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Your Environment. Your Health.

Goal 7 – Knowledge Management

Implementation Highlights and Accomplishments

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Use knowledge management techniques to create a collaborative environment for the EHS community, to encourage an interdisciplinary approach to investigate, analyze, and disseminate findings.

  1. Develop bioinformatics, biostatistics, and data integration tools to conduct interdisciplinary research for application to environmental health science.
  2. Develop and invest in publicly available resources and computational tools, for integrating and analyzing environmental health data.

Research Funding

Novel Methods for Obtaining Molecular Information from Archived Tissue Samples (R43/R44)
This Funding Opportunity Announcement (FOA) solicits Small Business Innovative Research (SBIR) grant applications from small business concerns (SBCs) to develop novel technologies to expand the capability for molecular analyses of banked frozen or formalin-fixed, paraffin-embedded tissues. There is a need for improved tissue preservation methods that maintain histologic features while preserving high quality DNA, RNA, protein and small molecules in archived tissue from rodent and human studies. In addition, novel approaches are needed to preserve DNA, RNA, and small molecules during collection and storage of biological samples. ES-16-012

Big Data to Knowledge (BD2K) Community-Based Data and Metadata Standards Efforts (R24)
This Funding Opportunity Announcement (FOA), under the Big Data to Knowledge (BD2K) initiative, is to provide time-limited, catalytic support for activities necessary to develop or extend/refine data and metadata standards and/or related tools in areas relevant to the NIH basic, translational, and clinical research mission. Projects can support activities at any point in the data standards lifecycle and should build on existing partnerships, infrastructure, and resources whenever possible. Projects must demonstrate a compelling science community interest and need for standards efforts in the specific domain(s) of interest, as well as a plan for meaningful engagement of the end-user communities and relevant stakeholders in the process. The data standard and any associated tools or products developed should be made freely available to the scientific research community via a curated, searchable portal. Projects should address long-term maintenance and sustainability of the data standard after the period of the NIH award; issues to be considered include approaches for dissemination, evaluation, and updating/refinement. Both short-term and longer-term projects are eligible. ES-16-010

Maintain and Enrich Resource Infrastructure for Existing Environmental Epidemiology Cohorts (R24)
The purpose of this Funding Opportunity Announcement (FOA) is to solicit grant applications that propose to: (1) support the maintenance of existing Environmental Epidemiology Cohorts (EECs) and to (2) enrich research infrastructure to improve scientific activities and resource sharing with the broader scientific communities.

The ultimate goal is to maintain and maximize NIEHS cohort investments within the environmental epidemiology community by supporting the infrastructure needed to prepare for future research opportunities and to promote broader scientific collaborations. ES-16-004

NIEHS SBIR Phase IIB Awards for Validation and Commercialization of Approaches to Reduce Animal Use in Toxicology Testing (U44)
This FOA provides additional support to SBIR/STTR Phase II grantees for the validation and commercialization of methods that either replace or reduce the number of animals (referred to as alternative test methods) used in in vivo toxicology screening and testing requirements set forth by US federal government agencies.

Proposed projects must address non-clinical toxicology testing requirements currently used or required by a US federal government agency. Applicants must submit a Validation and Commercialization Plan, which should include details on a specific US federal agency’s required endpoint(s) being assessed and a description of anticipated impact on the 3Rs of animal use (reduction, refinement and/or replacement) with adoption and implementation of the alternative test method. A listing of the different agency regulations and guidelines, by topic, can be found on the NTP website.

A minimum requirement for this funding opportunity is proposal of an alternative test method that can be utilized either as a stand-alone replacement or developed for use as part of a weight-of-evidence approach. Applications should consider validation guidelines outlined by the Organisation for Economic Co-operation and Development (OECD), in their validation plan. US federal agencies may have additional requirements for acceptance of alternative test methods that should be considered in the further testing and validation of these methods or ICH guidelines. Highest priority will be given to alternative test methods that can serve as stand-alone replacements for animal-based tests currently used or required by US federal agencies. As a cooperative agreement, small business concerns (SBCs) will be expected to work with NIH program staff and the Steering Committee, which may include members of the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM), to develop and implement the final validation plan for the proposed alternative test method. ICVAAM, which has representatives from multiple US federal agencies, will assist in coordinating validation steps including additional requirements that specific US federal agencies may have for acceptance of the alternative test method. ES-15-016

Big Data to Knowledge (BD2K) Enhancing the Efficiency and Effectiveness of Digital Curation for Biomedical Big Data (U01)
The purpose of this BD2K Funding Opportunity Announcement (FOA) is to support the development, improvement and implementation of tools and approaches that increase the efficiency and effectiveness of digital curation processes used to characterize and describe the digital data used in or resulting from biomedical research. LS-17-001

BD2K Open Educational Resources for Skills Development in Biomedical Big Data Science (R25)
The NIH Research Education Program (R25) supports research education activities in the mission areas of the NIH. The over-arching goal of this Big Data to Knowledge (BD2K) R25 program is to support educational activities that complement and/or enhance the training of a workforce to meet the nation’s biomedical, behavioral and clinical research needs.

To accomplish the stated over-arching goal, this FOA will support creative educational activities with a primary focus on Courses for Skills Development for biomedical researchers who need the requisite knowledge and skills to extract knowledge from biomedical Big Data. To extend the reach of the course, each educational activity is required to develop open educational resources (OERs) that adhere to FAIR (findable, accessible, interoperable, and reusable) principles. Ideally, OERs should be useful to individuals at all career levels, from predoctoral students to established investigators. HG-16-016

 

Children's Health Exposure Analysis Resource (CHEAR)
NIEHS is establishing an infrastructure, the Children's Health Exposure Analysis Resource (CHEAR), to provide the extramural research community access to laboratory and statistical analyses to add or expand the inclusion of environmental exposures in their research.  CHEAR is being solicited through three FOAs, this FOA solicits a network of laboratories providing a comprehensive suite of laboratory-based analytical services for samples derived from extant or ongoing children's health studies in the extramural research community. Each laboratory center (defined in this FOA as a Hub) within the network will provide analysis of environmental and endogenous exposures through both targeted and untargeted approaches.  Each Hub will also provide analyses of biological response indicators such as DNA damage, oxidative stress, immune/inflammation indicators and other molecular markers.  Hubs will incorporate a developmental core to develop novel measures for exposures and responses, expanding the number of current, commonly measured analytes, and developing new methods for detecting analytes in other biological matrices, in addition to serum, plasma or urine.

The Children's Health Exposure Analysis Resource (CHEAR) is a multi-unit infrastructure to provide access to comprehensive exposure analysis that can be performed using biological samples collected in studies of children's health.  The network has three units, a National Exposure Assessment Laboratory Network and an Exposure Data Repository and Resource for Statistical Analysis and Methods Development, as well as a coordinating center. ES-15-009, ES-15-010, ES-15-011

Worker Training Program (WTP) Ebola Biosafety and Infectious Disease Response Training (UH4)
The National Institute of Environmental Health Sciences (NIEHS) Worker Training Program (WTP) invites applications for cooperative agreements to support the development and implementation of occupational safety and health and infection control training programs for workers who may be at risk during infectious disease outbreaks.  NIEHS WTP will coordinate with the CDC,  the Department of Health and Human Services (DHHS) Office of the Assistant Secretary for Preparedness and Response (ASPR), the Occupational Safety and Health Administration (OSHA), and the National Institute of Occupational Safety and Health (NIOSH) to provide guidance materials, as developed or suggested under the cooperative agreements by federal partners,  such as targeted fact sheets, videos, podcasts and so forth, and assist awardees to develop an evidence-based curricula. RFA-ES-15-018

NIEHS SBIR Phase IIB Awards for Validation and Commercialization of Approaches to Reduce Animal Use in Toxicology Testing (U44)
This FOA provides additional support to SBIR/STTR Phase II grantees for the validation and commercialization of methods that either replace or reduce the number of animals (referred to as alternative test methods) used in in vivo toxicology screening and testing requirements set forth by US federal government agencies.

Proposed projects must address non-clinical toxicology testing requirements currently used or required by a US federal government agency. Applicants must submit a Validation and Commercialization Plan, which should include details on a specific US federal agency’s required endpoint(s) being assessed and a description of anticipated impact on the 3Rs of animal use (reduction, refinement and/or replacement) with adoption and implementation of the alternative test method. A listing of the different agency regulations and guidelines, by topic, can be found on the NTP website.

A minimum requirement for this funding opportunity is proposal of an alternative test method that can be utilized either as a stand-alone replacement or developed for use as part of a weight-of-evidence approach. Applications should consider validation guidelines outlined by the Organisation for Economic Co-operation and Development (OECD), in their validation plan. US federal agencies may have additional requirements for acceptance of alternative test methods that should be considered in the further testing and validation of these methods or ICH guidelines. Highest priority will be given to alternative test methods that can serve as stand-alone replacements for animal-based tests currently used or required by US federal agencies. As a cooperative agreement, small business concerns (SBCs) will be expected to work with NIH program staff and the Steering Committee, which may include members of the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM), to develop and implement the final validation plan for the proposed alternative test method. ICVAAM, which has representatives from multiple US federal agencies, will assist in coordinating validation steps including additional requirements that specific US federal agencies may have for acceptance of the alternative test method. ES-15-016

Selected Scientific Advances

2016

  • Strickland J, Zang Q, Kleinstreuer N (DNTP), Paris M, Lehmann DM, Choksi N, Matheson J, Jacobs A, Lowit A, Allen D, Casey W (DNTP). 2016. Integrated decision strategies for skin sensitization hazard. J Appl Toxicol 36(9):1150-1162. [Abstract]
    This study describes the process undertaken by ICCVAM to develop integrated decision strategies based on the adverse outcome pathway using in vitro, in chemico, and in silico information.
  • Kleinstreuer NC (DNTP), Ceger P, Watt ED, Martin M, Houck K, Browne P, Thomas RS, Casey WM (DNTP), Dix DJ, Allen D, Sakamuru S, Xia M, Huang R, Judson R. 2016. Development and Validation of a Computational Model for Androgen Receptor Activity. Chem Res Toxicol 30(4):946-964. [Abstract]
    Researchers integrated 11 high-throughput in vitro screening ToxCast/Tox21 in vitro assays into a computational network model to distinguish true androgen receptor pathway activity from technology-specific assay interference.
  • Vandenberg LN, M Agerstrand, A Beronius, C Beausoleil, A Bergman, LA Bero, CG Bornehag, CS Boyer, GS Cooper, I Cotgreave, D Gee, P Grandjean, KZ Guyton, U Hass, JJ Heindel (DERT), S Jobling, KA Kidd, A Kortenkamp, MR Macleod, OV Martin, U Norinder, M Scheringer, KA Thayer (NTP), J Toppari, P Whaley, TJ Woodruff and C Ruden. 2016. A proposed framework for the systematic review and integrated assessment (SYRINA) of endocrine disrupting chemicals. Environ Health Perspect 15(1):74. [Abstract]
  • Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W (DNTP), Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M (DNTP), Padilla S, Reif DM, Tanguay RL, Hamm J. 2016. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 33(4):435-452. [Abstract]
  • Smith MT, Guyton KZ, Gibbons CF, Fritz JM, Portier CJ, Rusyn I, DeMarini DM, Caldwell JC, Kavlock RJ, Lambert PF, Hecht SS, Bucher JR (DNTP), Stewart BW, Baan RA, Cogliano VJ, Straif K. 2016. Key characteristics of carcinogens as a basis for organizing data on mechanisms of carcinogenesis. Environ Health Perspect 124(6):713-721 [Abstract]
  • Swartley, OM, Foley, JF (DNTP), Livingston, DP, 3rd, Cullen, JM, Elmore, SA (DNTP). 2016. Histology atlas of the developing mouse hepatobiliary hemolymphatic vascular system with emphasis on embryonic days 11.5-18.5 and early postnatal development. Toxicol Pathol 44(5):705-725. [Abstract]

 

2015

  • Hsieh JH (DNTP), Sedykh A, Huang R, Xia M, Tice RR (DNTP). 2015. A data analysis pipeline accounting for artifacts in tox21 quantitative high-throughput screening assays. J Biomol Screen 20(7):887-897. [Abstract]
    Scientists implemented two graphical user interface applications, allowing users to rapidly analyze Tox21 high-throughput screening data.
  • Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. 2014. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 518(7539):355-359. [Abstract]
    Scientists developed a framework to dissect regulatory networks that can be applied to multiple cell fates and other data sets.
  • Bobb JF, Valeri L, Claus Henn B, Christiani DC, Wright RO, Mazumdar M, Godleski JJ, Coull BA. 2014. Bayesian kernel machine regression for estimating the health effects of multi-pollutant mixtures. Biostatistics 16(3):493-508. [Abstract]
    Here, scientists present a novel modeling approach to study mixtures and estimate the exposure-response as well as pinpoint components of the mixture that result in adverse health outcomes.

2014

  • Rooney AA (NTP), Boyles AL (NTP), Wolfe MS (NTP), Bucher JR (NTP), and Thayer KA (NTP). 2014. Systematic Review and Evidence Integration for Literature-Based Environmental Health Science Assessments. Environ Health Perspect 122(7):711-8. [Abstract]
    Scientists presented a standardized framework to guide literature-based risk assessment and translate evidence of health effects.
  • Cesta MF (NTP), Malarkey DE (NTP), Herbert RA (NTP), Brix A, Hamlin MH, 2nd, Singletary E, Sills RC (NTP), Bucher JR (NTP) and Birnbaum LS (DIR). 2014. The National Toxicology Program Web-based Nonneoplastic Lesion Atlas: A Global Toxicology and Pathology Resource. Toxicol Pathol 42(2):458-60. [Abstract]
    Scientists developed a publically available tool that will allow researchers to evaluate pathology results and compare those to a digital atlas of nonneoplastic lesions.

Other Implementation Activities

NIEHS Climate Change and Human Health Literature Portal
The Climate Change and Human Health Literature Portal is a knowledge management tool for locating the most relevant scientific literature on the health implications of climate change. It provides access to a database of studies from around the world, published between 2007 and 2014. The National Institute of Environmental Health Sciences (NIEHS) developed the database as a technical input to the U.S. Global Change Research Program's Sustained Assessment process. The portal is an effort to make this database more accessible to a wider global audience, and to provide updates on a regular basis to further the study of climate impacts on human health. Climate Change and Human Health Literature Portal 

Transform Tox Testing Challenge
Innovative thinkers are sought for a new federal challenge that will help advance the field of predictive toxicology. The Transform Tox Testing Challenge: Innovating for Metabolism, issued on Jan. 8, will provide up to $1 million in total prizes for modifications to existing high throughput screening (HTS) designs and prototypes that allow both chemicals and their metabolite products to be evaluated.

The National Toxicology Program (NTP) has joined with the National Center for Advancing Translational Sciences, also part of the National Institutes of Health, and the U.S. Environmental Protection Agency (EPA) to issue this new challenge. The goal is to improve the relevance and accuracy of toxicity data generated by automated chemical screening technology.

Climate Change and Environmental Exposures Challenge
On Feb. 23, NIEHS announced winners of its Climate Change and Environmental Exposures Challenge, naming a first place winner in both the national and local categories, and two second place winners in the local category, with a total of $30,000 in prizes.

The challenge invited innovators and environmental health specialists alike to develop data visualization tools and maps that will help decision-makers and the general public respond to the environmental health risks presented by climate change. NIEHS has posted links to the winning tools on the webpage linked above.

Comparative Toxicogenomics Database
Funded in part by NIEHS, scientists at the pharmaceutical corporation Pfizer Inc. and academic researchers affiliated with the Comparative Toxicogenomics Database (CTD) have integrated information about the toxicity of more than 1,200 pharmaceuticals into this publicly available research resource. The database provides chemical-gene-disease information and associated functional and pathway data. The Pfizer collaboration specifically added data for chemicals that may be involved in cardiovascular, neurological, kidney, and liver disorders. Molecular toxicologist Carolyn Mattingly, Ph.D., associate professor at North Carolina State University,has been directing the development of the CTD with NIEHS support since 2001. This is the only database that connects mechanisms of chemical action to potential impacts on human health. Comparative Toxicogenomics Database.

NIH Disaster Research Response
DR2 is a pilot project aimed at creating an environmental health disaster research system through platforms of ready-to-go research data collection tools and a network of specially trained research responders. This project was developed and will be administered by the NIEHS and NLM. NIEHS will build on our extensive program capabilities, research networks, and field experiences in leading this pilot. NLM will support the organization, management, and public interface of developed tools & communications. NIEHS leads disaster research response project.

U.S. Climate Resilience Toolkit and the Building Health Care Sector Resilience Toolkit
NIEHS has played a substantial role in several data initiatives developed in response to the President’s Climate Action Plan. The goal of the Building Health Care Sector Resilience toolkit is to help the health care sector better respond to extreme weather events and other impacts of climate change. This resource is part of the larger U.S. Climate Resilience Toolkit that provides public health officials, city planners, researchers, and others with information and decision-making tools. NIEHS supports White House event on climate change and health.

NIH Roadmap Epigenomics Program Resource
The NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. The group has described the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. It also established global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. This provides a resource for interpreting the molecular basis of human disease. Integrative analysis of 111 reference human epigenomes.

Epidemiology Resources Catalog
This online catalog of cohort, case-control, and cross sectional studies funded by NIEHS was launched in May 2015. It currently includes information on PI, life-stage of research subjects, exposures and health outcomes studied, and study location. The goals of the catalog are to facilitate new collaborations and data sharing in the EH community; maximize NIEHS investments, especially for studies where biosamples were collected; and provide junior investigators a path to initiate ancillary studies. Phase 2 will involve adding project details such as study design and number of subjects. NIEHS-Funded Epidemiology Resources.

NIH Big Data to Knowledge
As part of wide-ranging grants announced Oct. 10 by NIH, NIEHS is helping develop new strategies to analyze and make good use of the explosion in complex biomedical data sets, often referred to as Big Data. NIEHS is managing the career development portion of this nearly $32 million investment. NIEHS contributes to big NIH investment in biomedical research data.

Integrating Data from Multidisciplinary Research Superfund Risk e-learning Webinar Series:
Part of the SRP Risk e-Learning seminars, this webinar series explores challenges and opportunities for integrating datasets to solve complex environmental health problems. In the first session of this series, speakers introduced and discussed the concept of big data as it relates to environmental health science and provided examples of current initiatives.

Handbook for Conducting a Literature-Based Health Assessment Using OHAT Approach for Systematic Review and Evidence Integration
The NTP Office of Health Assessment and Translation (OHAT) has developed and released a “Handbook for Conducting a Literature-Based Health Assessment Using OHAT Approach for Systematic Review and Evidence Integration” that provides standard operating procedures that improve the reliability, ease, and efficiency of conducting systematic reviews in OHAT evaluations. Systematic Review and Evidence Integration for Literature-Based Environmental Health Science Assessments.

NTP Nonneoplastic Lesions Atlas
Nonneoplastic diseases are a major cause of morbidity and mortality in humans, and many of these are thought to have environmental causes. The NTP Nonneoplastic Lesion Atlas (NNLA) provides diagnostic guidelines for standardizing the terminology of microscopic nonneoplastic lesions in rats and mice to improve the understanding of nonneoplastic lesions and their relevance to human environmental diseases. NTP Nonneoplastic Lesions Atlas..

DREAM Toxicogenetics Challenge
An innovative, crowd-sourced computational challenge, the DREAM Toxicogenetics Challenge was conducted in 2014. DREAM stands for Dialogue for Reverse Engineering Assessments and Methods, and is a joint effort of Sage Bionetworks, NIEHS, the University of North Carolina at Chapel Hill, and the NIH National Center for Advancing Translational Sciences. The goal of the three-month challenge was to find better ways to predict the toxicity of chemicals, and to increase understanding of how a person’s individual genetics can influence cytotoxic response of exposure to widely used chemicals using a specific set of genomic and cytotoxicity data. The DREAM challenge included two subchallenges. Subchallenge 1 involved using the supplied data to accurately predict individual responses to compound exposure, based on genomic information. Subchallenge 2 called for development of a model to accurately predict how a particular population would respond to certain types of chemicals. DREAM challenge results published in Nature Biotechnology.

Office of Scientific Information Management
As part of the implementation of the knowledge management goals of the NIEHS Strategic Plan, a new Office of Scientific Information Management was created at the NIEHS in 2013, and Senior Advisor Allen Dearry, Ph.D., was named its Director. The new office is charged with facilitating a more collaborative approach to science through data sharing, and identifying the technology infrastructure required to enhance data analysis and discovery at the Institute.