UDP/Patient pages on the new site

monarch-initiative / monarch-ui

The previous version of the Monarch Initiative website

https://previous.monarchinitiative.org/

BSD 3-Clause "New" or "Revised" License

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UDP/Patient pages on the new site #199

Closed kshefchek closed 5 years ago

kshefchek commented 5 years ago

Should we be moving our UDP patient pages to the new site? For example, https://monarchinitiative.org/case/:MONARCH:c000017

https://github.com/monarch-initiative/operations/issues/113

monicacecilia commented 5 years ago

@mellybelly says: we should indeed migrate these pages over to the new website. To do so,

[ ] First: we should port these pages over in their current state.
- [ ] We need to update the data from UDP. (@kshefchek - UDP API is still down)
- [ ] Give the pages a minor face lift, adding an icon for 'patient pages,' other things? @mellybelly please comment
After v1.0 release, we should work on improving how we offer patient pages throughout the site by:
- Adding new pages from UDN,
- Adding the ones from MyGene2
- Maybe also adding new ones from Genomics England
- Maybe also adding new ones from SolveRD

monicacecilia commented 5 years ago

@kshefchek How are these pages generated? I imagine this is not static, we're pulling the patient pages. -- would you be able to please point @iimpulse in the right direction to look at including these pages in beta?

kshefchek commented 5 years ago

this would be driven by the biolink endpoints starting with 'case', for example:

https://api.monarchinitiative.org/api/bioentity/case/%3AMONARCH%3Ac000017/phenotypes?rows=100&facet=false&unselect_evidence=false&exclude_automatic_assertions=false&fetch_objects=false&use_compact_associations=false

It's odd that these ID's are indexed as :MONARCH:{id}, for example, :MONARCH:c000017. Given our curie map that should resolve to https://monarchinitiative.org/MONARCH:c000017, which doesn't resolve, but https://monarchinitiative.org/:MONARCH:c000017 does

kshefchek commented 5 years ago

see https://beta.monarchinitiative.org/MONARCH:c000017

monicacecilia commented 4 years ago

@kshefchek,

does the current page satisfy all of @mellybelly's requests (listed above)?
I see that the new page does not include the ability to download phenopackets, phenotypes and variants. Do we have plans to update this? Or did you and Melissa had a discussion about these and decided to do away with them?

kshefchek commented 4 years ago

does the current page satisfy all of @mellybelly's requests

Nope, none of these boxes can be checked at the moment - minor facelift is subjective, but we do not have a special icon for patient pages (@jmcmurry ?)

I see that the new page does not include the ability to download phenopackets, phenotypes and variants. Do we have plans to update this? Or did you and Melissa had a discussion about these and decided to do away with them?

The legacy site exports a very old version of phenopackets on patient pages, we also have tsv download buttons on every table. The new UI does not have either of these, but we should plan for them (especially the tsv's are useful)