[BioC] AnnBuilder questions...

[Dipl.-Ing. Johannes Rainer]

this sounds nice!

i will try it and report the outcome to you,
thanks, jo

Quoting Steffen Durinck <sdurinck at ebi.ac.uk>:

> Hi,
>
> If you want, you could also try out the biomaRt package see 
> developmental packages. biomaRt retrieves its annotation via direct 
> mysql queries to Ensembl. I don't know if that goes through your 
> firewall...
> rat2302 is present in Ensembl so you could query that for annotation 
> such as gene information, go, sequence,snp,... Ensembl also has 
> entrez-gene id's  (in the package they are still called locuslink but 
> in the database they are already entrez-gene).
> This package is still in an early phase so if you decide to use it 
> and have any comments, those would be very helpful for directing 
> further development.
>
> Below an example for rat230_2..
>
> Cheers,
> Steffen
>
> >library(biomaRt)
> > mart<-martConnect()
> -  Connected to ensembl_mart_29, ensembl_mart_29, ensembl_mart_29 and 
> ensembl_mart_29 -
>
> > getGene(id="1370752_a_at",array="rat230_2",mart=mart)
> An object of class "martTable"
> Slot "id":
> [1] "1370752_a_at"
>
> Slot "table":
> $symbol
> [1] "P53_RAT"
>
> $description
> [1] "CELLULAR TUMOR ANTIGEN P53 (TUMOR SUPPRESSOR P53). 
> [Source:SWISSPROT;Acc:P10361]"
>
> $band
> [1] "q24"
>
> $chromosome
> [1] "10"
>
> $start
> [1] 56420181
>
> $end
> [1] 56424324
>
> > getGO(id="1370752_a_at",array="rat230_2",mart=mart)
> An object of class "martTable"
> Slot "id":
> [1] "1370752_a_at" "1370752_a_at" "1370752_a_at" "1370752_a_at" 
> "1370752_a_at"
> [6] "1370752_a_at" "1370752_a_at"
>
> Slot "table":
> $GOID
> [1] "GO:0003700" "GO:0005634" "GO:0006350" "GO:0006355" "GO:0006915"
> [6] "GO:0045786" NA
>
> $description
> [1] "transcription factor activity"
> [2] "nucleus"
> [3] "transcription"
> [4] "regulation of transcription, DNA-dependent"
> [5] "apoptosis"
> [6] "negative regulation of cell cycle"
> [7] NA
>
> $evidence
> [1] "IEA" "IEA" "IEA" "IEA" "IEA" "IEA" NA
>
> $martID
> [1] "ENSRNOG00000010756" "ENSRNOG00000010756" "ENSRNOG00000010756"
> [4] "ENSRNOG00000010756" "ENSRNOG00000010756" "ENSRNOG00000010756"
> [7] "ENSRNOG00000010756"
>
>
>
>
>
> Dipl.-Ing. Johannes Rainer wrote:
>
>> hi,
>>
>> i wanted to build an annotation package for the Affymetrix rat2302 
>> chip. because i have problems to access ftp servers through the 
>> http_proxy i am behind (it works perfectly with http, but not 
>> through the ftp protocol) i downloaded the LocusLink and UniGene 
>> database files and created my UG and LL objects with the option 
>> "fromWeb=FALSE". i supposed that it would work, but i got an error 
>> "could not open connection to 
>> ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i supposed the 
>> function would not try to establish connections to the internet when 
>> i submit the attribute fromWeb=FALSE and define a local url 
>> beginning with file:// . maybe this is a bug, it may be better if 
>> one can submit also the url of a local info file to get the 
>> information about the built that was used... i wrote a wrapper 
>> function that overwrites the getUGBuilt() function to read a local 
>> info file, but it took me some time to understand why the call 
>> everytime failed
>>
>> another question: locuslink has been substituted by the Gene 
>> database... are there plans that AnnBuilder will annotate using the 
>> new database?
>>
>> thanks, jo
>>
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>>
>
>