mapping GO terms to classifications one rank down from the top- level GO categories

Question

[1215045934]

Hi all!

I would like to map a list of GO terms (>1000, won't be able to do it manually) from different GO ranks to one classifications one rank down from the top- level GO categories, i.e. direct children categories of Biological Process, Cellular Component, and Molecular Function. Here is an example from this paper . Then I would like to do a bar graph like this. Which software/package should I use?

Thanks a lot!

My GO list looks like this: [one GO term per line]

GO:0001505
GO:0006259
GO:0006403
...

Answer 1

[geneontologyhelp]

So the largest concern with this is how useful this task is. First of all, the level of the term doesn't really mean anything, it's just an artefact of how the ontology is constructed. See http://geneontology.org/docs/faq/#how-can-i-calculate-the-level-of-a-go-term and the linked Alterovitz et al.

A closely related but different concern is that the actual terms you'd get by just selecting children of the root terms may not even be used for annotations, or other concerns. Take GO:0005488 binding for example- it's a direct child of GO:0003674 molecular_function, so at the 'level' you're asking about. However, the comments for that term are

Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.

Instead, you might consider using a curated subset (Slim): see http://geneontology.org/docs/go-subset-guide. These contain a handpicked subgroup of terms in the specified aspect, but they are informative. The generic slim should be suitable for multi-organism files but there are a few Slims curated by specific MODs if you're only looking at one organism.