PhenClust, a standalone tool for identifying trends within sets of biological phenotypes using semantic similarity and the Unified Medical Language System metathesaurus. Issue 3 (15th September 2021)

• Record Type: Journal Article
• Authors: Wilson, Jennifer L; Wong, Mike; Stepanov, Nicholas; Petkovic, Dragutin; Altman, Russ
• Is Part Of: JAMIA open. Volume 4:Issue 3(2021)
• Publication Date: 2021-09-15
• Subjects: systems biology -- phenotype analysis -- high-throughput analysis -- network analysis -- computational tools -- Docker containers; Medical informatics -- Periodicals; 610.285
• DOI: 10.1093/jamiaopen/ooab079
• Languages: English
• ISSNs: 2574-2531

Abstract

Abstract: Objectives: We sought to cluster biological phenotypes using semantic similarity and create an easy-to-install, stable, and reproducible tool. Materials and Methods: We generated Phenotype Clustering (PhenClust)—a novel application of semantic similarity for interpreting biological phenotype associations—using the Unified Medical Language System (UMLS) metathesaurus, demonstrated the tool's application, and developed Docker containers with stable installations of two UMLS versions. Results: PhenClust identified disease clusters for drug network-associated phenotypes and a meta-analysis of drug target candidates. The Dockerized containers eliminated the requirement that the user install the UMLS metathesaurus. Discussion: Clustering phenotypes summarized all phenotypes associated with a drug network and two drug candidates. Docker containers can support dissemination and reproducibility of tools that are otherwise limited due to insufficient software support. Conclusion: PhenClust can improve interpretation of high-throughput biological analyses where many phenotypes are associated with a query and the Dockerized PhenClust achieved our objective of decreasing installation complexity.