[BioC] Error GO.db package "term is not member of any ontology"

[Sean Davis]

On Fri, Apr 9, 2010 at 8:50 AM, Ana Conesa <aconesa at cipf.es> wrote:
> Dear all,
>
> I am working with the package GO.db (version 2.3.5) to retrieve information
> from GO terms and I find a large number of my GO IDs that apparently are not
> in the database, i.e. I get the following error:
>
> Error in getGOParents(x) : GO:0090153 is not a member of any ontology
>
> But this term can be found at the Amigo site as "regulation of sphingolipid
> biosynthetic process". And there are many more in this situation. I
>
> is this a problem of GO database versions?. How could I find within R these
> l"lost" terms?

Hi, Ana.

You'll probably need to provide a reproducible example and the output
of sessionInfo() to get direct help.  However, this works fine for me:

> library(GO.db)
> get('GO0090153',GOTERM)
GOID: GO:0090153
Term: regulation of sphingolipid biosynthetic process
Ontology: BP
Definition: Any process that modulates the rate, frequency or extent of
    sphingolipid biosynthesis. Sphingolipid biosynthesis is the
    chemical reactions and pathways resulting in the formation of
    sphingolipids, any of a class of lipids containing the long-chain
    amine diol sphingosine or a closely related base (a sphingoid).
> sessionInfo()
R version 2.11.0 Under development (unstable) (2009-11-13 r50424)
i386-apple-darwin10.2.0

locale:
[1] en_US/en_US/C/C/en_US/en_US

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] GO.db_2.4.1         RSQLite_0.8-4       DBI_0.2-5
[4] AnnotationDbi_1.9.8 Biobase_2.7.3

Sean