[BioPython] Adding new database types to EUtils

[Sean Davis]

On Tue, Dec 4, 2007 at 9:49 AM, Luca Beltrame <luca.beltrame at unimi.it> wrote:
> Il Tuesday 04 December 2007 14:35:13 hai scritto:
>
>> release.  I have thought about making a python-based version, but I find R
>> a much more compelling framework for statistical computing and array-based
>
> I think it is mostly a matter of personal preference. I turned to Python (but
> I have been using GEOquery in the past) because I like the language more than
> R.
>
>> Metadata (and not values), then URLs can be constructed against their web
>
> I guess I did not make the statement clear enough in my original mail. Yes, I
> meant to fetch only the metadata because I wanted to gather the experiment
> descriptions from all the accessions I had (a rather large number) in order
> to look through them without having to query for each one.
> I will try looking at the queries via web and see if I can write something
> useful (although I still think that, as basic as it is, it would be nice to
> have EUtils GEO support in Bio.EUtils, at least for the metadata).
>
>> I'm not sure that exactly the same functionality is available via Eutils,
>> but I think not.
>
> I have played a bit with EUtils, but I haven't yet been able to use esearch to
> work with a GEO accession. Since I have just looked at them briefly, I can't
> guarantee it was just a mistake on my part, though.

This is a pretty old post, I know, but I thought I would toss in some
new information here.  We have parsed all of the GEO metadata into a
MySQL database which can be queried directly here:

http://meltzerlab.nci.nih.gov/apps/geo

In addition, for those who want programmatic access, on the same page
is a SQLite database file with the same information.  It can be used
from python (or any other language with SQLite bindings) for SQL-based
queries of GEO metadata.

Sean