ga4gh / ga4gh/phenopacket-schema

Phenopackets do not allow for representation of provenance of key data elements

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Dominant language
Java
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Description

The ability to represent per-element provenance of things like VariantInterpretation and Diagnosis are limiting with respect to how we've considered using phenopackets to store/transmit ClinGen-curated evidence.

For example, I am hesitant to include a VariantInterpretation which a ClinGen biocurator has abstracted from the literature because, in the absence of proper attribution the presence of this data in a ClinGen-produced phenopacket could easily be misinterpreted as ClinGen making an assertion of the pathogenicity of this variant.

Other elements that represent "judgement" could also arguably need the ability to represent provenance/attribution-- for instance, GenomicInterpretation, Diagnosis.

Contributor guide

Open the contributing guide

Research direction

Start by reviewing how VariantInterpretation, Diagnosis, and GenomicInterpretation are represented in the phenopacket schema. Define what per-element provenance and attribution should cover, then confirm that the schema can distinguish curated evidence from assertions made by the producing organization.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
backend-api-design
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
35/100

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