Gathering detailed phenotype data from any species is challenging. It can be an enormous problem to even standardize the descriptions you want to assign, never mind the actual collection of the information. Different research groups can have different growth conditions, different methods, different strain backgrounds. For many species trained curators are combing the literature for these details and putting them into the databases–WormBase collects great details for their gene pages this way. For some there are larger-scale projects to phenotype organisms. The benefits of this type of project are the infrastructure and standardization, and the creation of a resource that others can mine and explore the details further.
Today’s video tip of the week highlights one of these larger scale projects. A database of C. elegans phenotypes has been created using a video tracking system to automate as much as possible about the recording and scoring of the worm motions which can provide clues to the functions of the genes that are examined. The recent paper in Nature Methods (below) characterizes their database and explains their philosophy and summarizes the kinds of things they were examining. But you should also check out the paper on their dictionary of behavioral motifs (also in the references section). I thought the figures in this PNAS paper were really helpful to understand the ways the features are scored.
This video is a bit different than we usually use–generally we highlight videos walk through a database or some functions. But this one shows you how to build the video recording setup.
But you should go over and explore their database that stores the videos and data generated from this setup. An easy way to find something is to click on the genes that are circulating in the cloud on the main page. But I’ll also embed one of the videos here so you can see how that device records the worm locomotion details. Here is the page for an allele of the mir-124 gene. There’s summarized information about the data from the video, and on each page there is a link to the video. You may not want to watch the whole 15 minutes of this worm, but you can get a sense of the amount and type of information generated.
So if you are investigating worm genes–or if your gene of interest is related to one of these genes–you might want to have a look at their data. Another great things about this work, though, is it becomes a resource for other types of work too. I’ve written about the cool OpenWorm virtual 3D worm project in the past, and this helps them out as well. They can test out their simulations with different behaviors, and refine their tools based on differences in worm alleles.
— OpenWorm (@OpenWorm) July 14, 2013
Quick links to relevant sites:
C. elegans behavior database: http://wormbehavior.mrc-lmb.cam.ac.uk/
WormTracker 2.0: http://www.mrc-lmb.cam.ac.uk/wormtracker/
Yemini E., Jucikas T., Grundy L.J., Brown A.E.X. & Schafer W.R. (2013). A database of Caenorhabditis elegans behavioral phenotypes, Nature Methods, DOI: 10.1038/nmeth.2560
Brown A.E.X., Yemini E.I., Grundy L.J., Jucikas T. & Schafer W.R. (2013). A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion, Proceedings of the National Academy of Sciences, 110 (2) 791-796. DOI: 10.1073/pnas.1211447110