[Bioperl-l] PubMed records (was: MeSH terms)

Robert Bradbury robert.bradbury at gmail.com
Sun Oct 25 09:03:18 EDT 2009

On Sun, Oct 25, 2009 at 7:12 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Isn't this exactly what the NCBI's ELink is for?
> (snip)

Interesting.  I knew they had some of this but I didn't know they had
extended it so far (obviously the cloud of computers normally running blast
searches is keeping itself busy when there is nothing better to do).

[Aside: Does anyone know exactly what NCBI's computing capacity is?  Or how
this compares with the other major sites (Ensembl, Sanger, Broad, UCSC)

Now, extending Brian's helpful comment, is there anything within BioPerl or
CPAN in general which can take the "link cloud" and extend it into "degree
of connectivity cloud".  If anyone has ever used the Linux utility
"etherape" they will have an idea of what I'm talking about.  Etherape
displays the local network traffic in a grapical format with nodes for which
machines are communicating with each other and colors, sizes and brightness
of the links between them representing the traffic type, amount and age of
the communications.  I'm sure that agencies which shall not be named have
similar display programs which deal with the quantity and type of "chatter"
between "persons of interest".  This is all pretty standard stuff from a
"network graph" standpoint.

This type of graphical information can be highly useful from a "systems
biology" standpoint as well as an educational standpoint when one wants to
understand something like the components of a protein complex, the time
domain of gene expression, the activity of research in an area, etc.

So if the information is available I'm wondering what the tools are to make
it useful?  With the amount of computing power now available to home users
now one could begin to think of very creative ways of using this type of
information from a data mining standpoint.


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