PhenoTips: Patient Phenotyping Software for Clinical and Research Use.

We have developed PhenoTips, a deep phenotyping tool and database, specifically designed for phenotyping patients with genetic disorders. Our tool closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. The software provides a series of features that help reduce the clinician's workload during the clinical examination. Together with standardized phenotypic data, PhenoTips supports entering demographic information, medical history (including prior laboratory results), family history, various measurements, relevant images depicting manifestations of the patient's disorder, genetic tests and their results, as well as additional notes for each of these categories. A pedigree drawing tool which enables the collection of advanced family histories is currently under development. The software automatically plots growth curves for a variety of measurements, selects phenotypes reflecting abnormal measurements, instantly finds Online Mendelian Inheritance in Man (OMIM) diseases that most closely match the phenotypic description, and can suggest additional clinical investigations that can improve the diagnosis.

PhenoTips is already used both in research studies and in the clinic, including the phenotyping of patients for the FORGE (Finding Of Rare disease GEnes) Canada project (http://care4rare.ca/), and the Undiagnosed Disease Program at the NIH. Our source code and a demo version of PhenoTips are available at http://phenotips.org.