[Bioperl-l] PDB Parser

Bernd Mueller bernd at kirx.de
Mon Aug 20 15:03:29 EDT 2007


I attached my script.

Actually I tried to download all articles to a certain search term with
that script. The problem was that the retrieved documents were not free
as mentioned in the documentation of EUtilities on the NCBI page. So
many of the downloaded documents in xml-format were just dummies
containing only the abstract but not the fulltext article.

Bernd

Chris Fields wrote:
> Just curious, but what kind of query were you trying?  It might be worth 
> trying to work through it to add as an example to the cookbook page.
> 
> chris
> 
> On Aug 20, 2007, at 11:57 AM, Bernd Mueller wrote:
> 
>> Hello,
>>
>> Maybe you wanna try the Database-EUtilities module from bioperl. They
>> are described on http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
>>
>> I tried them for a similar search on pubmed but without any reasonable
>> results because my target was too focused.
>>
>>  From EUtilities documentation on
>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpentrez.section.EntrezHelp.The_Databases 
>>
>>
>> "Protein Database
>>
>> The Protein database contains sequence data from the translated coding
>> regions from DNA sequences in GenBank, EMBL, and DDBJ as well as protein
>> sequences submitted to Protein Information Resource (PIR), SWISS-PROT,
>> Protein Research Foundation (PRF), and Protein Data Bank (PDB)
>> (sequences from solved structures). "
>>
>> So PDB is included in eutilities from NCBI.
>>
>> Regards,
>> Bernd
>>
>> neeti somaiya wrote:
>>> Thanks for your response.
>>> Actually I am looking for something standalone and not on the web, as in
>>> something which I can download onto my machine and parse later to get 
>>> id and
>>> title.
>>>
>>> On 8/20/07, Oliver Wafzig <Oliver.Wafzig at sygnis.de> wrote:
>>>> On Monday 20 August 2007 06:33, neeti somaiya wrote:
>>>>> Another question I had was, I am interested only in pdb id and title,
>>>> and
>>>>> for this I am downloading and unzipping each of the full pdb structure
>>>>> files, parsing to get just id and title. Is there any other data 
>>>>> source
>>>> Hi Neeti,
>>>> this is a non bioperl way to download the data.
>>>> Use the SRS server on the EBI page to download only id and title lines
>>>> from
>>>> pdb.
>>>>
>>>> 1) Point your browser to the SRS page (http://srs.ebi.ac.uk).
>>>> 2) Search for 'PDB' on the 'library page' and select it.
>>>> 3) Use the standard query form. Select 'id' in the dropdown list and
>>>> insert '*' (wildcard).
>>>> 4) Create a view by selecting 'ID' and 'Title', then click the search
>>>> button.
>>>> 5) Click the save results button.
>>>> 6) Select 'file' in the 'output to' area and 'ALL' in the 'Number of
>>>> entries
>>>> to download' field. Press 'save'.
>>>>
>>>> If the download is slow, read the 'download tips' on the download 
>>>> page and
>>>> split the results in chunks.
>>>>
>>>> -- 
>>>> Oliver
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>>
>>
>> --Dipl.-Inform.(FH)
>> Bernd Mueller
>> phone: +49 179 2336692
>> email: bernd at kirx.de
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> 
> 

-- 
Dipl.-Inform.(FH)
Bernd Mueller
phone: +49 179 2336692
email: bernd at kirx.de


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