Investigate adoption/support/applicability of LinkML to maintain schemas for HTAN

[aclayton555]

This following this thread (internal Sage Slack): https://sagebionetworks.slack.com/archives/C01ANC02U59/p1712264979812149

Would be worth chatting with Robert and Anh Nguyet in an upcoming sprint.

[adamjtaylor]

We might also want to see how CoreModels is looking as it gets spun up for Sage over the summer

[aclayton555]

24-11/12 Cross-pollinate efforts with MC2: mc2-center/data-models#148

[aditigopalan]

Working on modularization/ new schema here (using HTAN first): Building up from CDS sequencing/ imaging templates and adding HTAN specific entities if required

[aclayton555]

24-11/12 Close-out: Work ongoing and proceeding into next sprint.

Upcoming conversations with CRDC expected to help clarify which standards will be used for the CRDC Submission Portal so we can gain clarity in mapping. Currently, various sources of truth: latest CDS templates we were previously provided, vs. the CDS Data Model Navigator (https://hub.datacommons.cancer.gov/model-navigator/CDS) vs. the CASDR resources (https://cadsr.cancer.gov/onedata/Home.jsp) vs the prior comparison between CDS and CRDC performed by Kristen: AmandaBell_CDS Template_CDScaDSR_CRDCcaDSR_Jul2024_AB1

[aclayton555]

25-1 Kick-off:

• Migration has been successful, with the CDS-Img template successfully generating. Regarding which standards to map to, CRDC has indicated that the latest CDS template standards are what will be used for the CRDC Submission Portal for now, but we should expect updates/remapping once CRDC settles on updated standards (timeline for this uncertain).
• Upcoming conversation with Tom to discuss any Schematic-related development/feature needs, and overall alignment on LinkML adoption at Sage (with ANV)
• Overall, continue approach of adopting LinkML and building the base foundation for the HTAN2 Data Model. Start with successful adoption of CDS-Seq and CDS-Img templates. Once clinical data RFC has been finalized, the integration of the clinical data schemas will be next. Overall transcription of schemas from HTAN1 and updated RFCs to be informed by attribute usage statistics.

[aclayton555]

2025.01.15 - Notes from our discussion with Tom tracked here and in related DPE ticket here: https://sagebionetworks.jira.com/browse/SCHEMATIC-225?focusedCommentId=232301

Currently some dependencies on DPE to perform gap analysis. @aditigopalan should we move this to Blocked for now? If there are other async updates to capture as we close our 25-1 sprint, can you please add them to this doc

[aclayton555]

25-1 Close-out: WIP comparison of LinkML and Schematic: https://sagebionetworks.jira.com/wiki/spaces/DPE/pages/3856367618/SCHEMATIC-226+Differences+between+Schematic+and+LinkML

Continue to monitor through 25-2/3 sprint.

[aclayton555]

Emerging actions from HTAN Data Model retrospective in August 2024: Support for Multiple Namespaces: Adding support for multiple namespaces and contexts within the data model will allow greater flexibility and reduce constraints on attribute reuse.

Ongoing LinkML exploration - would be helpful to understand if LinkML usage can help address this issue. If not, let's file a separate ticket for potential development in schematic.