Tools for clinical genomics

Using genomic data to improve health and research outcomes.

The challenge

The number of digital tools for data capture and analysis in healthcare has risen rapidly over the last two decades.

However, in Australia specific areas of practice remain largely manual and paper-based.

One such area is genomics – a burgeoning field of research and clinical care.

The lack of digitisation in the genomics space has slowed research teams in their attempts to study and evaluate genomic data. This represents a significant gap in our understanding of causes and treatment of specific diseases, such as some cancers.

A method for the simple retrieval and analysis of genomic data is needed so that the data can easily be applied in clinical and research settings.

Our response

We’ve developed a number of tools to capture, exchange and analyse genomics-related data.

These tools can be integrated with REDCap, one of the most frequently used databases for the collection of participant information in research studies.

The tools include:

  • FHIR-OWL: transforms OWL ontologies into FHIR code systems (OWL is used to author and distribute many genomics-related ontologies such as the Human Phenotype Ontology)
  • FHIR-HGNC: transforms the custom format used by the HUGO Gene Nomenclature into FHIR code system
  • Ontoserver REDCap plugin: enables capturing coded data in REDCap using standardised terminologies
  • Pedigree editor: pedigree editor for REDCap and SMART on FHIR based on Open Pedigree, with the ability to export to different formats, including the new Global Alliance for Genomics and Health pedigree standard
  • Redmatch: rules engine that enables transforming REDCap forms into FHIR resources
  • Pathling: FHIR-native analytics platform

The results

These tools enable the implementation of an end-to-end FHIR-based solution built on top of a standard REDCap installation. This provides smooth and efficient retrieval and collection of genomic and phenotypic data.


An image showing the graphics for tools CSIRO have created for clinical genomics. The graphics shown are for the tools Open Pedigree, Ontoserver, REDCap, Redmatch, FHIR and Pathling.

Clinical genomics tools developed by CSIRO. They enable the implementation of an end-to-end FHIR-based solution built on top of a standard REDCap installation.