BigMed

BIGMED

The precision medicine approach, also called personalized medicine, can improve the quality of patient care and increase safety. This approach to medicine refers to the way healthcare providers offer and plan specific care for their patients. Tailored treatments and diagnostics are based on the genes, proteins, and other substances in a person’s body.

The work in BIGMED was organized through four clinical areas: rare diseases, colorectal cancer, sudden cardiac death and frostbite. Solutions suggested by BIGMED have been based on the clinical needs identified in each disease area and focus on the following themes: digital technologies, ICT infrastructure and data provisioning, legal and ethical issues, bioinformatic pipelines and data sharing solutions for genomics.

For precision medicine to reach its full potential, we need supporting infrastructure to facilitate the flow and use of data.  SIRIUS addressed goals related to semantic data integration within the area of rare diseases.

Challenges

  • Technology transfer to healthcare tasks
  • Adopt ontology alignment techniques to contribute to the diagnostic process
  • Evaluate the coverage of links between phenotypes (HPO terms) and diseases (OMIM terms) obtained using ontology alignment systems.

Our Approach

SIRIUS researchers have been working on the BIGMED personalized medicine project (2016-2020) to create tools for identifying and specifying clinical phenotypes. Dag Hovland and Laura Slaughter worked on an ontology-driven form-based tool to be used by paediatricians to select phenotypes observed in newborns with suspected rare genetic disorder. The tool uses the Human Phenotype Ontology (HPO) and provides some guidance to selection of phenotypes to be used in the diagnostic process.

Characterizing the patient’s physical or biochemical characteristics as well as any responses to interventions is essential for tailoring treatment and diagnosing the patient Any observable trait, such as a behaviour, developmental delay or physical anomalies, is what is called a phenotype. Phenotypes are a manifestation of genetic variation and are essential data to collect that form the basis for personalized medicine.

SIRIUS researchers met with BIGMED clinicians and lab technicians to outline functionality of the phenotype tool which will be completed in 2019. Functionality includes using the ontology-driven system to track phenotype iterations throughout the diagnostic process, adding triggers that indicate a need for reanalysis, the addition of other input methods than the form check-boxes including free text.

Results

Demo

A demo is described in the Slaughter and Hovland (2019) publication

Source Code and Documentation

[Github] 

Publications​

Jiménez-Ruiz, E., Hovland, D., Slaughter, L., Håndstad, T., & Waaler, A. (2017, January). On improving the phenotype acquisition process using semantic web technology. In SWAT4LS.https://ceur-ws.org/Vol-2042/paper9.pdf

Slaughter, L., & Hovland, D. (2019). Suggesting Reasonable Phenotypes to Clinicians. In SWAT4HCLS (pp. 11-19). https://ceur-ws.org/Vol-2849/paper-02.pdf

Team

SIRIUS:

Laura Slaughter, Dag Hovland, Ernesto Jiménez-Ruiz, Tony Håndstad, Yngve Sejersted

Partners

Digital Solutions for Genomic Medicine, Oslo University Hospital

Acknowledgements

This work was partially supported by the SIRIUS Centre for Scalable Data Access (Research Council of Norway, project 237889) and BIGMED Lighthouse