Question: PSICQUIC - Provide own local database of interactions
0
16 months ago by

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

gene network psicquic • 389 views
modified 16 months ago by Paul Shannon370 • written 16 months ago by badredda0
Answer: PSICQUIC - Provide own local database of interactions
1
16 months ago by
Paul Shannon370
Paul Shannon370 wrote:

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


Dear Paul,

Thank you for your reply and sorry for the late comment ! I will check it as soon as possible and explore the package.

Best regards,

Alaa

Dear Paul,

You have mentioned about an earlier version that gives us the possibility to include our interactions using an RData file with the right format. Could you provide to me please this RData file ?

Thank you for your offer to help Paul but I wouldn't want to bother you with such a task as I want to explore it myself and learn. Thanks in advance !

Best regards,

Alaa