Video Tip of the Week: PhenX, standardizing phenotype measurements

This week’s tip is actually sort of a mega-tip. It’s not just one video–it’s a series of videos that the GeneticAlliance has provided (and there are more to come) with the theme: “Managing the Mass of Measures: Real People’s Real Data Made Useful”. It is part of their Standards and Tools webinar series that is offering outreach and knowledge on tools that aims to bridge the research–>patient gap.

Although I’ll select the PhenX webinar to highlight, PhenX is just one of the tools in a sort of ecosystem that is building more support from research knowledge to patient phenotypes, which can potentially link up with electronic health records (EHR) data, and hopefully lead to new insights and treatments. PhenX is a big team, with various moving parts, and their toolkit is the PhenX Toolkit, a way to standardize and collect important measurements about human biology and factors that influence health.

On their home page they describe this aspect of the work:

The Toolkit provides standard measures related to complex diseases, phenotypic traits and environmental exposures. Use of PhenX measures facilitates combining data from a variety of studies, and makes it easy for investigators to expand a study design beyond the primary research focus.

That should give you an idea of the types of things they intend to capture, but I would encourage you to have a look at their webinar to learn more about their project and how it fits into the scheme of translational medicine. But rather than me talking on about it, watch their presentation from the webinar series page, or embedded here:

Also in this webinar there were references to other projects and tools you might be interested in which relate to this: (aka eMERGE), PheKB (the Phenotype KnowledgeBase), and the PROMIS system (Patient Reported Outcomes Measurement Information System). These things are certainly downstream of most of the bioinformatics I’ve been involved with, but an important direction to get the research work tied more to the clinical side, to ultimately have impacts on human health.

Quick links:
PhenX team site:
PhenX Toolkit:


Hamilton C.M., Strader L.C., Pratt J.G., Maiese D., Hendershot T., Kwok R.K., Hammond J.A., Huggins W., Jackman D. & Pan H. & (2011). The PhenX Toolkit: Get the Most From Your Measures, American Journal of Epidemiology, 174 (3) 253-260. DOI: