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include-dcc / include-linkml

LinkML Schema for INCLUDE DCC
https://include-dcc.github.io/include-linkml/
MIT License
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Last updates before major release #181

Closed lopierra closed 1 month ago

lopierra commented 2 months ago

Hi @madanucd - I made the updates to Study/Dataset (and other components) that we've been discussing over the past few weeks - see commit messages. Let me know if you notice anything I missed.

Also, would you mind generating the schema and pydantic to make sure we don't have any errors in the YAMLs? I realized I haven't actually installed LinkML on my new laptop, but I don't want to hold up the release. Thank you!

twhetzel commented 2 months ago

@lopierra how soon do you need this reviewed?

lopierra commented 2 months ago

Sometime next week, if possible? It would be good to have a major release of the LinkML model to coincide with our next release of the Data Hub

madanucd commented 1 month ago

@lopierra Participant and Sample IDs: Is it advisable to incorporate both External and Global IDs for participants and samples within the Biospecimen, DataFile, and Participant classes?

Study Expected Number of Participants: What prompted the change of studyExpectedNumberOfParticipants from an integer to a string?

lopierra commented 1 month ago

@lopierra Participant and Sample IDs: Is it advisable to incorporate both External and Global IDs for participants and samples within the Biospecimen, DataFile, and Participant classes?

Study Expected Number of Participants: What prompted the change of studyExpectedNumberOfParticipants from an integer to a string?

Yes, good point.. we should have both Global and External IDs everywhere.

FOr studyExpectedNumberOfParticipants - I meant to change that back to integer but forgot

I will make these changes now

lopierra commented 1 month ago

@madanucd Sorry, I misunderstood your comment initially.. I do think we should include both Global and External IDs since the Global ID is used by FHIR and the External ID is more recognizable for humans. I added participantGlobalId to Condition for consistency.