Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes

  • A Correction to this article was published on 18 June 2020

Abstract

Purpose

Computational documentation of genetic disorders is highly reliant on structured data for differential diagnosis, pathogenic variant identification, and patient matchmaking. However, most information on rare diseases (RDs) exists in freeform text, such as academic literature. To increase availability of structured RD data, we developed a crowdsourcing approach for collecting phenotype information using student assignments.

Methods

We developed Phenotate, a web application for crowdsourcing disease phenotype annotations through assignments for undergraduate genetics students. Using student-collected data, we generated composite annotations for each disease through a machine learning approach. These annotations were compared with those from clinical practitioners and gold standard curated data.

Results

Deploying Phenotate in five undergraduate genetics courses, we collected annotations for 22 diseases. Student-sourced annotations showed strong similarity to gold standards, with F-measures ranging from 0.584 to 0.868. Furthermore, clinicians used Phenotate annotations to identify diseases with comparable accuracy to other annotation sources and gold standards. For six disorders, no gold standards were available, allowing us to create some of the first structured annotations for them, while students demonstrated ability to research RDs.

Conclusion

Phenotate enables crowdsourcing RD phenotypic annotations through educational assignments. Presented as an intuitive web-based tool, it offers pedagogical benefits and augments the computable RD knowledgebase.

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Fig. 1: The Phenotate annotator and comparator user interfaces.
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Change history

  • 18 June 2020

    The original version of this Article contained an incorrect supplementary file in the Excel file format. This has now been replaced in the HTML version of the Article.

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Acknowledgements

We thank Orion Buske, Marta Gîrdea, and other members of the Centre for Computational Medicine for their guidance during the development stage of this project. Furthermore, we thank the clinical geneticists who have submitted annotations to the project. We also thank Peter Roy, Karim Mekhail, Alistair Dias, Bernard Duncker, and Nagham Abdalahad for integrating Phenotate into their classes. We thank their students, as well as Chloe Ng, for contributing annotations. We also thank Sana Tonekaboni for her advice on ML methods, Andrei Turinsky for his advice on statistics, and Jixuan Wang for his assistance in integrating Phenotate into LMP408. We use web-based calculators on Social Science Statistics to computeP values. This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the ERA-NET Cofund action number 643578, E-Rare3; the Canadian component of the work was supported by the Canadian Institutes of Health Research (CIHR); and Genome Canada. A.X.L. received funding to work on Phenotate from a University of Toronto Faculty of Medicine Comprehensive Research for Medical Students (CREMS) Scholarship.

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Correspondence to Michael Brudno PhD.

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Chang, W.H., Mashouri, P., Lozano, A.X. et al. Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes. Genet Med (2020). https://doi.org/10.1038/s41436-020-0812-7

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Keywords

  • rare diseases
  • phenotype
  • crowdsourcing
  • medical education
  • machine learning