[Biopython-dev] KEGG support

[Giovanni Marco Dall'Olio]

On Wed, Feb 10, 2010 at 7:30 PM, Renato Alves <rjalves at igc.gulbenkian.pt>wrote:

> KEGG support in Biopython has been mostly untouched for the past 8 years
> with only a few changes and test additions. There is code in the tree to
> work with the Enzyme and Compound databases but not for others such as
> GENES, ORTHOLOGY, DRUG, ...
>

Hi,
I had a terrible experience with parsing Kegg pathway's files: in the end I
discovered that the files that are stored in their ftp don't correspond
exactly to the diagrams that you can find in the web interface, as for
example biochemical interactions don't have directionality while if you look
at them on kegg/pathway you will see arrows.

Some time ago I proposed to implement something similar to what you have
said for kegg/pathway, but in the end I abandoned the effort, because I had
problem both with suds and SOAPpy, and I wasn't satisfied by the annotations
in KEGG.


>
> Considering the fact that I will need to write some code to work with
> other formats I was planning to contribute and integrate it with the
> SeqIO interface. This will require some additional homework on my part.
>
>
If you are serious about that I may help you, but I can only work on the
weekends and you should tell me exactly what I have to do :-)

KEGG also has a SOAP based API [1]. It's functionality could be in some
> aspects compared to NCBI eutils. Using the python SOAP library suds [2]
> I had no problem interacting with it.
>


Are you sure? I tried it on KEGG an year ago and I was having problems to
execute slightly more complex queries. If you look at suds's bug tracker,
you will find some reports by me, like this one:
- https://fedorahosted.org/suds/ticket/213

I remember that I was looping between the KEGG support centre and the suds
bug tracker; both were very responsive to feedback and very keen to answer
me, but in the end they didn't speak to each other and the bug reports that
I have filed are still unfixed.

Which library can you use for the soap queries? I had the feeling that
SOAPpy (which I think it is included in the standard lib) worked well with
KEGG, however it development has stopped many years ago (
http://sourceforge.net/projects/pywebsvcs/files/SOAP.py/), it is a mess if
you want to use it behind an http_proxy (I should have a patch somewhere if
you are interested) and I am sure it won't be kept compatible with the
future versions of python.

Another alternative may be beautiful soup, but I have never tried it. This
question on stackoverflow may provide you some ideas:
-
http://stackoverflow.com/questions/206154/whats-the-best-soap-client-library-for-python-and-where-is-the-documentation-fo

I am not sure about which is the standard soap library for python, and which
one is included in the standard lib. If you are going to use SOAPpy, it is a
bad bet toward compatibility and maintenance for the future releases. Suds
is the best option but it is not in the standard lib, and they still have to
fix the bugs I have reported an year ago. I have the feeling that there is
no good alternative for python.

Moreover, the WSDL functions that I have seen for KEGG are not especially
useful. They seems to allow for the basic queries, but for most of the tasks
it is better to download the ftp locally and work there.



> So just in case someone was already working on this secretly :) I would
> like to know to make my life easier. If not I would also like to know if
> you would be interested in the addition and finally what's your thought
> about the SOAP interface and the suds (optional) dependency.
>
> Just a word on suds. Even though the project has been around for a few
> years now, it's still not available in most Linux distros. On my
> personal experience with it it's probably the simplest and easy to use
> SOAP library for python out there.
>
> Cheers,
> Renato
>
> [1] - http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
> [2] - https://fedorahosted.org/suds/
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-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it