MGI plugin for BIoGPS

[Dan Beisner]

Hi all,

 

I might be wrong on this, but I was pretty sure the MGI plugin used to be populated when you clicked on a human gene but it appears to no longer be the case.  Is that something that has changed recently?  Would be great to get it back if possible.

 

Thanks,

Dan

 

 

Dan Beisner

Senior Scientist

Vividion Therapeutics

10550 Torrey Pines Rd

San Diego, CA 92037

(858)784-2969

 

[Dan Beisner]

Slight follow up on issue from yesterday.  We have an informatics person in our group who set up  an autolink to BioGPS in a list of hit genes for a screen we’ve done.  He uses the Ensembl ID for the BioGPS search.  This used to pull up multiple species if there were homologues, but it now only pulls up the human one. 

 

Best,

Dan

[G Tsueng]

Hi Dan,

Thanks for reaching out to us.  Can you tell me when the last time you were able to get the MGI plugin in BioGPS to behave as you described?

To my knowledge, BioGPS has given species-specific results when species-specific identifiers (entrez gene id, ensemble gene id) are used since MyGene.info (was upgraded from V1 to V2 back in 2013). Hence, if the MGI plugin has only recently stopped giving mouse results for human genes, it might have to do with changes to MGI's site itself.  If you prefer to get species-non-specific results, using gene symbols or gene names in your search should do the trick.

To address your second issue, can you clarify what sort of result you were getting when the Ensembl ID was used? Were you getting something like the gene selection page you'd find with a gene symbol? Eg (http://biogps.org/?query=CDK2 ) Were you getting multiple, species-specific gene reports in in different tabs/windows like (http://biogps.org/#goto=genereport&id=1017 and http://biogps.org/#goto=genereport&id=12566 ?)

If you'd just like something like what you'd get with a gene symbol, one way to do so is to have your informatics person use MyGene.info to convert the Ensemble ID to gene name or symbol, and then use those gene names or symbols in biogps deeplinks (http://biogps.org/faq/)


best wishes,
ginger

[Andrew Su]

Hi Dan,

Just to follow up on the first point, I confirmed that this is a bug on our end.  MGI, RGD, Flybase, etc. should all render correctly even when clicking on the human gene.  We are looking into this...

Best,

-andrew

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[Andrew Su]

Hi Dan,

Thanks for the bug report -- the issue has now been fixed.  When viewing a human gene, the plugins for non-human plugins like MGI, Flybase, etc. will now render properly.  Please let us know if that's not the case...

For your help eradicating bugs, may we send you a BioGPS mascot (which doubles as a monitor screen cleaner)?  If so, please email me your mailing address and mascotpreference (http://sulab.org/2008/12/biogps-swag-just-in-time-for-the-holidays/) directly to me (off list).

Best,

-andrew