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Change log for beacon v2 Model

This document is planned as a manually maintained list of changes to the Beacon version 2 Model repo.
It should only include changes that affect or could affect implementations, and the log would be updated after the corresponding pull request is approved and merged. This log only include the changes added after December, 1st 2021.

2022-03-11/2022-03-25: removing 'cohort' prefix from some cohort properties issue #102

Adapting the default schema for cohorts to the style used in property names for other entry types

  • cohortId to id
  • cohortName to name
  • cohortInclusionCriteria to inclusionCriteria
  • cohortExclusionCriteria to exclusionCriteria

The properties that could be misleading if the prefix was removed like type or size are keeping the prefix.

2022-03-11/2022-03-14: More Phenopackets alignments PR #84 && PR #85 && PR #86

This follows some discussions with Phenopackets developers (@pnrobinson & @julsejacobsen) and a general agreement "to adopt as good as possible for easier re-use though understood not to be Phenopackets per se".

  • gestationalAge
  • modification of treatment and dependencies
  • addition of karyotypicSex for representing cytogenetic/genomic assessment of sex chromosome composition represented from a list of values

2022-03-08: Re-structuring genomicVariation for VRS compatibility PR #72

This modification allows the use of VRS variation classes, while also keeping an updated version of the current Beacon schema (using VRS location instead of the legacy position) as an option. This proposal addresses feedback from the GA4GH PRC process.

The change here introduces the root level variation property as a wrapper for the different options of "allelic" representtaions:

"variation": {
  "oneOf": [
    {"$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation" },
    {"$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation" },
    {"$ref": "#/definitions/LegacyVariation" }
  ]
},

2022-03-04: Correcting structure for ageOfOnset in disease PR #77

In the schema for disease, ageOfOnset referenced age instead of timeElement (with age, expressed as iso8601duration parameter being one of the options):

  • corrected disease and timeElement schemas for correct structure and examples

2022-03-04: Correcting use of singular for unit PR #67

2021-12-22: Fixing errors in filteringTerms.json for Cohorts and Datasets PR #65

Fixing incorrect definitions inside of the files below. They miss mandatory "ftType": "ontologyTerm".

Affected file/s:

2021-12-22: Improved specificity of variant IDs in genomicVariations default schema PR #63

Fixing a discrepancy between the definition of clinVarIds and the expected format.

Affected file/s:

The definition of variantAlternativeIds moves from one string to an array of proper external references (externalReference).

´clinVarIds´ is deprecated and replaced by clinvarVariantId which is string that references the ClinVar VariantId and not any other identifier. Other types of ClinVar identifiers must go into variantAlternativeIds.