Meetings & Conferences Semantics and Ontologies Standards

Alexander Diehl (GO/MGI): Biological Processes subtree in GO (CBO 2009)

Gene Ontology (GO) has developed over time to become more of a true ontology. Its purpose is: as a common language to share knowledge, to support cross-referencing.

Terms of interest for CBO in GO include cellular processes and their regulation, cell differentiation, cellular extravasation, among other things. Cellular process, multicellular organismal process and multi-organism process are disjoint from each other. Some of these terms can be problematic: for instance, localization is a subtype of multi-organism process, which could also be one of the other types, depending on the definition: it all comes down to the definition…

Terms in GO may have multiple parents, some of which are from other ontologies such as the Cell Ontology. These links to external ontologies will not be present in the standard download, but you can download a version of GO that has the links (you’ll probbaly have to download the additional external ontologies separately).

There are 16419 terms in the biological process ontology. They don’t just develop GO as annotators need them or users request them. They also have domain workshops that focus on getting a particular type of domain covered (e.g. lung development and muscle development). GO developers use OBO-Edit 2.0, which isn’t as fully-functional as Protege and OWL, but which is useful for people only developing in OBO.

Annotations of gene products to GO are genome specific. With regards to the CBO and GO, we shouldn’t reinvent the wheel. We also need to think very carefully about the definition of behaviour, which in GO means “the specific actions or reactions of an organims in response to external or internal stimuli…”

Basically, they are just cellular processes, which might be a little more restrictive than we want.It would be really useful to make as much use of GO as possible because you get a lot of benefits: you get automatic linking to all the rest of GO, and all the analyses etc that people do and then annotate with GO. You might also want to look into the extracellular matrix organisation terms.

Question: why did you decide to put cell type outside of GO? Well originally, it was created to describe aspects of particular gene products, and cell type doesn’t seem to be within scope. In a longer term, they want to bring the Cell Ontology under the auspices of the GO Consortium.

MGI website.

In other news, during lunch James Glazier has said that CBO should only be for behaviour of cells, not behaviour in cells, and that we will not be attempting to hang CBO underneath the biological process section of GO.

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

By Allyson Lister

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