[Bioperl-l] parsing xml output

[Christopher Fields]

Um, I don't think it works that way.  I'm pretty sure the XML is generated from 
the ASN1 output.  I don't think (like Warren says) that you can directly get to the 
tax information.  Indirectly is another matter...

Chris

---- Original message ----
>Date: Fri, 19 May 2006 14:42:09 -0600
>From: Hubert Prielinger <hubert.prielinger at gmx.at>  
>Subject: Re: [Bioperl-l] parsing xml output  
>To: Warren Gish <gish at watson.wustl.edu>, bioperl-l at bioperl.org
>
>hi warren,
>that means if I alter the DTD (if that is possible) by adding the 
>taxonomic id to the DTD..... then I should have the taxonomic id tag in 
>the xml file (theoretically)
>but I guess this is only possible with a local search (blastall) but not 
>with an online search.
>
>greetings
>
>Warren Gish wrote:
>>
>> On May 19, 2006, at 11:52 AM, Hubert Prielinger wrote:
>>
>>> hi,
>>> I wondered whether is it also possible in the xml output (either WU 
>>> or NCBI - Blast) to get the species (taxononmy) for every hit, if I 
>>> do a general search.
>>> regards
>>>
>> The taxonomic id is not an entity in the NCBI XML DTD.  If the 
>> information was embedded in deflines, one could conceivably parse for 
>> it, but I believe the NCBI only distributes taxids in their ASN.1 data 
>> and in their pre-formated BLAST databases, and NCBI BLAST only reports 
>> taxids in its ASN.1 output format, where taxid is available as an entity.
>>
>> --Warren
>>
>>
>
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