Transformation Projects

Informatics Project

Develop and evaluate a proof of principle mechanism for converting current genetic test reports into a structured format

Informatics Project

Project Background

Results from genetic testing laboratories are typically represented within a PDF document (unstructured data) which is uploaded to an electronic health record (EHR) with information hard-coded into the document and not easily extractable other than through manual means on an individual basis.

Structured and standardised genomic data formats are needed to enable novel clinical and research use, such as improving identification of those suitable for pharmacogenomic or other therapeutic interventions and support wider genomic-associated research activity at scale.

Project Overview

To overcome these issues, the North Thames GMS is developing a proof of principle mechanism to transform how genomic tests are represented. This process will extract structured data elements from genomic reports for easy integration into electronic health records using existing open technical standards such as Fast Healthcare Interoperability Resource (FHIR).

Progress to Date

  • Analysis of current genomic reports to identify key data elements for extraction
  • Description of data element’s metadata for describing clinical genomic sequence information
  • Structural modelling of PDF Genomic report file and mapping it to FHIR
  • Prototype python web application that maps from a manually extracted genomic report – PDF to csv/json then to FHIR
  • Bulk FHIR data exportation between FHIR servers.
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