[BiO BB] extracting data from NCBI taxonomy

[Lipika Ray]

Hi Malcolm,

Thanks a lot! Now I get my required results.
Thanks again.

Lipika Ray
Postdoctoral Fellow
SUNY, UAlbany

>
>You will need to script eutils
>http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
>
>For starters:
>
>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&ter
>m=txid7711[Organism:exp]&rettype=count
>
>tells you there are 902185 such proteints
>
>You can then get any subrange of those 902185 of them with URLS.  For
>instance, you can get the second 50 such gi numbers (in wordy xml) in
>your browser using
>
>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&ter
>m=txid7711[Organism:exp]&retstart=51&retmax=50&rettype=uilist
>
>however, "The maximum number of retrieved records is 10,000."
>(http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html)
>
>So you need a loop, so you need a script (which you'll need to parse the
>wordy xml anyway), which means you will need to study eutils a little
>more and learn how to use the web environment feature.

>I don't think there is another way, but I hope I can be proved wrong.
>
>Cheers,
>
>Malcolm Cook