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openvar / VVweb

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Requested features #2

Open Peter-J-Freeman opened 4 years ago

Peter-J-Freeman commented 4 years ago

Hi Teri,

I have been teaching this week and have had a couple of requests. Firstly, can we provide a link to the Ensembl genome browser. I think this is reasonable.

Second, can we link directly to gnomAD? Again, this is reasonable but currently would only be achievable if we are provided with a GRCh37 primary assembly variant description.

I would also like to consider providing a link out to the Decipher browser.

What do you think?

Peter-J-Freeman commented 4 years ago

I think it might also be useful to think about linking out to ClinVar.

Peter-J-Freeman commented 4 years ago

I'm going to poll colleagues to see which resources might be useful. For example, we could also think about linking to VEP.

Peter-J-Freeman commented 4 years ago

Requests from Andrew D.

We ideally need a genome browser embedded for visualisation. This will likely be J-Browse We also need to discuss the tracks we provide in the browser and how the links to external resources may work.

When we provide links, it would be very useful if these were accompanied by the genomic level query, e.g. a link to UCSC could be complemented with chr1:216,595,554. GnoMAD 1-216422237-G-A. This would allow the users to record how they accessed the exrternal resource so that they can do so again.

TeriForey commented 4 years ago

Hi Pete, Could you be more specific please? I.e. for variant NM_000088.3:c.589G>T exactly what links do you need? I've had a quick look at some of the sites you've mentioned and I'm not sure exactly how we'd link to a specific page, or do you just want a selection of links to their search/query page?

I'd like to get the new web version up and running on Lamp158 this week so adding a lot of new tools/browsers might not be possible for this version.

Peter-J-Freeman commented 4 years ago

Hi Teri

Don't worry about this for now. It will be a future release now.

Peter-J-Freeman commented 4 years ago

Move to requested features

https://github.com/openvar/VVweb/issues/6#issuecomment-560355783

Peter-J-Freeman commented 4 years ago

https://github.com/openvar/VVweb/issues/6#issuecomment-562627076