[BiO BB] Programmatic access to pubmed

[Manjula P. Thimma]

Dear Dr.Christoph,

Thanks for the message. I tried to access the application(not sure it is a
downloable java app with jar or web-based app), via the link you gave. It
invariably takes me to a 3-D protein structure viewer!.

Could you please let me know, how do I get hold of this tool?

Best Regards
Manjula


On 4/29/10 11:47 AM, "Dr. Christoph Gille" <christoph.gille at charite.de>
wrote:

> 
> In our team we reconstruct metabolic networks and therefore we need to screen
> hundreds of pubmed references to find evidences for certain
> metabolic reactions in the literature.
> 
> We use this simple Java-application:
> http://www.bioinformatics.org/strap/strap.php?pubmed=t
> 
> We proceed as follows:
> We make a list of Pmid-numbers.
> 
> We move the mouse over the list and then we go for a coffee to
> give the system sufficient time to cache the Abstracts.
> 
> Then we move again the mouse over the list of PMID numbers.  This
> time we observe color text high-lightings (defined by
> Ctrl-F "Find") to appear in the abstract panel.
> 
> If abstract is too big, then the high-lightings may appear in the
> vertical scroll-bar of the text panel.
> 
> 
> The system might automatically identify full text links by following the links
> provided by NCBI.
> In all cases PDF can be manually associated.
> 
> In this case this visual text-mining can be performed for full text.
> 
> 
> 
> http://www.bioinformatics.org/strap/strap.php?pubmed=t
> 
> Appart from this, professional Literature managers such as Jabref or Mendeley
> are able to load lists of pubmed abstracts.
> 
> 
> 
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