ResearchPhenoDB Download

About ResearchPhenoDB :

ResearchPhenoDB is a research tool developed by the Baylor-Hopkins Center for Mendelian Genomics for the Centers for Mendelian Genomics. It is comprised of Phenotype Module which is designed to collect, store and analyze standardized phenotypic information and an ELSI Module to collect consents and committee discussions. These are described in:

Hamosh A, Sobreira N, Hoover-Fong J, Sutton VR, Boehm C, Schiettecatte F, Valle D. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat. 2013 Apr;34(4):566-71. doi: 10.1002/humu.22283. Epub 2013 Mar 4. PMID: 23378291

In addition, ResearchPhenoDB also includes an Analysis Module for variant filtering and evaluation and a Sample Tracking Module for tracking consents and samples through the research pipeline. These are described in detail in a paper under review.

ResearchPhenoDB is available for download only, after registration. To try out the Phenotype and Analysis Modules, please create an account at MyPhenoDB. MyPhenoDB is hosted at Johns Hopkins for those who want to test out the software and those without IT support or sufficient volume to merit installation at their own center. It is toggled to a fully de-identified state and does not allow upload of data. It is available for download and can be toggled to a fully identified state. Because it is not designed for a research project both the ELSI and Sample Tracking Modules are excluded from MyPhenoDB.

Licensing :

The PhenoDB software is distributed under the Creative Commons Attribution-NonCommercial-ShareAlike license.

Downloads Registration :

(for us to track for funding purposes)

Fill in all fields above and click the 'Submit Registration' button.

You will be given the link to download the software once your have submitted your registration. Additionally we will be sending you an email containing the same download instructions, and we will be sending you an email when new versions of PhenoDB are released in the future.

Software Requirements :

PhenoDB is built on the Django web application framework and uses MySQL as the underlying database. It is designed to run on recent releases of RedHat, Centos and Fedora Code. It requires 20GB of disc space and 4GB of memory to run (8GB if you need to run analyses.)

The distribution is composed of a compressed 'tar' file which contains both the PhenoDB software and all the software tools to run it.

The root directory of the software includes a README.TXT which contains instructions on how to install the software with the included installer, and how to install the software manually should you want a custom installation. You will need to read this file before doing an installation.

If you are upgrading your PhenoDB installation, you will need to check the VERSIONS.TXT file which contains information on each version of PhenoDB as well as special instructions on how to upgrade from version to version.