Genomic Resource Grant for PhenX Toolkit (U41) – New Award
On July 1, 2013, the National Human Genome Research Institute (NHGRI), which funds PhenX, awarded RTI a 4-year cooperative agreement for $5.3 million to continue to expand and improve the PhenX Toolkit. The goals of the proposed work are to:
Address four new research domains;
Review and update measures in the Toolkit;
Extend Toolkit capabilities (e.g. integrating Chinese and Spanish translations of PhenX protocols and providing some PhenX protocols as web-based protocols);
Map PhenX measure variables to additional studies in the database of Genotypes and Phenotypes (dbGaP);
Expand and nurture existing collaborations;
Build new collaborations across the National Institutes of Health (NIH) and with other government agencies, and continue to engage and inform the scientific community.
Widespread adoption of PhenX measures will increase the overall impact of individual studies by making it easier to compare and combine data from different studies. With continued support, PhenX will promote and advance collaborative research across the biomedical research community.
On July 31, 2013, a new feature called "Register Your Study" was released in the PhenX Toolkit. This provides investigators that use PhenX measures the opportunity to share information about their studies with other Registered Users of the PhenX Toolkit. Investigators will be able to find other studies using the same measures and identify opportunities for cross-study analysis. Registered Users simply login and click on the My Studies page, enter information about their study and begin collaborating!
On April 29, 2013, the Toolkit released a new module called "Featured Measure." Updated quarterly, this module is an opportunity for the PhenX Toolkit to highlight measures not on the Top 5 list but are nonetheless interesting and suitable to a wide range of research areas. The current Featured Measure is Healthy Food Environments, which was selected by the Social Environments Working Group to capture the influence of the built and social environments in promoting obesity and being overweight. You can find the Featured Measure in the lower left corner of the PhenX Toolkit homepage.
PhenX Toolkit News and Views
This year, PhenX has seen an increase in the number of NIH Funding Opportunity Announcements (FOAs) that encourage investigators to employ PhenX measures to promote the collection of comparable data across studies. PhenX has been mentioned in FOAs from NHGRI, National Institute on Drug Abuse (NIDA), National Institute on Alcohol Abuse and Alcoholism (NIAAA), National Center for Complementary and Alternative Medicine (NCCAM), National Institute of Mental Health (NIMH), and the National Cancer Institute (NCI), as well as the Department of Defense (DoD). They have all incorporated the PhenX Toolkit into their FOAs as a resource for investigators involved in genomic and biomedical research. To date, 45 FOAs reference PhenX measures.
We are also tracking published articles that cite the Toolkit. PhenX has been cited in 49 publications and has been mentioned in 26 articles. This list of scientific articles and funding opportunities can be found on the News and Views Page along with other media announcements and sources that mention PhenX.
Top Domains and Top Measures
Top Domains and Measures are calculated based on the number of times they are included in reports generated by user Toolkits, cumulatively. The top Domains and Measures are listed on the PhenX Toolkit home page and are recalculated and updated with each new release. The top 5 domains and measures for July 2013 are listed below.
Top 5 Domains in the PhenX Toolkit
Alcohol, Tobacco and Other Substances
Top 5 Measures in the PhenX Toolkit
Alcohol-30-Day Quantity and Frequency
Peripheral Arterial Disease
PhenX in dbGaP
The NIH database of Genotypes and Phenotypes (dbGaP) serves as a data repository for genotype, sequence, and phenotype data and the associations between them. Genome-Wide Association Studies (GWAS) funded by the NIH are required to deposit collected genotype and phenotype data in dbGaP (http://www.ncbi.nlm.nih.gov/gap). In spite of the many risk factors common to multiple diseases, historically studies have included few, if any, measures in common. The ability for the PhenX Toolkit to serve as a resource for studies to include standard measures of phenotypes and environmental exposures for use in genomic and biomedical research, along with the task of annotating PhenX variables in dbGaP will help investigators identify opportunities to combine and compare studies. This ongoing collaboration between PhenX and dbGaP has led to:
dbGaP study variables that are identical, comparable, or related to PhenX being identified
dbGaP data fields in Advanced Search enabling dbGaP users to search variables from different studies that are mapped to the same PhenX variables
Investigators using PhenX measures can annotate variables collected by PhenX protocols as identical, comparable, or related to PhenX variables as part of the dbGaP submission process.
This comprehensive mapping and development of dbGaP Advanced Search tools provides a powerful resource that allows investigators to identify studies with common or related measures. With this information, researchers will be able to identify additional studies for cross-study analysis or include common measures at the study design phase.
PhenX in BioPortal
BioPortal is a web portal that provides access to a library of biomedical ontologies and terminologies via the NIH National Center for Biomedical Ontology (NCBO) Web services (http://www.bioontology.org/). BioPortal enables the research community to participate in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms, and to provide ontology reviews. The NCBO Web services provide multi-layered access to the ontology content, from getting all terms in ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection. Having PhenX in BioPortal will enable access to PhenX terms linking to other terms in the relevant biomedical and phenotype ontologies, and provide a one-stop search across different standards and resources. For instance, a PhenX term may have links to the corresponding terms in SNOMEDCT or MeSH, and vice versa. PhenX measures are in BioPortal with 137,405 mappings from 211 ontologies including Medical Subject Headings (MeSH) and Systematized Nomenclature of Human Medicine (SNOMED) Clinical Terms (SNOMEDCT).
In May, PhenX Investigator, Dr. Wayne Huggins, presented an overview of the PhenX Toolkit, including a live tour, to researchers at RTI International. It has been archived here on the PhenX Toolkit. This seminar and live tour provides researchers with hands-on experience using the web-based, freely-available Toolkit. Since the start of 2013, PhenX Investigators have also participated in the following workshops and conferences:
KOMP2 Translational Workshop, NHGRI – Rockville, MD – June 17-18
Advancing Environmental Health Data Sharing and Analysis: Finding a Common Language, EPA-NIEHS – RTP, NC – June 25
Be on the lookout for PhenX at the American Society of Human Genetics (ASHG) in Boston, MA, October 22-26, 2013. The PhenX booth is #1052, and we will be presenting a Poster, #1826W, on Wednesday, October 23. We look forward to seeing you there!
The PhenX Toolkit
The PhenX (Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is a catalogue of well-established, standard measures of phenotypes and exposures recommended for genomic and other biomedical research studies. The PhenX Toolkit includes 21 research domains (fields of research) and 295 measures. An additional 44 measures provide depth in support of Substance Abuse and Addiction research. The Toolkit is funded by NHGRI through a Genomic Resource Grant to RTI International. Additional support is provided by the National Institutes of Health's (NIH) Office of Behavioral and Social Sciences Research (OBSSR) and NIDA.
The Toolkit provides detailed protocols to ensure that the data collected are comparable across studies. Investigators who come to the Toolkit when designing or expanding a study can be confident that PhenX measures are high quality, having been broadly validated in previous studies. This is particularly helpful for investigators who want to expand their study beyond the primary research focus. The PhenX team is striving to ensure that this resource meets the needs of the scientific community: please provide feedback when you use the Toolkit.