Owner NHGRI Website www.phenxtoolkit.org | Available in English Commercial no | |
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PhenX (consensus measures for Phenotypes and eXposures) is a community-driven effort to provide standard measures for use in biomedical research. The goals are to help investigators identify opportunities for collaborative biomedical research and improve the consistency of data collection. The PhenX Toolkit is a web-based catalog of high-priority measures related to complex diseases, phenotypic traits and environmental exposures. These measures were selected by working groups of experts using a consensus process. 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. The Toolkit is funded by the National Human Genome Research Institute (NHGRI) with additional support from the Office of Behavioral and Social Sciences Research (OBSSR); the National Institute on Drug Abuse (NIDA); the National Institute of Mental Health (NIMH); the National Heart, Lung, and Blood Institute (NHLBI); the National Institutes of Health (NIH); and the NIH Office of Disease Prevention's (ODP's) Tobacco Regulatory Science Program (TRSP). The PhenX Toolkit is available to the scientific community at no cost.
Contents
Objectives
For genome-wide association studies (GWAS) and other studies involving human subjects, the use of standard measures can facilitate cross-study analyses. Such analyses compare independent findings to validate results or combine studies to increase sample size and statistical power. This increased power makes it possible to identify more subtle and complex associations such as gene-gene and gene-environment interactions.
PhenX Measures
The Toolkit has a broad scope and currently provides assessments for 23 research domains.
Specialty collections
In addition, the Toolkit includes more focused add-on collections for specialists in 4 areas.
The Toolkit
The PhenX Toolkit is a catalog of measures recommended by domain experts, with browse and search capabilities and bioinformatics support. PhenX measures and protocols are included in the Cancer Data Standards Repository (caDSR) Common Data Elements (CDE) Dictionary and the National Center for Biomedical Ontology (NCBO) BioPortal. PhenX protocols are available as REDCap Instrument Zip files, and work is underway to map PhenX variables to all studies in dbGaP. PhenX provides easy access to standard measures with the potential to increase the overall impact of individual studies via cross-study analyses. For each measure, the PhenX Toolkit provides a brief description, the protocol for measurement with supporting images and tables, the reasons for selecting the protocol, details about training and equipment, and selected references. Users can browse research domains, measures, or collections, search using a “Smart Search” or a full text search, collect measures of interest in “My Toolkit”, and request custom data dictionaries and custom data collection worksheets.
The Toolkit can be particularly helpful when an investigator wants to expand a study to include measures that are outside his or her primary area of expertise. Whereas study specific measures are needed to address the primary research goal, common measures are needed to increase the overall impact of the study; both types of measures are important to overall study design.
The new "Register Your Study" feature allows registered users to share their study with other registered users or find other studies using the same protocols and identify opportunities for cross-study analysis.
Protocols
In addition to measures, PhenX also defines protocols. There may be multiple protocols defined for a measure. For example, for smoking cessation, there is an adult protocol (id: 030901) and adolescent protocol (id:030902).
Variables
PhenX also provides a datatype (e.g., integer, string, date, enumerated, or encoded values) for each PhenX variable. For example, variable 'PX070501_Pregnancy_Outcome_1' for 'Outcome of Pregnancy?' is of type enumerated with value set of four possible values (Live birth,Still born,Miscarriage,Induced abortion).