unmarshalling XML

[iain.d...@gsk.com]

I am about to create some code to preprocess PSI-MI document before they are imported into cPath, adding new ids etc.  I was about to start playing with castor/apache digester to turn the xml into usable objects, when I realised you must do something similar in cPath.

I know that you supply your xml unmarshalling classes as a jar rather than as source code, so I was wondering if these are supplied as source with any other projects?

I understand if this is intellectual property you wish to keep ownership of, I was just looking not to re-invent something already in existence.

Many thanks

Iain

[Gary Bader]

Hi Iain,
Yes, we have castor generated code for dealing with PSI-MI XML as
part of our data services library, which we keep separate from cPath so
that it can be used in other projects (e.g. Cytoscape). It is also
open-source, but we haven't posted it on the web yet. Ethan did the
castor mapping, which required some special castor configuration options
and some tweaks to the generated code to avoid name clashes, etc. I
temporarily posted the code here:
http://www.cbio.mskcc.org/~bader/pub/personal/soft/

but we'll work to get it up on a real website. Let us know if you have
any problems with the code.

You might be generally interested in the data service code, which
currently supports PSI-MI level 1, but will be eventually expanded to be
a general interface to other PSI-MI levels and BioPAX.

Best,
Gary

[iain.d...@gsk.com]

Thanks for the code Gary.

Hopefully I'll be able to play with it next week. Thanks for the offer, I'll let you know if I get truly stuck using it.

Many thanks

Iain

"Gary Bader" <ba...@cbio.mskcc.org> 12-Jan-2005 15:41 Please respond to cpat...@googlegroups.com

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