[BioC] GO terms not found in goTools and GO

[Lina Hultin-Rosenberg]

Thank you so much for the information! I did not now exactly how the 
different packages worked, now I know and understand better the problems 
I ran into. I use biomart ensembl for the GO queries.

Best regards,
Lina

Seth Falcon skrev:
> Wolfgang Huber <huber at ebi.ac.uk> writes:
> 
>> Dear Lena,
>>
>> the point to realize is that biomaRt queries an online database (you
>> didn't tell us which one you use), while the GO package is assembled and
>> packaged by friendly curators in Seattle every couple of months.
>>
>> According to this site
>> http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0060070
>> your term was last modified 2007-03-16, which could explain why it is
>> not yet in the latest GO package (version 1.17.0).
>>
>> If you want an consistent set of GO terms throughout, please use the
>> humanLLmappings (soon to be humanEGmappings) package for gene-GO
>> associations, not biomaRt. If you use biomaRt, you need to spend more
>> effort dealing with the dynamic nature of genome annotation (this is not
>> our fault, this is the state of the science).
> 
> Good advice.  I want to clarify one detail:
> 
> We are working on new Entrez Gene based organism specific annotation
> packages for human, mouse and rat.  They are intended as New And
> Improved versions of <organism>LLMappings.  We have not finalized how
> we will name them, and almost surely they will not be humanEGmappings.
> I will start a thread on bioc-devel today with some proposed naming
> schemas for those that are interested.
> 
> Best,
> 
> + seth
>