Standardising clinical phenotype: CSIRO’s Ontoserver and Shrimp

News > Published on 05 May 2017 > By merryn.pearce

Scientists from the CSIRO Australian e-Health Research Centre have included the Human Phenotype Ontology as part of their clinical terminology software tools — designed to help clinicians better search for, retrieve, and apply standardised clinical terminology in their practice.

Ontoserver is a terminology server that queries, searches, filters and ranks standard clinical terminologies such as SNOMED CT. Ontoserver has now been extended to include the Human Phenotype Ontology (HPO), and hence cover a wider range of rare diseases. A key use case for Ontoserver is to translate clinical descriptions of a phenotype into a standardised terminology with associated codes. It does so through fast, incremental searches, and context-specific result ordering.

Using Ontoserver to search clinical terminologies, supports greater use of standardised, coded medical data, rather than relying on natural language which is difficult to compute, and is prone to variation. Standardisation facilitates the development of genotype-phenotype databases and supports the sharing of these datasets - vital to yielding the benefits of clinical genomics to the Australian health system.

The CSIRO Australian e-Health Research Centre is a member of Australian Genomics, its CEO Dr David Hansen, co-leads Program Two. David said “These tools enable all software developers and vendors implementing health applications to easily capture standard terminology based data – data which will be core to relating clinical data to genomics data. This is a key outcome for program two of Australian Genomics in providing tools to the wider genomics community.”

What are the key features of Ontoserver?

  • Ontoserver uses a FHIR-based, RESTful API. This makes it quick and easy to add sophisticated data capture fields to any other software system.
  • It supports multiple clinical terminologies and versions.
  • It has a state-of-the-art ranking algorithm that ensures the right codes appear in the top ranked search results.
  • It is distributed using Docker, making it easy to deploy.

A complementary tool, named “Shrimp”, has also been developed by CSIRO scientists and works as a clinical terminology search, visualisation, and exploration tool. It runs in a browser, and talks to Ontoserver.

Take a tour of Shrimp here:, and explore Ontoserver at Ontoserver is free to use in Australia and by licence elsewhere.

Find out more about The Australian e-Health Research Centre