Dear Bioconductor community,

I have recently started using PSICQUIC (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml) to produce an integrative network of multiple -omics datasets. I would like to know i) if there's any way to provide our own database of interactions to PSICQUIC that is available locally on our server; ii) some services are offline and PSICQUIC can't reach them; could we, for example, download the databases from the main website of these offline services and provide them to PSICQUIC locally ? Thank you in advance.

Best regards,

Alaa

Hi Alaa,

You may find the Bioconductor RefNet package fits your needs.  It is a wrapper around PSICQUIC and it provides a straightforward method for adding your own interactions.   Inspired by PSICQUIC, RefNet defines a data.frame format.

These interactions have been expressed in the standard RefNet 19-column format for easy querying, as explained in the vignette.  

The only wrinkle is that "extra" sources - other than PSIQUIC - must currently come from the bioc annotationHub.  In an earlier version, an RData file holding a data.frame of the right format could also be used.   We could probably restore this quite easily.  Let me know if you would like me to give this a try, perhaps with a sampling of your  new interactions.

These are the fields (columns) needed in a data.frame for incorporation in RefNet.  They are inspired by PSICQUIC.

* a.canonical
* b.canonical
* relation
* bidirectional
* detectionMethod
* pmid
* a.organism
* b.organism
* a.common
* a.canonicalIdType
* b.common
* b.canonicalIdType
* cellType
* a.modification
* a.cellularComponent
* b.modification
* b.cellularComponent
* provider
* comment