PhenoTips

PhenoTips

   PhenoTips

PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders. The user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. This easy-to-use front-end, compatible with any device that runs a Web browser, is coupled with with a standardized database back-end where phenotypic information is represented using the Human Phenotype Ontology (HPO).

Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and free-form notes.

In addition to data collection, PhenoTips automatically analyzes a wide range of measurements and plots live the corresponding growth curves. It also supports accurate diagnosis based on the entered data, and can suggest additional clinical investigations that can improve the diagnosis.

Features preview

Team

PhenoTips is developed in the Computational Biology Lab at University of Toronto's Computer Science Department, in collaboration with geneticists and clinicians form SickKids and CARE for RARE.

Citing PhenoTips

If you wish to mention PhenoTips in a scientific article, please refer to our paper published in May 2013 in Human Mutation:

Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K. M., Chénier, S., Chitayat, D., Faghfoury, H., Meyn, M. S., Ray, P. N., So, J., Stavropoulos, D. J. and Brudno, M. (2013), PhenoTips: Patient Phenotyping Software for Clinical and Research Use. Hum. Mutat., 34: 1057–1065. doi: 10.1002/humu.22347

News

Oct 07 2014

PhenoTips 1.0 (stable) released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.0 release, after 3 years, more than 1000 issues closed, and 19 development releases.

For those new to the project, PhenoTips is an open source software tool for collecting and analyzing phenotypic and genotypic information for patients with genetic disorders. The main goal of PhenoTips is to empower clinicians and scientists to perform deep phenotyping of their patients, using a rich, structured phenotype ontology, so that the gathered data can be used both by humans and machines. To support this, other features of the software include:

  • Gathering demographics information about the patients and their families
  • Entering multiple sets of measurements, which are automatically translated into percentiles and standard deviations, and plotted on standard growth charts
  • Uploading previous medical records, lab results, radiographies or photographs
  • Prenatal and perinatal phenotypes and related information
  • Selecting a list of genes, either with known mutations, or that should be investigated further
  • Differential diagnosis tools, suggesting both phenotypes to investigate, and possible disorders
  • A rich pedigree editor, able to import and export PED files
  • PDF exports for printing or archival, XLS exports for analyzing/sharing multiple related patients, and JSON exports for sharing data between different PhenoTips instances or different applications
  • Patients can be easily pushed between PhenoTips instances
  • Simple, yet powerful data privacy and collaboration settings, which allow sharing a patient with other users or workgroups
  • A dynamic homepage providing quick access to patients
  • A powerful table which allows advanced filtering of all the patient records (accessible by the current user)
  • The whole patient form is configurable and extensible, with Studies giving the option of having more than one such configuration available at the same time
  • A powerful Administration section which allows changing most of the features of the software

The 1.0 branch will continue to be maintained with regular bugfix releases, while the main development effort goes into the 1.1 release, expected towards the end of the year.

Sep 26 2014

PhenoTips 1.0 Release Candidate 2 released

The PhenoTips development team is happy to announce the availability of the first and second release candidates for PhenoTips 1.0. A release candidate is a test release of what will be the first "stable" version of PhenoTips 1.0, and unless any major bugs are found in the next few days, this will be the 1.0 release, so please test this release thoroughly. The 1.0 release is expected in early October. The highlights of this release, compared to the previous milestone, are:

  • Replaced the CSV export with a more user-friendly Excel export
  • VCF files can be uploaded to a patient record; the data is not yet processed, though
  • Better help/info buttons for the patient record fields and phenotypes
    • Added info buttons for OMIM diseases and gene names, and for phenotypes displayed as search results and differential diagnosis
  • Multiple patients can be pushed to PhenomeCentral in a batch
  • Pedigree improvements:
    • Genes and Phenotypes can now be entered for every person
    • Added support for importing and exporting from a BOADICEA file
    • Added explicit generation numbering to nodes in pedigrees
    • More pedigree templates: proband with one or two generations, plus a consanguineous marriage
    • Improved the UI with simpler, scalable icons, a reorganized menu, and a tabbed person menu
    • Added a placeholder affected disease which allows marking affected persons without specifying an exact OMIM disease
    • Info buttons are shown for disorder, gene, and phenotype search results, as in the main patient record
    • Better support for touchscreens
    • Better display of the pedigree image in the patient record
    • Added a service for requesting the pedigree image for a patient
  • More information exposed through the JSON export
  • By default, attached files are stored on the filesystem instead of the database
  • An extension repository (app-store) is setup, allowing future extensions to be easily installed; more extensions will show up soon
  • Many other bugfixes, performance and UI improvements

See the full list of issues on GitHub.

Jul 29 2014

PhenoTips 1.0 Milestone 13 released

The PhenoTips development team is happy to announce the availability of the thirteenth milestone of PhenoTips 1.0. Since there are still a few open issues preventing a final 1.0 release, and it has been more than two months since the previous milestone, we decided to release another milestone, so that our users can benefit from the latest improvements and bugfixes sooner. The highlights of this release are:

  • Selected phenotypes appear in their corresponding top level anatomical system category instead of the generic Other, even if those categories are not present by default in the form
  • Added severity, temporal pattern, spatial pattern, and locality qualifiers for phenotypes
  • Removed the mode of inheritance qualifier from phenotypes, since it shouldn't be applied to symptoms but to diseases
  • More abnormal measurements automatically select their corresponding phenotypes
  • Terms in phenotype subcategories are now expandable
  • Added help/description buttons for many of the fields in the patient record
  • The disease search doesn't list most genes, loci and proteins anymore, just actual disease names
  • Fixed two bug where a user's own patient records, and patients owned by a user's group wouldn't appear in data tables
  • A link to browse all patients has been added in the top menu, where it is always accessible
  • Pedigree improvements:
    • Support for importing pedigrees from a few formats: PED, GEDCOM, and our own custom format
    • Added the ability to enter ethnic background for each person
    • By default siblings are ordered by age, if possible
    • Improved the generated layout
  • Changed the default date format to the international year-month-day
  • Added a RPM package compatible with RHEL 7 and derived distributions
  • The separate Solr .war has now been merged into the main PhenoTips one, making it easier to install PhenoTips
  • Java 1.7 is now the minimum version of Java supported, since 1.6 has been discontinued
  • Plus many other minor bugfixes and improvements

See the full list of issues on GitHub.

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Reproducing or distributing this clinical information without permission from the institution that owns it is strictly forbidden.
PhenoTips version 1.0