[Biojava-dev] retrieving species (common name)

[Hubert Prielinger]

hi,
sorry for replying that late,
I have XML blast outputs, which you can retrieve information like 
accession id, protein name, length of sequnence aso....
but there is no possibility to retrieve the taxonomy (especially the 
scientific name or common name)
I need the common and scientific name from each blast hit. I have found 
in biojava-live/src/org/biojava/bibliography/taxa  a few code examples 
that could suit my
task (e.g: simpleTaxon.java)

eg: I have the accession id: YPOL_IBDVS
and I want to get the taxonomy of that protein, not neccessarily the 
entire taxonomy but mentioned above scientific and common name.
and I don't know exactly how to get the taxonomy, it seems that there is 
no directly way from the accession id, but over the taxon id, but I 
don't know how to get that either.....
it must be possible to map the accession id to the taxon id and then 
request with the taxon id the taxonomy, if I get it right.....

thanks in advance
regards
Hubert


Richard Holland wrote:
> I'm not sure what you're asking for here. Could you explain in a little
> more detail? Maybe write some example program code that assumes BioJava
> works the way you'd like it to work in this situation, making up the
> names of classes/methods that you might call in BioJava but don't yet
> exist, then we can help you fill in the gaps. 
>
> cheers,
> Richard
>
> On Mon, 2006-06-05 at 16:49 -0600, Hubert Prielinger wrote:
>   
>> hi,
>> Is it possible with biojava to retrieve the species not the entire 
>> taxonomy, only the common name if I only have the accession id or the 
>> name of the protein and if yes
>> how to start.....
>> In my case:
>> I would retrieve the accession id from my local database then assign as 
>> parameter to the program, retrieve common name and write the common name 
>> back into the database....
>> the thing I want to know is the retrieving possible with biojava?
>>
>> thanks for help
>>
>> Hubert
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