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Environmental Factor, July 2015

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New data tools top the agenda at NTP board meeting

By Ernie Hood

Bucher

Bucher announced that DNTP was awarded some of the funds redirected after cancellation of the National Children’s Study (NCS) by NIH in December. Remaining true to the original intent of the study, DNTP will use the funds to expand the Tox21 program to encompass a Developmental Toxicity Program. (Photo courtesy of Steve McCaw)

Thayer

Thayer enjoyed one of the lighter moments in a detailed discussion of new data analysis tools that promise to advance systematic review. (Photo courtesy of Steve McCaw)

Daniel Kass

Ad hoc BSC member Daniel Kass, deputy commissioner of the New York City Department of Health and Mental Hygiene, paid close attention at his first meeting and contributed several incisive comments. (Photo courtesy of Steve McCaw)

New and maturing tools to aid the process of systematic review and overall NTP research efforts took center stage at the June 16 meeting of the National Toxicology Program (NTP) Board of Scientific Counselors (BSC).

Representatives of the NTP Office of Health Assessment and Translation (OHAT) briefed the board on several quickly developing innovations. The board also approved two contract concepts and heard updates on topics, such as NTP’s analysis of the chemicals in the 2014 Elk River chemical spill (see story) and an NTP research project to update the levels of concern categories used in NTP conclusions about the hazard identification of environmental exposures.

Hopeful signs on the budget

Later in the morning, after NIEHS and NTP Director Linda Birnbaum, Ph.D., reported on recent and upcoming developments at NTP, she shared an up-to-the-minute news flash from Capitol Hill. The full House Appropriations Committee had just released its fiscal year 2016 Labor, Health, and Human Services funding bill, which includes funding recommendations for the National Institutes of Health (NIH), the parent agency of NIEHS.

In his report, NTP Associate Director John Bucher, Ph.D., announced that Kristina Thayer, Ph.D., was named Deputy Director for Analysis in the Division of the NTP (DNTP). In her new position, Thayer will oversee both OHAT and the Office of the Report on Carcinogens, and she will be responsible for continuing to advance the use of systematic review in environmental health sciences.

Expanding the toolkit

Thayer kicked off a session devoted to briefing the board on new software advances to make the process of conducting a systematic review more efficient, focusing on tools for text mining and machine learning, structured data extraction, and data display.

OHAT has been working extensively to implement systematic review methods, including release of a handbook on conducting systematic reviews in January 2015. “Parallel to adopting principles of systematic review, we’ve made a pretty large investment in tool development,” said Thayer. “These tools have really matured in the past year, to the point now that they can regularly be seen as part of OHAT projects.”

One of the new tools, called SWIFT (Sciome Workbench for Interactive Computer-Facilitated Text Mining), will be released for use later this year and will be freely available. Contractor Ruchir Shah, Ph.D., from Sciome LLC, described the tool as a user-friendly workbench to explore, categorize, search, and perform topic discovery. SWIFT also provides methods to prioritize documents to facilitate screening, with the goal of making the screening process more efficient.

“We started taking concepts from the fields of text mining, information retrieval, and machine learning to statistically analyze large collections of documents,” Shah explained. Among other applications, SWIFT will be used to help generate a new form of OHAT document called a scoping report, which provides an overall sense of the literature on a specific topic. 

OHAT researcher Katherine Pelch, Ph.D., told the board about the first scoping report using the SWIFT text-mining tool to effectively winnow down an enormous number of potential references for a systematic review, in this case, on environmental influences on the epigenome.

Data scientist Andy Shapiro, from the NTP Program Operations Branch presented another tool being developed called HAWC (Health Assessment Workspace Collaboration), a web-based content management system for human health assessments, and its recent application to OHAT assessments.

(Ernie Hood is a contract writer with the NIEHS Office of Communications and Public Liaison.)


  • BSC group photo
    1/8

    Late spring in North Carolina presented the perfect opportunity for a group photo of the BSC, along with Birnbaum and Bucher. Shown seated, from left, are Sonya Sobrian, Ph.D.; Lisa Peterson, Ph.D.; Birnbaum; and Iris Udasin, M.D. Standing, from left, are Dale Hattis, Ph.D.; Bucher; Paul Howard, Ph.D.; George Corcoran, Ph.D.; David Dorman, D.V.M.; and Kass. (Photo courtesy of Steve McCaw)

  • Dorman
    2/8

    Dorman, of North Carolina State University, brought a touch of color to the proceedings with his Wolfpack red shirt. (Photo courtesy of Steve McCaw)

  • Birnbaum, Bucher, Peterson and Walker
    3/8

    A moment of humor during the meeting was enjoyed by, from left, Birnbaum, Bucher, Board Chair Lisa Peterson, Ph.D., and DNTP Deputy Director for Science Nigel Walker, Ph.D. (Photo courtesy of Steve McCaw)

  • Chapin
    4/8

    Comments from board member Robert Chapin, Ph.D., from Pfizer, are always good-natured yet scientifically penetrating. (Photo courtesy of Steve McCaw)

  • Shah
    5/8

    Shah noted that SWIFT is still undergoing development and expansion of its capabilities, including eventual integration with HAWC. (Photo courtesy of Steve McCaw)

  • Hattis and Holmgren
    6/8

    The dialogues during breaks are often as important as the proceedings themselves. From left, Hattis, of Clark University, confers with Stephanie Holmgren from the NIEHS Office of Scientific Information, and Corcoran, of Wayne State University. Holmgren made a presentation to the board on how to systematically search the literature, a key step in the systematic review process. (Photo courtesy of Steve McCaw)

  • Shapiro
    7/8

    Shapiro was particularly proud to display the new HAWC logo. The project is an expansion of his master’s thesis at the University of North Carolina at Chapel Hill, and the software is currently being used by the World Health Organization International Agency for Research on Cancer monographs program, as well as by OHAT. (Photo courtesy of Steve McCaw)

  • HAWC logo
    8/8


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