Tip of the Week: Database of mouse databases


We are acutely aware of the thousands of bioinformatics resources out there, and we are often asked for guidance on finding a particular type of tool for some function or other.  There are some excellent lists out there which attempt to catalog the various tools–the NAR Database Issue and corresponding list, the Resource Collection at the Univ. of Pittsburg, and others.  But recently we saw one developed with a specific focus, which claims to bring together over 200 resources for the mouse.  The Mouse Resource Browser collects and categorizes a number of different types of things–not just databases, as we’ll see.  Find them here: http://bioit.fleming.gr/mrb

The curated collection of sites that may  be of use to mouse researchers has a number of features.  The developers used a questionnaire to elicit some information from the resource providers, and when they don’t have that input they have created some basic information for the records themselves. You can do a basic search for resources with a quick search box. There is an advanced search option.  I found the option of browsing by category (they have 22 categories) the most informative to figure out what kind of resources they had collected.

The data for a given record is organized across a series of tabs:

  • General: description, highlights and subject matter of the resource
  • Ontologies and Standards: if the resource relies on any of the important vocabularies or standards formats in the field, they are listed here
  • Technical: details of implementation, type of database, access methods, if there is a web services component, whether there are downloads or not
  • CASIMIR DDF: this is an interesting tab that assesses some of the features of the resources such as currency/updates, quality control process, versioning, technical documentation, user support, and more.

Although the focus is mouse, you’ll see some more broad types of resources in there.  For example, UCSC Genome Browser is listed as there is a mouse database there.  Reactome is listed.  These have a species range and include mouse, but are certainly not focused on mouses.  Other types of resources include commercial suppliers such as Charles River. So it isn’t limited just to things like sequence databases and things of that nature–it’s got more aspects that researchers employing mouse as a model system might find useful.

There are some choices they have made that I’m not sure I would have.  They list the MGI mailing list as a separate feature from MGI.  But as I thought more about it, I could see why.  There is good information there, and if you don’t know of it already a pointer might help.  But as I was thinking of the 200+ resources just for mouse, I thought that sort of affected the total.

If you use mouse as your model system, you will probably find some useful databases and other web sites that are handy for your work.  If you don’t work with mice, there are probably still some useful resources for your work as well.  Check out MRB’s site for more information: http://bioit.fleming.gr/mrb

Reference:
Zouberakis, M., Chandras, C., Swertz, M., Smedley, D., Gruenberger, M., Bard, J., Schughart, K., Rosenthal, N., Hancock, J., Schofield, P., Kollias, G., & Aidinis, V. (2010). Mouse Resource Browser–a database of mouse databases Database, 2010 DOI: 10.1093/database/baq010

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  1. Pingback: Tip of the Week: A year of tips III (first half of 2010) | The OpenHelix Blog

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