’d post something fun to get started this week: Species names.

As I mentioned last week, the number of species with complete genomes is rising rapidly, but so far as I can tell, none with some obviously ‘tongue-firmly-in-cheek’ names such as:

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