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Glossary of PhenX Terms and Acronyms

The following terms are defined for the PhenX project. A list of acronyms can be found here.

PhenX Term Definition
Archive: A location for the previous version of measures and protocols after the Expert Review Panel has convened and made recommendations.
Archived measure or protocol: A measure or protocol that is no longer recommended for use, and is placed in the Archive. Measures or protocols in the archive may be viewed but not added to "My Toolkit."
Back-compatibility: If a protocol is updated or replaced the back-compatibility of the previous protocol with the new/updated protocol must be assessed. The three categories are: "back compatible", "partially back-compatible", and "not back-compatible". If the protocol is either partially or not back-compatible there will be changes to the data dictionary.
Collection: A grouping of measures with a shared characteristic, target population or topic. The measures included in a Collection may cut across research domains.
Common Data Element (CDE): In the PhenX Toolkit, each PhenX Measure has at least one corresponding CDE registered in the NCI cancer Biomedical Informatics Grid (caBIG). The CDEs are developed according to guidelines set by caBIG. The purpose of defining CDEs is to unambiguously represent the data captured by a specific Measure Protocol. Each CDE is constructed by uniquely pairing the specific Data Element with its associated Value according to a hierarchical scheme. The PhenX CDEs are deposited in the cancer Data Standards Repository (caDSR).
More information: https://cdebrowser.nci.nih.gov/CDEBrowser/
Comparable PhenX-dbGaP variable mapping: These variables are conceptually the same and can be compared directly or after a transformation or unit conversion. Examples of comparable variables are variables collected using the same protocol; or variables that are recognized as generally providing the same information such as birth date, birth year and age (transformation), or weight in kilograms and pounds (unit conversion).
Core Collection: These measures are appropriate for all research of a specific characteristic, target population or topic. They are a collection of measures that are essential to the study of a particular field of research.
Data Collection Worksheet (DCW): A prototype data collection tool (in MS Word) for the PhenX protocol. It identifies and captures each data item required and collected by the protocol.
Data Dictionary (DD): Lists each variable included in the protocol DCW and its attributes. Data dictionaries are available in two formats: 1) the Word format captures skip patterns commonly used in Epidemiology studies; 2) the CSV format is compatible with the database of Genotypes and Phenotypes (dbGaP) data submission packet.
database of Genotypes and Phenotypes (dbGaP): The database of Genotypes and Phenotypes (dbGaP) presents results of genome studies and is maintained by the National Center for Biotechnology Information (NCBI). dbGaP and PhenX researchers collaborate with one another to provide more resources for the research community.
More information: http://www.ncbi.nlm.nih.gov/gap
Derived Variable: A variable that can be calculated using a combination of the results from multiple PhenX Measures or a combination of results from PhenX Measures and non-PhenX Measures. BMI is an example of a Derived Variable for the PhenX Measures Height and Weight.
Essential Data: Essential Data includes variables that are not necessarily specified by the protocol, such as date of exam or blood pressure cuff size, but that need to be collected and recorded along with the main phenotypes/variable(s)
Essential Measure: Essential Measures are other PhenX Toolkit measures that are needed to interpret the results of the measure of interest, such as age when measuring height or weight.
Expert Review Panel (ERP): The group of experts who review one or more of the domains of existing PhenX measures to assess the scope of the domain, determine if new measures should be added, existing measures retired, descriptions of the measure be changed, or if the protocols need to be updated, replaced, or retired. All ERP recommendations must be approved by the PhenX Steering Committee.
Key Words/Related Concepts: The words, terms, and phrases searched by the PhenX Toolkit query tool.
Mental Health Research (MHR): The MHR project was launched to expand the breadth and depth of MHR measures in the Toolkit by adding two Specialty Collections and a Core Collection of MHR measures.
NHGRI: The National Human Genome Research Institute (NHGRI) is the NIH Institute which provides funding for PhenX through a cooperative agreement (# 1U01 HG004597-01).
More information: http://www.genome.gov/
NIDA: The National Institute on Drug Abuse (NIDA) is an NIH Institute which provided additional funding for the PhenX Substance Abuse and Addiction (SAA) project through an administrative supplemental to the National Human Genome Research Institute (NHGRI) cooperative agreement (U01 HG004597).
More information: http://www.drugabuse.gov/
NIH Liaison: NIH Institutes and Centers (ICs) have supported, and continue to support GWAS and epidemiological studies. Liasons from the ICs are invited to participate in PhenX to lend their substantial expertise and experience to the PhenX consensus building process.
More information: https://www.phenx.org/Default.aspx?tabid=66
OBSSR: The Office of Behavioral and Social Sciences Research (OBSSR) in the NIH Office of the Director provided additional funding for PhenX through administrative supplements to the National Human Genome Research Institute (NHGRI) cooperative agreement (U01 HG004597).
More information: http://obssr.od.nih.gov/index.aspx
PhenX: PhenX is pronounced "phoenix" and refers to "consensus measures for Phenotypes and eXposures"
PhenX Domain: A PhenX Domain is a field of research with a unifying theme and easily enumerated quantitative and qualitative measures (e.g. demographics, anthropometrics, organ systems, complex diseases and lifestyle factors).
PhenX Measure: A PhenX Measure refers broadly to a standardized way of capturing data on a certain characteristic of, or relating to a study subject.
PhenX Project: The project developing the PhenX Toolkit. PhenX is led and managed by a team of RTI scientists through a cooperative agreement (# 1U01 HG004597-01) from the National Human Genome Research Institute.
PhenX Protocol: A PhenX Protocol is a standard procedure recommended by a Working Group for investigators to collect and record a PhenX Measure.
PhenX Toolkit: The PhenX Toolkit is a web-based catalog of high-priority measures for consideration and inclusion in genome-wide association studies (GWAS) and other large-scale genomic research efforts. For each measure, the PhenX Toolkit provides standard protocols to collect the measures, Common Data Elements and supporting documentation.
More information: https://www.phenxtoolkit.org/
PhenX Variable: A PhenX Variable is developed for each data element collected by the PhenX protocols. PhenX variables can be found in the PhenX Data Dictionary files at the "My Toolkit" page when the PhenX protocol is selected. For each PhenX variable, the data dictionary includes a unique variable name, variable ID, variable description, and other related attributes such as data types, units, and permitted values when applicable.
Quick Start: Quick Start is a series of pages designed to help introduce you to the PhenX Toolkit and get you up and running quickly. The pages lead you through real toolkit pages, helping you to actually log in, browse and search, add measures and protocols into your Toolkit,and download your Toolkit selections as reports.
Related PhenX Measure: An additional PhenX Measure that the user may find helpful based on the selection of a particular PhenX Measure. Related PhenX Measures can include additional Measures that are needed to calculate a Derived Variable (e.g., Weight and Height are needed to calculate BMI), Measures that are commonly used in presentations and publications to present the value of the chosen Measures (e.g., Height and Weight by Race and Ethnicity), Measures that are conceptually related to the chosen Measure (e.g., Current Educational Attainment is conceptually related to Annual Family Income and Arm Span is conceptually related to Height), Measures that are physiologically and/or biologically related to the chosen Measure (e.g., Stroke and Heart Disease). Related PhenX Measures are suggestions only.
Related PhenX-dbGaP variable mapping: These variables are associated with bioassay protocols. Because bioassays may use different protocols to acquire the data, the actual data collected may or may not be comparable. The intent is for investigators to carefully review the methods used to acquire the data before directly comparing or combining data.
Replaced protocol: A description used by the Expert Review Panel that means to replace the previous protocol with a new protocol from a different source. A protocol that has been replaced is archived.
Retired measure or supplemental information: A measure or supplemental information that includes a protocol that is no longer recommended for use. Retired measures still appear with the other measures of the domain but are clearly annotated as "retired" and cannot be added to "My Toolkit". Retired supplemental information is removed from the Supplemental Information section in the Toolkit.
RTI International: The Research Triangle Institute, also known as "RTI International" or "RTI" is an independent nonprofit research institute dedicated to improving the human condition. PhenX is led and managed by a team of RTI scientists.
More information: http://www.rti.org
Selection Criteria for PhenX Measures: Measures are selected for the PhenX Toolkit using the following criteria: clearly defined, well established, broadly applicable, validated, reproducible, specific, reliable, and include standard measurement protocols.
Sickle Cell Disease Research (SCDR): The SCDR project was launched to expand the breadth and depth of SCD measures in the Toolkit by adding two Specialty Collections and a Core Collection of SCD measures.
Smart Query Tool (SQT): A tool for searching for PhenX measures. It offers a high specificity search option and a high sensitivity search option as well as the option to filter on selected attributes of the measures.
Specialty Collection: A collection of measures with a shared characteristic, target population, or topic. that is related to substance abuse and addiction. The use of these measures is study-specific.
Steering Committee: The PhenX Steering Committee is a 12 member team responsible for selecting PhenX domains, establishing the domain-specific Working Groups, communicating PhenX to the larger research community, and setting guidelines for the PhenX Toolkit.
More information: https://www.phenx.org/Default.aspx?tabid=57
Substance Abuse and Addiction (SAA): The SAA project was launched to expand the breadth and depth of SAA-related measures in the Toolkit, by adding six Specialty Collections and a Core Collection of SAA measures.
Supplemental Information: The Supplemental Information describes the scope of each PhenX Domain, includes other Measures considered by the Working Group (not selected for the Toolkit) and additional comments from the Working Group.
More information: https://www.phenx.org/Default.aspx?tabid=281
Tobacco Regulatory Research (TRR): The TRR project was launched to expand the breadth and depth of TRR related measures in the Toolkit by adding five Specialty Collections and a Core Collection of TRR measures.
Updated protocol: A description used by the Expert Review Panel that means to update the previous protocol with a more current protocol from the same source or some minor edits to descriptions or references of the protocol.
Well-Established : A well-established protocol is one that is readily accepted and recognized by the researchers within a given area of expertise. It may have been used by many investigators and studies over time, come from a highly-regarded source or long-running study (NHANES, Framingham, etc.), and be a protocol that you, as an expert in the field, would recommend to others.
Working Group: A PhenX Working Group is assembled for each domain. Each Working Group includes 6-8 scientists with relevant expertise. The Working Group reviews well-established measures, and proposes measures for outreach to the research community. After the research community has reviewed these measures, the Working Group selects the high priority measures to include in the PhenX Toolkit. Measures that were not chosen are available in the Supplemental Information.
More information: https://www.phenx.org/Default.aspx?tabid=58
www.phenx.org: This is the primary web portal for information about the PhenX project. PhenX Steering Committee Members and Working Group Members have access to a private area of the PhenX portal. The portal also supports the consensus process needed to review and finalize measures for Domains.
More information: https://www.phenx.org


Acronyms

Acronym Meaning
CDE: Common Data Element
DCW: Data Collection Worksheet
DD: Data Dictionary
dbGaP: database of Genotypes and Phenotypes
GWAS: genome-wide association studies
ICs: Institutes and Centers
MHR: Mental Health Research
MHRP: Mental Health Research Panel
NHGRI: National Human Genome Research Institute
NIDA: National Institute on Drug Abuse
NIH: National Institutes of Health
OBSSR: Office of Behavioral and Social Sciences Research
P3G: Public Population Project in Genomics
PhenX: consensus measures for Phenotypes and eXposures
RTI: Research Triangle Institute
SQT: Smart Query Tool
SAA: Substance Abuse and Addiction
SCDR: Sickle Cell Disease Research
SSP: Substance Abuse and Addiction Scientific Panel
TRR: Tobacco Regulatory Research
TRRP: Tobacco Regulatory Research Panel

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