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

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 >