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monarch-initiative / phenopacket-store

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
https://monarch-initiative.github.io/phenopacket-store/
BSD 3-Clause "New" or "Revised" License
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WWOX notebooks #25

Closed pnrobinson closed 9 months ago

pnrobinson commented 1 year ago

PMID_25411445 -- this notebook contains data about the PMID_17470496 Is the original file available somewhere?

ldingemans commented 1 year ago

same as #24 probably, so will see if I got the original notebook somewhere - otherwise will recreate it this week

ldingemans commented 1 year ago

uploaded correct notebook with 44ebaa70de46312baa09bbd077e2011966cc963a, but saw now only one variant is added - need to verify that it the two mutations are both in the phenopacket (I think not right now)

pnrobinson commented 11 months ago

Hi @ldingemans I have been working on the pyphetools package and updated many of the functions. I think it is time to start to finalize phenopackets for the final analysis. This is a notebook with the latest version https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/MAPK8IP3/Platzer_2019_MAPK8IP3_PMID_30612693.ipynb Can we touch bases about going through everything and getting phenopackets ready for clustering?

ldingemans commented 11 months ago

Of course, sounds like a good idea - I will send you an email to see when you're available!

pnrobinson commented 9 months ago

@ldingemans updates?

ldingemans commented 9 months ago

@pnrobinson maybe I misunderstood - I send you an email on Sep 20 to try and schedule a meeting, but I did not get a reply I think? I can send you another one to reschedule of course but not sure what is best?

pnrobinson commented 9 months ago

I have revised all of the scripts and notebooks over the last few weeks and added a lot of Q/C code to pyphetools, and I think things are now correct. For now let's concentrate on finishing the analysis. I will continue to add data to the repo.