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Frequently Asked Questions (FAQ)

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Questions

Do I have permission to use all forms and measures in the Toolkit? If not, what are the restrictions?

Do I need to register to use the PhenX Toolkit?

How are PhenX Domains chosen?

How are the PhenX Portal and the PhenX Toolkit related?

How are the Top 5 Measures and Top 5 Domains determined?

How can I find the measure or protocol I'm looking for?

How do I cite use of the PhenX Toolkit?

How will the Tutorial help me?

Is there a standard format for display of Measures and Protocols?

Is there any guidance on using the PhenX Toolkit?

What are the Substance Abuse and Addiction (SAA) collections, and how are they different from the 21 research domains?

What are the Top 5 Measures and the Top 5 Domains?

What does the PhenX Toolkit offer researchers?

What Domains have been chosen by the PhenX Steering Committee?

What is a Conceptual Group?

What is a Saved Toolkit?

What is PhenX?

What is Quick Start?

What is Supplemental Information?

What is the difference between a Measure and a Protocol?

What is the difference between Essential Measures and Essential Data?

What is the relationship between the Substance Abuse and Addiction (SAA) collections and the Alcohol, Tobacco, and Other Substances (ATOS) domain?

Who are the members of the Working Groups?

Who determines what is included in the Toolkit?

Why do the Protocol images look small?

Why should I join the PhenX Toolkit User Network?

Why should I register on the PhenX Toolkit?

Why should I use the PhenX Measures?

Answers


Do I have permission to use all forms and measures in the Toolkit? If not, what are the restrictions?     « Back to top

In general, PhenX measures are freely available. For any proprietary measures, the Toolkit provides contact information to request permission to use that specific measure.

Do I need to register to use the PhenX Toolkit?     « Back to top

No. You are able to search, browse, choose and report on Measures from the Toolkit.

How are PhenX Domains chosen?     « Back to top

Domains are chosen by the PhenX Steering Committee based on the following criteria:
  • Public health significance
  • Evidence of substantial genetic influence on key phenotypes associated with the domain
  • Evidence of environmental influence on key phenotypes associated with the domain
  • Available, well-established measures and protocols
  • Cross-cutting relevance to several diseases or exposures
  • Broad inclusion in non-GWA studies of diseases
  • Potential for translation to clinical research

How are the PhenX Portal and the PhenX Toolkit related?     « Back to top

The PhenX Portal provides general information about the PhenX project and the consensus process. The PhenX Toolkit presents a recommended set of standard measures for use in Genome-wide Association Studies (GWAS) and other large-scale genomic research efforts.
More information: http://www.phenx.org

How are the Top 5 Measures and Top 5 Domains determined?     « Back to top

The Top Measures and Top Domains are identified by reviewing My Toolkits and calculating the number of times each measure or domain is added to My Toolkits, cumulatively. The measures and domains with the highest inclusion in reports are those listed as Top Measures and Top Domains. This list is recalculated and updated with each Toolkit release. Toolkit release notes and dates can be found at the following link
More information: https://www.phenxtoolkit.org/index.php?pageLink=about.releases

How can I find the measure or protocol I'm looking for?     « Back to top

There are two features one can use to find PhenX measures and protocols:
  1. Browse - Browse by domain or browse the full listing of measures.
  2. Search - Specify the search by using the Smart Query Tool. This tool provides you with the option to using a high specificity search through protocol and measure names, or a full text search through measures and protocols. Use quotation marks to search for the exact phrase.

How do I cite use of the PhenX Toolkit?     « Back to top

Measures from the PhenX Toolkit version June 30 2010, Ver 3.3 (www.phenxtoolkit.org) were included in this analysis. PhenX (consensus measures of Phenotypes and eXposures) is supported by NHGRI award No. U01 HG004597.
More information: https://www.phenxtoolkit.org/index.php?pageLink=help.guidance

How will the Tutorial help me?     « Back to top

The Tutorial provides an example of how to use the PhenX Toolkit to plan studies.

Is there a standard format for display of Measures and Protocols?     « Back to top

Yes. A standard format was adopted to ensure uniform appearance and consistency between Domains. This has resulted in appearance changes between the PhenX Protocols and the original source. This is a cosmetic change only and is primarily a change to the layout of the text. There is no loss of information or meaning.

Is there any guidance on using the PhenX Toolkit?     « Back to top

Yes. Toolkit Guidance is available on the home page. The guidance reminds investigators of their responsibilities and provides links to helpful resources available on the Toolkit, e.g., information to ensure compliance with regulations.
More information: https://www.phenxtoolkit.org/index.php?pageLink=help.guidance

What are the Substance Abuse and Addiction (SAA) collections, and how are they different from the 21 research domains?     « Back to top

Measures pertaining to SAA are found in seven of the research domains, including the Alcohol, Tobacco, and Other Substances domain. The SAA Specialty Collections provide additional measures to use in SAA studies, depending on the research objective. The SAA Core Collection contains measures from across the research domains and the SAA Specialty Collections that are appropriate for all SAA or other research studies.

What are the Top 5 Measures and the Top 5 Domains?     « Back to top

As users download protocols from the Toolkit, statistics are kept on the top Measures and Domains that are included in user "My Toolkits". The top five downloaded measures and domains are listed on the home page of the PhenX Toolkit
More information: https://www.phenxtoolkit.org/

What does the PhenX Toolkit offer researchers?     « Back to top

The Toolkit offers measures that have the potential to be cumulatively combined with other current and future studies that incorporate the same PhenX measures. In addition, the Toolkit:
  • greatly increases the opportunities for cross-study comparison
  • increases statistical power for detection of moderate and complex gene-gene and gene-environment associations
Use of PhenX Measures will help make your study compatible with other studies that also incorporate PhenX Measures. As PhenX measures are widely adopted by the scientific community, this will foster productive collaborations and interdisciplinary research that will greatly increase the opportunities for cross-study comparisons.

What Domains have been chosen by the PhenX Steering Committee?     « Back to top

Twenty-one Domains have been chosen. They include:
  1. Anthropometrics
  2. Alcohol, Tobacco and Other Substances
  3. Cancer
  4. Cardiovascular
  5. Demographics
  6. Diabetes
  7. Environmental Exposures
  8. Gastrointestinal
  9. Infectious Diseases and Immunity
  10. Neurology
  11. Nutrition and Dietary Supplements
  12. Ocular
  13. Oral Health
  14. Physical Activity and Physical Fitness
  15. Psychiatric
  16. Psychosocial
  17. Reproductive Health
  18. Respiratory
  19. Skin, Bone, Muscle and Joint
  20. Social Environments
  21. Speech and Hearing

More information: http://www.phenx.org

What is a Conceptual Group?     « Back to top

Conceptual Groups include measures that cut across the 21 Research Domains and provide Toolkit users with an alternative to browsing the Toolkit by Domain. Measures that are related by topic or that share a specific characteristic are grouped together. We include measures in a Conceptual Group if any part of a protocol or measure fits the definition of that Conceptual Group. A brief description of each Conceptual Group is provided below.

Life stage   A measure is included in a given life stage Conceptual Group if it has at least one protocol valid for participants (or their proxies) who are within the given life stage/age range. Life stages with many measures are subdivided by domain.

Data Collection Mode   The data collection mode Conceptual Group describes the degree and type of interaction with the study participant that is required to administer the protocol(s) for the measure.

Physical Assessment   The physical assessment Conceptual Group classifies measures by the type of physical assessment. It includes measures of the participant, such as height, or of environmental exposures, such as ultraviolet light.

Time   This group classifies measures by the time needed to complete the protocol(s) for the measure.

Source   This Conceptual Group classifies measures by the study or questionnaire from which the protocols for the measure were taken. Sources used for ≥ 5 measures are included.

Risk Factors   This Conceptual Group includes measures associated with one or more diseases or conditions.


What is a Saved Toolkit?     « Back to top

A Saved Toolkit is a named list of Measures and Protocols that were selected during a toolkit session. Once you create a Saved Toolkit, you can return to the Toolkit at any time to review and/or revise the contents of that Toolkit.

What is PhenX?     « Back to top

PhenX is pronounced "phoenix" and refers to "consensus measures for Phenotypes and eXposures"
More information: http://www.phenx.org

What is Quick Start?     « Back to top

Quick Start is a series of pages designed to help introduce you to the PhenX Toolkit. The pages guide you through the actual Toolkit, helping you to log in, browse and search, add measures and protocols into Your Toolkit, and download Your Toolkit selections as reports.
More information: https://www.phenxtoolkit.org/index.php?pageLink=help.wizard

What is Supplemental Information?     « Back to top

The Supplemental Information includes the scope of the Domain, other Measures considered by the Working Group but not selected for the Toolkit and additional comments from the Working Group.
More information: https://www.phenxtoolkit.org/index.php?pageLink=help.wizard

What is the difference between a Measure and a Protocol?     « Back to top

The Measure is "what" is being evaluated. The Protocol is "how" the Measure is obtained. The Protocol may also describe other data, called "essential data" that are required to interpret the Measure.

What is the difference between Essential Measures and Essential Data?     « Back to top

Essential data and Essential measures are critical to the collection of the measure or are necessary for the interpretation of results. 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 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.

What is the relationship between the Substance Abuse and Addiction (SAA) collections and the Alcohol, Tobacco, and Other Substances (ATOS) domain?     « Back to top

The ATOS domain from the original PhenX project includes 14 high-priority measures to use as outcome variables or important environmental covariates to include in genomic studies. The SAA collections contain additional SAA-related standard measures to expand the breadth and depth of the Toolkit for SAA and other researchers.

Who are the members of the Working Groups?     « Back to top

Each WG is assembled to include a balance of diverse perspectives and the expertise needed to cover and broadly represent the scope of the research domain. Each WG is comprised of six to eight researchers. WG members may come from academic institutions, private organizations and the federal government.

Who determines what is included in the Toolkit?     « Back to top

Each WG is tasked with selecting 15 high-priority measures for inclusion in the PhenX Toolkit. Consensus building leads to the final selection of measures. This effort requires coordination between the PhenX Steering Committee and the Working Groups; input from the scientific research community; leadership from RTI International; and support from NHGRI.

Why do the Protocol images look small?     « Back to top

For readability we have adopted the use of thumbnails in the Protocol Detail display pages. You can click on these thumbnails to see the corresponding full-sized image. When you request a report, the full-size images are included.

Why should I join the PhenX Toolkit User Network?     « Back to top

Joining the PhenX Toolkit User Network will allow you to share your profile with other users of the Toolkit - potentially facilitating interactions and collaborations. Network users can view only the profile information you choose to share. Members can opt out of the User Network at any time.

Why should I register on the PhenX Toolkit?     « Back to top

Registered Users have access to additional features such as the ability to save and share multiple Toolkits and attach notes. Becoming a Registered User also helps the toolkit team to serve you better.

Why should I use the PhenX Measures?     « Back to top

The PhenX Toolkit is a valuable resource for any researcher who is planning or expanding a study and would like to incorporate well established measures that have been recommended by experts in the field. Because cross-study analysis can significantly improve statistical power, the inclusion of standard measures will facilitate replication studies, detection of modest associations, and detection of gene-gene and gene-environment interactions.
More information: http://www.phenx.org

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