Is it possible to load PSI-MI data into chado

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Is it possible to load PSI-MI data into chado

longbow leo
Hi,

PSI-MI is "Proteomics Standards Initiative-Molecular Interactions", which provides a standard for protein-protein interaction records. The website is http://www.psidev.info/ and there are two file formats available: tabular-delimited file (PSI-MITAB) and XML (PSI-MI XML).

Details:

PSI-MITAB: http://wiki.reactome.org/index.php/PSI-MITAB_interactions

PSI-MI XML: http://www.psidev.info/index.php?q=node/60

Are there any modules of Chado ready to install this kind of data? How about the related loader?

If there is no module or scripts available, how could I begin to do this?

Thanks!


Haizhou Liu


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Re: Is it possible to load PSI-MI data into chado

Dave Clements, GMOD Help Desk-3
Hi Haizhou,

I'm not a proteomics person, but I will take a stab at your questions.  First, I doubt that there are any existing scripts to load PSI formats into Chado.  This is the only mention I can find of "PSI" on this list, ever.  I think this means we don't have an established way to do this.

However, it doesn't seem like a stretch to me at all to store this type of information in the sequence module.  At a high level, proteins are derived from genomic regions and thus qualify as features in the Chado model.  Interactions are relationships between proteins/features and would thus become feature relationships in Chado.  This should work fine as the interactions are already defined in an ontology and thus can be loaded into the CV module.

So, at a high level, I think we're on solid ground.  I suspect that the challenge will happen with the details.  I haven't looked at the PSI formats in details, but it may be that many of the attributes will become feature relationship properties in Chado.  That's workable, but may be unattractive if most data ends up in a property table.


Anyone else have thoughts on this?

Thanks,

Dave C.


On Tue, May 25, 2010 at 12:25 AM, longbow leo <[hidden email]> wrote:
Hi,

PSI-MI is "Proteomics Standards Initiative-Molecular Interactions", which provides a standard for protein-protein interaction records. The website is http://www.psidev.info/ and there are two file formats available: tabular-delimited file (PSI-MITAB) and XML (PSI-MI XML).

Details:

PSI-MITAB: http://wiki.reactome.org/index.php/PSI-MITAB_interactions

PSI-MI XML: http://www.psidev.info/index.php?q=node/60

Are there any modules of Chado ready to install this kind of data? How about the related loader?

If there is no module or scripts available, how could I begin to do this?

Thanks!


Haizhou Liu


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