ga4gh / ga4gh/phenopacket-schema

Create/Update/Disseminate Export Tools

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Dominant language
Java
Stars
101
Forks
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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

Open the contributing 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

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