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CSIRO Ontoserver

CSIRO Ontoserver is a clinical terminology / ontology server developed by CSIRO. In the sBeacon architecture it builds the ontology index that powers advanced metadata queries — expanding a query term into its hierarchical descendant terms (and their codes) so that a query for a broad concept matches all narrower concepts beneath it. (Source: sources/2026-09-18-aws-how-csiro-built-scalable-cost-optimized-genomic-variant-querying-on-aws)

Role in sBeacon

  • Onboarding: after metadata is written to S3 in ORC, an orchestrator Lambda calls Ontoserver to build the ontology index; the resulting index files are written back to S3.
  • Querying: the Microservice Lambda looks up the query's ontology terms in DynamoDB to get the matching descendant terms and codes, then uses those codes to query the metadata tables on Athena. This is what lets a query such as "individuals with a specific BRCA1 mutation who have stage 3 cancer" resolve hierarchical clinical/phenotypic terms.

sBeacon is not tied to Ontoserver specifically: it supports the API schema of the Ensembl OLS V4 specification, so other terminology servers implementing that schema can be substituted.

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