PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features

Abstract

To interpret whole exome/genome sequence data for clinical and research purposes, comprehensive phenotypic information, knowledge of pedigree structure, and results of previous clinical testing are essential. With these requirements in mind and to meet the needs of the Centers for Mendelian Genomics project, we have developed PhenoDB (http://phenodb.net), a secure, Web-based portal for entry, storage, and analysis of phenotypic and other clinical information. The phenotypic features are organized hierarchically according to the major headings and subheadings of the Online Mendelian Inheritance in Man (OMIM®) clinical synopses, with further subdivisions according to structure and function. Every string allows for a free-text entry. All of the approximately 2,900 features use the preferred term from Elements of Morphology and are fully searchable and mapped to the Human Phenotype Ontology and Elements of Morphology. The PhenoDB allows for ascertainment of relevant information from a case in a family or cohort, which is then searchable by family, OMIM number, phenotypic feature, mode of inheritance, genes screened, and so on. The database can also be used to format phenotypic data for submission to dbGaP for appropriately consented individuals. PhenoDB was built using Django, an open source Web development tool, and is freely available through the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine (http://phenodb.net).

Figure 1

The initial page after login as a submitter. New submission has been highlighted to show the next screen. This page also shows all the programmed searches.

Figure 2

The first page of submission. Please note that a family number has been automatically generated (top of the page) and that the submitter must affirm that consent to share medical information has been obtained.

Figure 3

The family information that is collected. An example is prepopulated to show that sample information is also collected. The link to add features (required of all affected individuals in a family) is highlighted.

Figure 4

A: The individual specific page, including the highest level of the phenotype hierarchy. B: An example of feature selection using the hierarchy. Selecting abnormal for any category opens a tree below. C: Alternatively the search box can be used to find the desired terms. D: Selection of a term automatically selects it (and those higher up) in the hierarchy.

Figure 5

The summary data view for review before submission. This is also the view seen by members of the PRC when reviewing families and by members of the Analysis & Interpretation Committee. A. Top of page. B. Bottom of page.