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Question: PSICQUIC - Provide own local database of interactions
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gravatar for badredda
14 days ago by
badredda0
badredda0 wrote:

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

ADD COMMENTlink modified 13 days ago by Paul Shannon350 • written 14 days ago by badredda0
1
gravatar for Paul Shannon
13 days ago by
Paul Shannon350
Paul Shannon350 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
ADD COMMENTlink written 13 days ago by Paul Shannon350

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

ADD REPLYlink written 8 days ago by badredda0

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

ADD REPLYlink written 7 days ago by badredda0
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