Re: [Psidev-ms-dev] mzData issues

[simon a. (B. <sim...@bb...>]

On 15 Dec 2005, at 13:41, Chris Taylor wrote:

> Hiya. The viewer looks nice -- I got it to work with one of the 
> example files (myo_full) and it is clean and simple. No need to RTFM  
> :)

Probably a good job as there isn't a FM yet :)

Actually a couple of reports have suggested that it has problems with 
other mzdata files (it was written using the examples off psidev as we 
use an ABI machine and don't have an official mzData converter yet).  
It would be really useful to get some more examples on the psidev 
examples page from the major instrument manufacturers to help with 
developing mzData tools.


> On PIMS, I saw this first on a poster at BSPR and meant to follow up 
> on a particular issue; are you aware of the FuGE project 
> (fuge.sf.net)? The model will soon be at milestone 2 (hopefully all of 
> the issues sorted, and all the required functionality in).

You mentioned it when we spoke at BSPR.  I have looked at it but 
haven't gone any further in implementing it in PIMS.  The scope of Fuge 
seems to be somewhat larger than what we had intended for PIMS.  PIMS 
is really a glorified sample tracking system which also stores data.  
It does model the experimental process, but in a very simple way.  I'm 
eventually aiming to extend it to store the analysis of MS data as well 
(mzIdent and the like), but trying to strictly model the whole workflow 
would make it more complex than we would either need or want.


> Another thing would be the (very new) FuGO project (ontology). This 
> project needs contributors and in that respect I'm wondering how much 
> of a controlled vocabulary you've accumulated in developing PIMS?

We've incorporated existing ontologies wherever we can (eg Brenda for 
tissues, EBI taxonomy and the appropriate limits from the psidev 
ontology), but haven't developed our own.  FuGO sounds interesting - 
I'm happy to extend our ontology support with whatever comes out of it 
though I don't know how useful I'd be at contributing to the actual 
ontology construction.


> P.S. Where do you put stuff collected through PIMS -- do you have a 
> bespoke repository? Is that public? Is it anything like this: 
> http://www.ebi.ac.uk/pride/ ?

There isn't a central repository - you can download the PIMS server 
from our site and create your own.  I'm aiming to eventually allow 
automated export from PIMS into pride (I think we already collect all 
of the necessary information in a suitable form), but that's still on 
the to-do list.  Our schema is included as part of the PIMS server 
download.

TTFN

Simon.
-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

sim...@bb...
+44 (0) 1223 496463