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Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm
  • Toyofumi Fujiwara,
  • Jae-Moon Shin,
  • Atsuko Yamaguchi
Toyofumi Fujiwara
Database Center for Life Science

Corresponding Author:[email protected]

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Jae-Moon Shin
Database Center for Life Science
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Atsuko Yamaguchi
Tokyo City University
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Abstract

Over 7,000 rare genetic diseases have been identified, and millions of newborns are affected by severe rare genetic diseases each year. A variety of Human Phenotype Ontology (HPO)-based clinical decision support systems (CDSS) and patient repositories have been developed to support clinicians in diagnosing patients with suspected rare genetic diseases. In September 2017, we released PubCaseFinder (https://pubcasefinder.dbcls.jp), a web-based CDSS that provides ranked lists of genetic and rare diseases using HPO-based phenotypic similarities, where top-listed diseases represent the most likely differential diagnosis. We also developed a Matchmaker Exchange (MME) application programming interface (API) to query PubCaseFinder, which has been adopted by several patient repositories. In this paper, we describe notable updates regarding PubCaseFinder, the GeneYenta matching algorithm implemented in PubCaseFinder, and the PubCaseFinder API. The updated GeneYenta matching algorithm improves the performance of the CDSS automated differential diagnosis function. Moreover, the updated PubCaseFinder and new API empower patient repositories participating in MME and medical professionals to actively use HPO-based resources.
30 Sep 2021Submitted to Human Mutation
04 Oct 2021Submission Checks Completed
04 Oct 2021Assigned to Editor
07 Oct 2021Reviewer(s) Assigned
23 Oct 2021Review(s) Completed, Editorial Evaluation Pending
12 Nov 2021Editorial Decision: Revise Minor
14 Jan 20221st Revision Received
18 Jan 2022Submission Checks Completed
18 Jan 2022Assigned to Editor
06 Feb 2022Review(s) Completed, Editorial Evaluation Pending
08 Feb 2022Editorial Decision: Accept
22 Feb 2022Published in Human Mutation. 10.1002/humu.24341