Data Collection and Processing
This section principally presents material supporting design and conduct of data (questionnaire, physical measures, etc.) collections and processing.
Conceptualization
Please visit the following section:
Design and Conduct
Questionnaires
In Theory
Data classification index and general documentation on collection of epidemiological data.
Please visit also the following section(s):
Consensus measures for phenotype and exposure (PhenX) 
This website aims to contribute to the integration of genetics and epidemiologic research. A recommended minimal set
of high priority measures for use in Genome-wide Association Studies (GWAS) and other large-scale genomic research
effort are presented in the
PhenX toolkit
under different domains. Standard procedure protocols are provided for each measure in the toolkit. PhenX is led by
RTI International and funded by the National Human Genome Research Institute (NHGRI).
Recommendation for
indicators, international collaboration, protocol and manual of operations for chronic disease risk
factor surveys
Part II of this document deals with issues related to defining every step of the survey organization, from the
target population to the recruitment
per se. Part III contains protocols and operational guidelines for individual measurements and biological
samples collection. A European Health Risk Monitoring-written document, the Copyright is reserved for the Finnish
National Public Health Institute (2002).
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Comparison Chart of Guidelines
This document compares selected reference guidelines written by well-known organizations. These guidelines cover all biobanking steps, i.e. biological sample collection, labelling, processing, and storage applied to a wide range of sample types. A P3G-prepared document (2008). |
Classification indexes
Anatomical Therapeutic Chemical Classification
System (ATC/DDD Index 2006)
This website gives access to information about, and documents refering to, the classification of drugs. There is an
important focus on adopting a standardized approach based on the Anatomical Therapeutic Chemical (ATC)
classification and on the Defined Daily Dose (DDD), a technical unit of measurement for drug utilisation studies. A
World Health Organization Collaborating Centre for Drug Statistics Methodology website. The website is situated at
the Norwegian Institute of Public Health.
Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR)
This website contains the handbook for mental health professionals listing different categories of mental disorder and
the criteria for their diagnoses. Published by the American Psychiatric Association and presented on the
BehaveNet®Inc website.
International Classification of Diseases (ICD)
This website presents the last version of the ICD-10, a detailed description of known diseases and injuries. Every
disease (or group of related diseases) is described together with its diagnosis and its unique code. A World Health
Organization classification.
International Standard Classification
of Occupations (ISCO)
This website presents the classification structure for organizing jobs into a defined set of groups according to the
tasks and duties undertaken in the job. Developed by the International Labour Organization.
ISCED97
This document presents the International Standard Classification of Education (ISCED), a framework for the compilation
and presentation of national and international education statistics and indicators. It contains standard concepts,
definitions and classifications. Designed by UNESCO Institute of Statistics (1997).
National Occupational Classification (NOC)
This website provides a complete listing of all the categories under which Canadian jobs are classified and their
description. A Statistics Canada-maintained website.
Standard Occupational Classification (SOC)
This website details a standardized system for classifying occupations in the United Kingdom. An Office of National
Statistics-maintained website.
International Classification of
Functioning, Disability and Health (ICF)
This website details a standardized system for classifying of health and health related domains that describe body
functions and structures, activities and participation. The domains are classified from body, individual and
societal perspectives. Since an individual's functioning and disability occurs in a context, ICF also includes a
list of environmental factors. ICF is a new member of WHO Family of International Classifications.
In Practice
Real-life examples related to collection of epidemiological data.
Please visit the following sections:
-
P3G Questionnaire Catalogue
- P3G Repository of Reference Questionnaires
- Repository of P3G Comparison Charts
Automated Self-administered 24-hour Dietary Recall (ASA24)
ASA24 is a software tool that enables automated and self-administered
24-hour dietary recalls. ASA24 consists of a Respondent Web site used by
study participants to complete recalls and a Researcher Web site used by
researchers to manage study logistics. This software has been developped
by NCI in collaboration with USDA investigators and under contract with
Archimage in Houston, TX, and Westat in Rockville, MD (2005).
Database of Genotypes and Phenotypes (dbGaP)
This website lists studies investigating the interaction of genotype and phenotype. Open access data includes a
study description, phenotypic variables of interest, study documents (questionnaire, standard operating procedures,
consent forms, etc), and genotype-phenotype analyses. The database can be searched by studies, disease, or keywords
and access to datasets can be requested. This website is maintained by the National Center for Biotechnology
Information (NCBI). (2006).
UK Biobank: Report of the
integrated pilot phase
This document reports on, and provides recommendations based on, the results obtained from the pilot phase of UK Biobank.
The pilot phase was conducted between February and June 2006, in order to assess the basic design of the study and
the approaches to data and sample collection. Prepared by UK Biobank (2006).
UK Biobank: Protocol for a large-scale prospective
epidemiological resource
Part 1 of this document outlines the scientific rationale for constructing a very large cohort-based biobank in
middle aged adults in the UK. It also considers the basic design of such a study, reviewing and justifying decisions
about baseline quetionnaires, physical measures and biological samples. Prepared by UK biobank (2007).
National Health and Nutrition Examination
Survey (NHANES)
This website of the American survey displays all serum/plasma collection and biochemistry procedures, from cholesterol to
heavy metals, electrolytes, metabolic enzymes. It also provides among others questionnaire administration methods
and individual physical and cognitive measurements US Department of Health and Human Services-maintained website
(2006).
The National Children's Study
This section of the website of the National Children's Study (NCS) displays the "Reviews and Analytic Reports". It offers
access to a wide variety of literature reviews and "white papers" on study design and conduct relevant to the
construction of a large (approx 100 000 live births) national birth cohort. Other sections of the website deal with
issues specific to the NCS itself (e.g. study hypotheses). The website is cosupported by the U.S. Environmental
Protection Agency, U.S. Department of Health and Human Services and USA.gov Agency.
Questionnaire Modules
This section of the website is a collection of research questionnaires intended to serve only as models and be adapted by researchers to suit
their particular needs. This tool is provided by the National Cancer Institute's Division of Cancer Epidemiology and
Genetics.
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Comparison Chart of Key Health Organizations/Projects Involved in Biobanking This document presents selected Key Health Organizations/Projects involved in Biobanking. For each organization/project, the table addresses the general mission and indicates if it is particularly involved in the four following domains: (1) Guidelines and scientific tools creation to support biobanks, (2) Networking and harmonization, (3) Scientific Discoveries and (4) Biobanking. A P3G-prepared document (2010). |
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Mental Disorders Assessment Comparison Chart
This document compares selected reference Mental Disorders instruments. For each instruments, the table addresses the main fields of comparison, i.e. authors, objectives, domains covered, population targeted, time recall, number of items, administration mode, available translations, copyright, condition of use and references. A P3G-prepared document (2009). |
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Social Support Assessment Comparison Chart
This document compares selected reference social support instruments. For each instrument, the table addresses the main fields of comparison, i.e. authors, objectives, domains covered, population targeted, time recall, number of items, administration mode, available translations, copyrights, condition of use and references. A P3G-prepared document (2009). |
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Nutrition Assessment Comparison Chart
This document compares the different approaches for dietary assessments. For each approach, the table addresses the main fields of comparison, i.e. objectives, quantitative/semi-quantitative approaches, time recall, strengths/weaknesses, number of items, administration mode, references and references of studies using this approach. A P3G-prepared document (2009). |
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Physical Activity Assessment Comparison Chart
This document compares selected reference physical activity instruments developed to enable comparisons across culturally diverse populations. For each instrument, the table addresses the main fields of comparison, i.e. authors, objectives, domains covered, population targeted, time recall, number of items, administration mode, available translations, copyrights, condition of use and references. A P3G-prepared document (2008). |
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Physical Fitness Assessment Comparison Chart
This document introduces the main tests which can be used in the assessment of physical fitness and compares their representation among a reference studies/organisms panel. For each test, the objective and a brief description are given. A P3G-prepared document (2009). |
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Health-Related Quality of Life (QoL) Assessment Comparison Chart
This document compares selected reference health-related quality of life instruments. For each instrument, the table addresses the main fields of comparison, i.e. authors, objectives, domains covered, population targeted, time recall, number of items, administration mode, available translations, copyrights, condition of use and references. A P3G-prepared document (2008). |
HuGE Navigator
This website provides access to a continuously updated knowledge base in human genome epidemiology
through three main section. The HuGEpedia,
including Phenopedia and
Genopedia,
is an encyclopedia of human genetic variation in health and disease. HuGEtools allow users to search and
mine the literature in human genome epidemiology (
HuGE Literature Finder,
GWAS Integrator,
HuGE Investigator Browser,
Gene Prospector,
Genotype Prevalence Catalog,
HuGE Watch,
Variant Name Mapper,
HuGE Risk Translator
). A series of HuGE related informatics utilities and projects such as
GAPscreener,
HuGE Track,
and Open Source are available
in the HuGEmix section. Website developed and maintained
by the Human Genome Epidemiology Network (HuGENet™)(2009).
IT Tools
Selected software for data entry.
Epi Info™
Epi Info™ is a versatile software which was developed for work at the interface between epidemiology and public health. It can be
used to quickly develop a simple questionnaire or form, to customize the data entry process or to undertake basic
analyses. The emphasis is on speed and ease of use, it is not a platform for sophisticated modelling. The software
and website are now maintained by the Centers for Disease Control and Prevention (CDC) in the United States.
PEDSYS
PEDSYS is a database system developed to provide a software environment in which to manage and analyse genetic and
demographic data, particularly in relation to pedigree (family-based) data. The system supports integrated
collection, management and analysis of constantly evolving data sets. The software and website are supported by the
Southwest Foundation For Biomedical Research.
Progeny Anywhere
Pregeny Anywhere is a pedigree drawing component (ActiveX Control or JavaBean). It allows to produce pedigrees directly or from
downloaded information. It is a free online tool from Progeny Software.
Physical and Cognitive Measures
In Theory
General documentation and guidelines regarding collection of physical and cognitive measures.
Please visit also the following section(s):
Consensus measures for phenotype and exposure (PhenX)
This website aims to contribute to the integration of genetics and epidemiologic research. A recommended minimal set
of high priority measures for use in Genome-wide Association Studies (GWAS) and other large-scale genomic research
effort are presented in the
PhenX toolkit
under different domains. Standard procedure protocols are provided for each measure in the toolkit. PhenX is led by
RTI International and funded by the National Human Genome Research Institute (NHGRI).
Recommendation for indicators, international
collaboration, protocol and manual of operations for chronic disease risk factor surveys
Part III of this document contains protocols and operational guidelines for individual measurements. A European Health Risk
Monitoring-written document, the Copyright is reserved for the Finnish National Public Health Institute (2002).
|
|
Comparison Chart of Guidelines
This document compares selected reference guidelines written by well-known organizations. These guidelines cover all biobanking steps, i.e. biological sample collection, labelling, processing, and storage applied to a wide range of sample types. A P3G-prepared document (2008). |
In Practice
Real-life examples related collection of physical and cognitive measures.
Please visit the following section:
Database of Genotypes and Phenotypes (dbGaP)
This website lists studies investigating the interaction of genotype and phenotype. Open access data includes a
study description, phenotypic variables of interest, study documents (questionnaire, standard operating procedures,
consent forms, etc), and genotype-phenotype analyses. The database can be searched by studies, disease, or keywords
and access to datasets can be requested. This website is maintained by the National Center for Biotechnology
Information (NCBI). (2006).
Atherosclerosis Risk in Communities (ARIC)
This is the website of the American ARIC study. It displays biochemical procedures such as Blood Collection and
Processing, Lipid and Lipoprotein Determinations, Hemostasis Determination and Clinical Chemistry Determinations
that were used during the recruitment and the follow up. A Collaborative Studies Coordinating Center-maintained
website, based at the University of North Carolina.
National Health and
Nutrition Examination Survey (NHANES)
This website of the American survey displays all serum/plasma collection and biochemistry procedures, from cholesterol to
heavy metals, electrolytes, metabolic enzymes. It also provides among others questionnaire administration methods
and individual physical and cognitive measurements US Department of Health and Human Services-maintained website
(2006).
Analysis
Please visit the following section:
Dissemination
In Theory
NHMRC Biobanks Information Paper
The aim of this paper is to provide information relevant for the
establishment, management and governance of biobanks in Australia.
National and international documentation, as well as other relevant case
studies are used to identify best practices with regard to
standardization of biobank policies, practices and procedures. Prepared
by the NHMRC (2010).
In Practice
Please visit the following section:
Database of Genotypes and Phenotypes (dbGaP)
This website lists studies investigating the interaction of genotype and phenotype. Open access data includes a
study description, phenotypic variables of interest, study documents (questionnaire, standard operating procedures,
consent forms, etc), and genotype-phenotype analyses. The database can be searched by studies, disease, or keywords
and access to datasets can be requested. This website is maintained by the National Center for Biotechnology
Information (NCBI). (2006).
The Human Genome Variation database of Genotype-to-Phenotype information
This website lists and describes genetic association studies. Studies can be searched by phenotypes,
genetic markers, or results of interest. Study designs and results can be compared using the browser tool.
It is maintained by a team led by Professor Anthony Brookes.
GAPPNET
This organization aims to accelerate and streamline effective and responsible use of validated and
useful genomic knowledge and applications. GAPPNET has 4 functions: knowledge synthesis and dissemination,
evidence-based recommendations development, translational research and translational programs;
for which some tools have been developed such as ACCE,
EGAPP,
USPSTF.
GAPPNet was formed by CDC's Office of Public Health Genomics, NCI's Division of Cancer Control and
Population Sciences, and other stakeholders in 2009.
HuGE Navigator
This website provides access to a continuously updated knowledge base in human genome epidemiology
through three main section. The HuGEpedia,
including Phenopedia and
Genopedia,
is an encyclopedia of human genetic variation in health and disease. HuGEtools allow users to search and
mine the literature in human genome epidemiology (
HuGE Literature Finder,
GWAS Integrator,
HuGE Investigator Browser,
Gene Prospector,
Genotype Prevalence Catalog,
HuGE Watch,
Variant Name Mapper,
HuGE Risk Translator
). A series of HuGE related informatics utilities and projects such as
GAPscreener,
HuGE Track,
and Open Source are available
in the HuGEmix section. Website developed and maintained
by the Human Genome Epidemiology Network (HuGENet™)(2009).
IT Tools
ORCID
This website aims
to solve the author/contributor name ambiguity problem in scholarly
communications by creating a central registry of unique identifiers for
individual researchers and an open and transparent linking mechanism
between ORCID and other current author ID schemes. ORCID is an
independent organization.
