ArticleBMC genomics2018
An online tool for measuring and visualizing phenotype similarities using HPO.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed.
- Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.BMC bioinformatics · 2024Article
- DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity.Bioinformatics (Oxford, England) · 2024Article
- PhenoExam: gene set analyses through integration of different phenotype databases.BMC bioinformatics · 2022Article
- Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.Scientific reports · 2020Article
- Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.BMC systems biology · 2019Article
- An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations.Frontiers in genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Human Phenotype Ontology (HPO) is one of the most popular bioinformatics resources. Recently, HPO-based phenotype semantic similarity has been effectively applied to model patient phenotype data. However, the existing tools are revised based on the Gene Ontology (GO)-based term similarity. The design of the models are not optimized for the unique features of HPO. In addition, existing tools only allow HPO terms as input and only provide pure text-based outputs.
resultsWe present PhenoSimWeb, a web application that allows researchers to measure HPO-based phenotype semantic similarities using four approaches borrowed from GO-based similarity measurements. Besides, we provide a approach considering the unique properties of HPO. And, PhenoSimWeb allows text that describes phenotypes as input, since clinical phenotype data is always in text. PhenoSimWeb also provides a graphic visualization interface to visualize the resulting phenotype network.
conclusionsPhenoSimWeb is an easy-to-use and functional online application. Researchers can use it to calculate phenotype similarity conveniently, predict phenotype associated genes or diseases, and visualize the network of phenotype interactions. PhenoSimWeb is available at http://120.77.47.2:8080.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.