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

Martin Morgan mtmorgan at fhcrc.org
Fri Apr 9 18:43:52 CEST 2010


On 04/09/2010 08:30 AM, Ana Conesa wrote:
>  Dear Jim and Vicent,
> 
> Yes, I guess this is the thing. I was wondering if there was a more up-to-date 
> GO.db package...
> If case you find it interesting, I found around 200 terms not present in the 
> current GO.db... (see attached)

The GO.db has just been rebuilt for the forthcoming release. It's
available through biocLite when using R-2.11.0 pre-release. I get

> get("GO:0090153", 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).

with

> packageDescription("GO.db")$Version
[1] "2.4.1"

and

> GO_dbInfo()
             name
1    GOSOURCENAME
2     GOSOURCEURL
3    GOSOURCEDATE
4        DBSCHEMA
5  GOEGSOURCEDATE
6  GOEGSOURCENAME
7   GOEGSOURCEURL
8 DBSCHEMAVERSION
                                                              value
1                                                     Gene Ontology
2 ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
3                                                          20100320
4                                                             GO_DB
5                                                         2010-Mar1
6                                                       Entrez Gene
7                              ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
8                                                               2.1

Martin
	

>  Thanks again
> 
> Ana
> 
> 
> 
> On Friday 09 April 2010 17:19:25 James W. MacDonald wrote:
>> I think she gives the command below.
>>
>> There is a problem with the form of the call to get(); the keys are of
>> the form GO:0090153, while the key used is missing the colon. So even if
>> the term did exist in the GO.db package, it wouldn't be found using that
>> key.
>>
>> However, I think the real reason this term isn't found is that it is a
>> new term, added after the current version of the GO.db was produced.
>>
>> If you look at the term information on the AmiGO website, the source is
>> stated to be ascb_2009. Since the GO.db package is now 6 months out of
>> date, I wouldn't be surprised if this term were added after we built
>> this package last.
>>
>> Best,
>>
>> Jim
>>
>> Vincent Carey wrote:
>>> What is the exact command you are running that generates the error?
>>> Present it in a way that another person not using your computer can
>>> generate it.
>>>
>>> On Fri, Apr 9, 2010 at 9:17 AM, Ana Conesa <aconesa at cipf.es> wrote:
>>>> Thanks Sean for your fast reply
>>>>
>>>> This is my sessionInfo()
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.10.0 (2009-10-26)
>>>> x86_64-pc-linux-gnu
>>>>
>>>> locale:
>>>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] GO.db_2.3.5         RSQLite_0.7-1       DBI_0.2-4
>>>> [4] annotate_1.24.1     AnnotationDbi_1.8.2 Biobase_2.6.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] xtable_1.5-5
>>>>
>>>>> get('GO0090153',GOTERM)
>>>>
>>>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>>>>  value for "GO0090153" not found
>>>>
>>>> Any hint?
>>>>
>>>> Ana
>>>>
>>>> On Friday 09 April 2010 15:03:20 Sean Davis wrote:
>>>>> get('GO0090153',GOTERM)
>>>>
>>>> --
>>>> Ana Conesa
>>>> Bioinformatics and Genomics Department
>>>> Centro de Investigaciones Principe Felipe
>>>> Avda. Autopista Saler 16,
>>>> 46012 Valencia, Spain
>>>> Phone: +34 96 328 96 80
>>>> Fax:   +34 96 328 97 01
>>>> http://bioinfo.cipf.es/aconesa
>>>> http://www.blast2go.org
>>>> ==========================================
>>>> FIRST INTERNATIONAL COURSE IN AUTOMATED
>>>> FUNCTIONAL ANNOTATION AND DATA MINING
>>>> Valencia/Orlando, September/October 2009
>>>> http://bioinfo.cipf.es/blast2gocourse
>>>>
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>>>
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> 
> 
> 
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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