Actionability

Table of Contents

• A. Actionability APIs
• B. Actionability Messaging Services
  • B.1 BRL Internal Pulsar
  • B.2 ClinGen Data Exchange Kafka Services
    • B.2.1 Actionability topic
      • Version 1.0.0
      • Version 2.0.0
      • Version 2.1.0
• C. Chromosomal Abnormalities

A. Actionability APIs

Check out documentation on - Actionability APIs here

B. Actionability Messaging Services

B.1 BRL Internal Pulsar

B.2 ClinGen Data Exchange Kafka Services

B.2.1 Actionability topic

This topic tracks curation events of an actionability topic. The events are tracked per context - Adult or Pediatric.

Check API PRODUCTION endpoint that generates the message content based on the current status of the topic:

• Adult - https://actionability.clinicalgenome.org/ac/Adult/api/doc/AC002.json?flavor=wag
• Pediatric - https://actionability.clinicalgenome.org/ac/Pediatric/api/doc/AC002.json?flavor=wag

Given below are the STAGE equivalent of the production API endpoints:

• Adult - https://actionability.test.genome.network/ac/Adult/api/doc/AC002.json?flavor=wag
• Pediatric - https://actionability.test.genome.network/ac/Pediatric/api/doc/AC002.json?flavor=wag

Version 1.0.0

Version 1 of the actionability topic message is gene-condition specific. Follow the schema and example documents given below:

• Schema - schema_1.0.0_AV1.json5
• Example messages

1. In Prep state - AC1056_in_prepration.json
2. Released state - AC001_released.json
3. Released - under revision state - AC061_released_under_revision.json

Version 2.0.0

Version 2 of the actionability topic message supports both gene-condition AND variant-condition specific curation topics. Follow the schema and example documents given below:

• Schema - schema_2.0.0.json5

1. Gene-Condition Released state - AC001_gc_released.json
2. Variant-Condition Released stateAC1060_vc_released.json

Summary of schema change (1.0.0 to 2.0.0)

• Property jsonMessageVersion domain definition changed to semantic version
• New property curationType
• New property variants. Note it is EITHER genes or variants based on the curationType property.
• All the properties, conditions, preferred_conditions, assertions and scores will EITHER contain the gene or variant properties.
• Scoring group structural change - not backward compatible

Version 2.1.0

Version 2.1.0 of the actionability topic message schema has additional attributes to support curator authorship. Authorship is graded as primary and secondary curators. schema_2.1.0.json5

C. Chromosomal Abnormalities