ga4gh / ga4gh/phenopacket-schema
Create/Update/Disseminate Export Tools
- Dominant language
- Java
- Stars
- 101
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
Description
FHIR to Phenopackets export
May come from https://github.com/P2GX/phenoboard/blob/main/src-tauri/Cargo.toml
Collab with EPIC (Brooke) and Care Evolution (Benjamin)
OMOP to Phenopackets export
Read: https://pubmed.ncbi.nlm.nih.gov/38777085/
CanDIG (Marion Shadbolt; [slides](https://docs.google.com/presentation/d/19c0h-4_jzLAit9ROaiFK5o8yrkPm6T0ZrR9YF_I2LUw/edit?slide=id.p#slide=id.p)): To join the Digital Health & Discovery Platform, CanDIG transformed the Marathon of Hope Cancer Centres Network (MOHCCN) clinical data into domain-agnostic OMOP CDM. Since OMOP is query-based, a Python microservice was built to map concepts into Phenopackets v2 for external exchange.
another one from BaylorCM (??)
Already exists:
TopMed to Phenopackets (and TM to LinkML) export (Joshua Proulx; TopMed)
Link?
Contributor guide
Research direction
Start by reviewing the phenoboard Cargo.toml reference, the cited OMOP-to-Phenopackets paper, and the CanDIG slides. Clarify the scope, ownership, and links for FHIR and OMOP exports, including the possible BaylorCM contribution. Done should be a concrete, agreed export-tool plan with the existing TopMed work distinguished.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, rust
- Domain
- backend-api-design, data-engineering
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100