BioGRID PSICQUIC Registry Entry

[star...@gmail.com]

Hi,

Our entry in the PSICQUIC registry is listed as BioGRID on the official listing here:

http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS

Unfortunately, due to server maintenance issues and the original maintainer of the server moving on, our implementation has not been up and running. I would like to get that corrected, however, but I have a couple of questions I was hoping I could get help with:

1) If I modify our access urls, how do I go about broadcasting this information to the registry under our old listing? I'd prefer if the transition is the least disruptive as possible.

2) Where do I specify things like our snapshot version and tags etc, or is that done manually via the registry entry process?

Thanks in advance for your help.

Chris

[Rafael Jimenez]

Hello Chris,

On 9 August 2013 07:32, <starkfree@gmail.com> wrote:

Hi,

Our entry in the PSICQUIC registry is listed as BioGRID on the official listing here:

http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS

Unfortunately, due to server maintenance issues and the original maintainer of the server moving on, our implementation has not been up and running. I would like to get that corrected, however, but I have a couple of questions I was hoping I could get help with:

1) If I modify our access urls, how do I go about broadcasting this information to the registry under our old listing? I'd prefer if the transition is the least disruptive as possible.

Let us know and we will change the URLs accordingly in the registry. This will propagate to all the clients using the registry like Cytoscape or PSICQUIC view.

 

2) Where do I specify things like our snapshot version and tags etc, or is that done manually via the registry entry process?

Your PSICQUIC service will provide information about the version as well as the number of interactions. ie:

http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/version

http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/*?format=count

Regarding the TAGs, have a look to the TAGs your service has already assigned in the registry...

http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS&name=BioGrid

If there is any addition or change you would like to make let me know. More information about TAGs ...

https://code.google.com/p/psicquic/wiki/PsicquicServiceTags

Regards,

Rafael.

 

Thanks in advance for your help.

Chris

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[star...@gmail.com]

Hi Rafael,

Thanks for the info. Okay, I see my mistake. I thought the version number listed in the registry was our data version and not our implemented version of psicquic :) I've instead added a "build" property to the properties list for that functionality.

We've setup our service here at its new home:

http://tyersrest.tyerslab.com:8805/psicquic/webservices

http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/properties

http://tyersrest.tyerslab.com:8805/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=1000

Please let me know if you notice any problems and feel free to update our links as well in the registry.

Thanks again for your help!

Chris

[Rafael Jimenez]

Hello Chris,

I just had a quick look and it looks good to me. I will proceed to update the registry with the new URL. A part from updating the registry I would like to check with you a couple of details:

I see you are using NCBI gene IDs and BioGrid IDs as primary identifiers. The "Data distribution best practices" guideline suggests to provide a single reference in the the unique identifier column using UniProt or RefSeq. This is just a recommendation aiming to make easier querying and integrating interactions from different services. I imagine for you still makes more sense to use NCBI gene IDs specially for genetic interactions. Looking at your website I see it is possible to search by UniProt and refSeq, so I was wondering, would be possible to add these cross references at least to the alias column?

I see you followed the PSI-MI TAB 2.5 format. This is good, but I was wondering how difficult would be to add some more information following the PSI-MI TAB 2.7 format. https://code.google.com/p/psicquic/wiki/MITAB27Format

Thanks,

Rafael.

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[star...@gmail.com]

Hi Rafael,

Thanks for your help in setting that up. I'll definitely check into the 2.7 format, and if we have access to everything we need to make it a go, we'll incorporate the changes into future updates.

Thanks again!

Chris