New Gene Ontology connections

No doubt you’ve seen all those Gene Ontology (GO) terms in the databases.  There’s a nice story behind the development, structure and use of GO terms which we describe in our full tutorial on the topic.  But another important feature of GO is that is continues to evolve and improve, and a new feature is in the process of rolling out.

I learned about this from the a GO mailing list.  If you find yourself relying on GO terms for tools you support or queries you may do to annotate lists of genes, you may want to keep up with changes like this.

On February 17th the GO team implemented major new features, one of which is expanding the use of “regulates” to the Molecular Function hierarchy.  Earlier in GO development the relationships didn’t indicate a “regulates” relationship at all.  There were only “is a” or “part of” relationships between terms.  But they added regulates to the Biological Process group some time ago.  Here’s a sample of how that looks:

go_regulates

The really big new aspect of this, though, is not just this functionality within Molecular Function terms.  It is that now they are creating a “regulates” function between the Molecular Function and Biological Process terms–these are called intra-ontology links.

This is a nifty new way to be able to annotate genes and gene products.  It carries more information than just a single definition would. But, it is also rather a challenge for software developers because it is a largee conceptual leap than the straight hierarchies are.  So it may take a while to fully roll out to your favorite database that uses GO.  But watch for it–it is a big deal.

For more details if you are interested (or you have software that may break because of this) you can see more details and an example in the GO wiki:

http://wiki.geneontology.org/index.php/Overview_of_Function-Process_regulates_links

One example is this:

Specifically, we have made the implicit regulatory relationships between ‘regulation of molecular function’ BP terms and the corresponding MF terms explicit. For example:

   * regulation of kinase activity (BP) regulates kinase activity (MF)

It makes sense in English, I know. But it’s not so simple for a computer. They have to be told this. And that’s what this change can do.

I’ll concede that this may not be among the most exciting things in your life lately.  But it is big for what we do.  So I just thought I’d mention it….