Updating and unifying biomarker representation across parsers

[DSuveges]

Background

@JarrodBaker drew my attention to the fact that there’s a discrepancy on how biomarkers are represented in different evidence sets. In the cancer_biomarkers there are biomarkerName and biomarkers, which is not a list, but an object in which there are two properties: variant (array) and a geneExpression (array). In the new evidence set prepared for the partner preview, biomarkers is a list with objects with properties name and description . This discrepancy needs resolved.

On the partner preview front-end biomarkers are shown as chips, where the descriptions are shown upon hover-over. In case of cancer_biomarker evidence is displayed on a more detailed way.

Tasks

• [ ] Solidify a consistent schema for both use cases
• [ ] If reasonable unify the front-end visualisation of biomarkers across all evidence.

Acceptance tests

1. Get JSON schema that describe the biomarker object
2. Update all relevant parsers to accommodate the updated schema
3. Validate evidence against the new schema

[d0choa]

@DSuveges close?

[DSuveges]

This issue is not yet ready to be closed. The two schemas are still divergent, but it is not so important at the moment jump on it.

To be honest, I am not 100%sure how to properly model biomarkers.