[BioC] Error in BioMart and wormbase

[Marc Carlson]

Hi Christof,

I am not sure what sort of data you were looking for from biomaRt, but
there is also an organism annotation package for worm.

http://www.bioconductor.org/packages/release/data/annotation/html/org.Ce.eg.db.html


  Marc



Christof Winter wrote:
> Dear Steffen,
>
> I had the same problem as Ana. I did as you suggested and installed
> the dev version of biomaRt (downloading the .tar.gz and installing
> with R CMD INSTALL, running Debian Linux). Now I cannot even connect
> to BioMart anymore (I checked with another machine, there connecting
> still works, so it's not BioMart being down):
>
> > library(biomaRt)
> > listMarts()
> Error in value[[3]](cond) :
>   Request to BioMart web service failed. Verify if you are still
> connected to the internet.  Alternatively the BioMart web service is
> temporarily down.
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i486-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_1.99.4
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-0 XML_1.99-0
>
> After getting this error, i also installed the dev versions of the
> packages XML and RCurl, but the error remains.
>
> Do you have any idea how to solve this? Could it be because of the
> base package "methods", which is not dev as well?
>
> Thanks,
> Christof
>
> steffen at stat.berkeley.edu wrote, On 28.01.2009 06:37:
>> Dear Ana,
>>
>> It looks like there is a problem with the XML configuration file for
>> that
>> dataset.  If you upgrade to using the dev version of biomaRt
>> (http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should
>> be fine for this dataset, as that version does not depend on this XML
>> file
>> anymore.
>>
>> worbase_gene works for me see below:
>>
>>> library(biomaRt)
>>>
>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")
>>
>> Checking attributes ... ok
>> Checking filters ... ok
>>> att = listAttributes(wormbase)
>>> att[1:10,]
>>                 name                          description
>> 1            species                              Species
>> 2               gene                           Gene WB ID
>> 3      sequence_name                 Sequence Name (Gene)
>> 4        public_name                     Gene Public Name
>> 5                cds                  Sequence Name (CDS)
>> 6           cgc_name                        Gene CGC Name
>> 7         transcript           Sequence Name (Transcript)
>> 8        name_dmlist                  Gene Names (merged)
>> 9         cds_dmlist        Sequence Names (CDS) (merged)
>> 10 transcript_dmlist Sequence Names (Transcript) (merged)
>>
>>> sessionInfo()
>> \R version 2.8.0 (2008-10-20)
>> powerpc-apple-darwin8.11.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] biomaRt_1.99.4
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.92-0 XML_1.98-1
>>
>>
>>
>>> Dear all,
>>>
>>> I've been experience a problem with BioMart when I tried to access
>>> wormbase. I am getting an error when I tried to use a specific dataset
>>> (wormbase_gene). This problem do not exist when I access any other
>>> dataset from wormbase. Besides, few months ago a used this code without
>>> problems.
>>>
>>>
>>>> library(biomaRt)
>>>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")
>>> Checking attributes and filters ...Error in if (xmlGetAttr(xml,
>>> "displayType") == "list" && type != "boolean") options =
>>> parseOptions(xml) :
>>>   missing value where TRUE/FALSE needed
>>>
>>>> listDatasets(wormbase)
>>>                 dataset        description version
>>> 1        wormbase_paper              Paper
>>> 2         wormbase_gene               Gene
>>> 3 wormbase_anatomy_term       Anatomy Term
>>> 4 wormbase_expr_pattern Expression Pattern
>>> 5      wormbase_go_term            GO Term
>>> 6         wormbase_rnai               RNAi
>>> 7    wormbase_phenotype          Phenotype
>>> 8    wormbase_variation          Variation
>>>
>>>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper")
>>> Checking attributes and filters ... Ok
>>>
>>>
>>>
>>> I will appreciate any help.
>>>
>>> Ana.
>>>
>>>
>>> ##############################
>>>> sessionInfo()
>>> R version 2.8.0 (2008-10-20)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MON
>>>
>>> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
>>>
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>> other attached packages:
>>> [1] biomaRt_1.16.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_0.91-0 XML_1.94-0.1
>>>
>>> _______________________________________________
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>>
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>
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