Fwd: From Uniprot entries to PSI-MI objects

[Dominik Mertens]

Hey guys,

i would like to create PSI-MI files with my interactor proteins by using
information from UniProtEntry objects.
My question is the following: is there an easy way in order to get the
information from a UniprotEntry
object into PSI-MI objects which can then be used to write a well
defined PSI-MI file? organism objects, for example, are not the same for
PSI-MI and uniprotjapi, and taxonomic numbers are not supported in the
uniprotjapi organism object but needed in PSI-MI. Or could it be just
sufficient to reference to the uniprot entry by the xref and leave out
the other information? This would mean that all information needed
afterwards have to be requested by Uniprot webservices and would last a
bit,therefore it is not my preferred way.
If transformation from UniprotEntry to PSI-MI objects would work easily,
i just had to write the ExperimentDescription myself and this would make
automation much easier.

Maybe this question better fits to the uniprot mailing list, but i just
wanted to give it a try in this one. I hope one of you guys is familiar
with this problem.

Thank you for your efforts!

Cheers,
Dominik

[Samuel Kerrien]

Dear Dominik,

First of all, thanks a lot for your interest !

I believe your question is addressed to us correctly, UniProt would probably have directed to us anyways...

As for your questions, I am not aware of code that directly converts a UniProt protein entry into the PSI-MI equivalent (neither for XML nor TAB).

I will consider from this point on that you are talking about PSI-MI XML, should you have meant PSIMITAB, I believe the concepts can be transfered fairly easily.

The mapping between a uniprot entry and a PSI-MI XML interactor [1] is rather straight forward, here are the main things I would consider looking into some of the code we wrote in Intact to convert a UniprotEntry into a light object that extract much of what is needed to fill up an interactor's shortlabel, interactorType, organism, xrefs...

The class is UniprotRemoteService [2], please have a look and let us know if you need more.

You can also find PSI-MI XML examples on our FTP site [3].

I assume to up here that you knew about our PSI-MI XML Java library, if it is not the case, please have a look at it. It is a Maven project, the source code is on SVN: http://psimi.googlecode.com/svn/trunk/psi25-xml

or you can download our last release (1.7.9) with all dependencies: http://code.google.com/p/psimi/downloads/list

Cheers

Sam

[1] http://psidev.sourceforge.net/mi/rel25/doc/#element_interactor_Link03B11FE8

[2] http://goo.gl/Va5dR

[3] ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25/pmid/2011/

[dominik...@biologie.uni-freiburg.de]

Thanks a lot or the quick reply, Samuel! Good to know that IntAct
support works quite well and made the correct decision to choose
IntAct ;-)

If I´m running in any further problems i will let you know!

Cheers,
Dominik