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

Fri Apr 9 17:30:45 CEST 2010

 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)
 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
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > 	[[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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
==========================================
-------------- next part --------------
 Error	in	getGOParents(x)	:	GO:0004299	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0005837	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008575	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030693	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044281	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006803	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006118	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044283	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044282	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071103	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006441	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006510	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004680	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004682	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070925	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071554	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006512	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003754	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090066	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071174	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071173	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0015482	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003773	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071212	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071216	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071496	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071514	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003763	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090092	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003929	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003926	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0045045	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008605	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003936	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0005065	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071555	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070972	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071539	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070993	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008248	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006371	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070897	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0005551	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030508	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003685	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004239	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003901	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004681	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004600	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0042027	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0045034	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004229	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008567	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003928	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004213	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006804	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070918	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071359	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071310	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003208	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003206	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003205	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003231	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003229	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003321	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044212	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090100	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0061008	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003333	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070997	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090079	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071375	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071495	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003158	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003401	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003254	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090218	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071445	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003407	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090087	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0060986	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071378	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0060969	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0060968	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071466	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090224	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003338	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0060993	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090181	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090101	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071385	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071384	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071383	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071158	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090068	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071156	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0000051	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090077	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003341	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003352	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003228	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003209	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003230	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071256	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070988	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071322	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090130	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044179	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0070938	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090162	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030161	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090109	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044215	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044216	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044217	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0044182	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004263	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0019131	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030188	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004192	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004218	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004295	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008133	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003818	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004277	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004215	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0050425	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030601	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004214	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004228	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003816	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004281	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008464	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004186	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0016512	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004240	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0090174	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003804	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004286	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030189	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004230	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004276	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0016919	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030602	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004246	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004217	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003815	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004237	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008451	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004289	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008125	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003812	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008067	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008581	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003817	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071267	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0071265	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004238	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008423	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0017114	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0005061	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004231	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008132	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0006125	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0016804	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004254	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003160	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003157	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003159	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0042315	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0050517	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0042576	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0008472	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004287	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030019	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030191	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003803	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0030192	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0005155	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004278	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004178	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0003802	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0017165	is	not	a	member	of	any	ontology
Error	in	getGOParents(x)	:	GO:0004182	is	not	a	member	of	any	ontology