[BioC] network (interaction) data repositories for bioc?

[Wolfgang Huber]

Hi Paul

The RIntact package might be of interest to you:
http://www.bioconductor.org/packages/2.1/bioc/html/Rintact.html

It reads PSI-25 XML from IntAct and with more effort could probably also
be made to read instances of this format from other sources such as Mint
or DIP.

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber



Paul Shannon ha scritto:
> I use a lot of interaction data, assembled from hither and yon and  
> usually
> on an ad hoc basis -- ranging from kinate-substrate relationships in  
> yeast
> to human protein-protein interactions from pulldown experiments.
> Perhaps other do the same, which might mean there's a lot of duplicated
> effort in this area.
> 
> I wonder: is there any bioc effort to collect, curate and organize  
> networks?  I found
> the ppiData in bioc ExperimentData; perhaps that project could be  
> extended?
> Or alternatively, the PSI-MI (The Molecular Interaction XML format  
> from the Human Proteome
> Organization) might suggest good minimal data structures.
> 
> Does bioc have anything like this going on right now?
> 
> Cheers,
> 
>   - Paul
>