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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Different number of PanelApp panels in /api and /WebService paths #4988

Open Jakob37 opened 21 hours ago

Jakob37 commented 21 hours ago

I am investigating starting to run Scout's built in method to update the PanelApp Green panel, similarly to how we are updating the OMIM-AUTO panel.

When looking closer, I found that although most genes are shared between our panels, a significant number differ. We have a few hundred additional genes in our local panel, while missing a handful. (Both end up ~4000).

Looking closer, the difference seems to be where we access the PanelApp services.

Scout it seems is using this one end-point to grab panels (yielding 175 panels):

While in Lund we are using the /api end points. The panel ones here yields 400+ panels:

Looking at the names, the 400+ is mostly (except one panel) a superset of the 175 ones.

Are you guys familiar with this difference? Any reason for why you are getting the data from the /WebServices URL rather than the /api? Unsure whether I am overlooking something fundamental here 🤔 Would like to start using the Scout-based PanelApp Green update tool, but would of course need to understand where all the panels and genes go first ...

dnil commented 20 hours ago

Thats a bit odd, thank you for checking! From a cursory look I have the feeling the "api" urls are their new API, and "web services" the old one. But the latter has not been discontinued, and certainly returns also new updates, so the difference in retrieval is not super clear. There is some mention of "old style" and "new style" panel ids. Let's check some FAQs and then ask them?

dnil commented 20 hours ago

A clue might also be found in the signed-unsigned panels? The official NHS signed ones are somewhere around 175 (173?). EDIT: scratch that, old new - they are way more now (300).

Jakob37 commented 20 hours ago

From a cursory look I have the feeling the "api" urls are their new API, and "web services" the old one. But the latter has not been discontinued, and certainly returns also new updates, so the difference in retrieval is not super clear.

Yes, I got the same feeling.

There is some mention of "old style" and "new style" panel ids. Let's check some FAQs and then ask them?

Sounds good!

I'll poke around a bit more in the JSON-data as well and see if some more patterns emerge.

Jakob37 commented 19 hours ago

Under API on the main site, it seems they are pointing towards using the Swagger (i.e. /api) endpoint:

https://panelapp.genomicsengland.co.uk/

Didn't find anything about the WebServices.

Anyway, I'll send them an email and ask!