Bert Hakkinen - Institute of Medicine

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1) NLM Databases, and
2) NLM Review Process for Haz-Map
Pertti (Bert) Hakkinen, Ph.D.
Senior Toxicologist and Toxicology and
Environmental Health Science Advisor
Friday, March 16, 2012
IOM, Committee on Review of the Department of Labor’s Site
Exposure Matrix (SEM) Database
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PERSONAL BACKGROUND
Many years in the consumer products industry, working with
companies, trade associations, government agencies, etc.
Several years at the European Commission’s Institute for Health
and Consumer Protection
Now: National Institutes of Health, National Library of Medicine
and
Adjunct Associate Professor in Biomedical Informatics
Uniformed Services University of the Health Sciences (USUHS)
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Disclaimer:
The views expressed are the
personal opinion of the speaker
and
do not necessarily reflect the opinions of NLM,
NIH, or other parts of the U.S. Government.
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Goals of Presentation


Introduction to NLM databases & tools
of likely interest to you
Haz-Map review process
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U.S. National Library of Medicine (NLM)
NLM’s Mission: Collect, organize, and disseminate healthrelated information.

World’s largest biomedical library
 Millions of items in collection

Services: PubMed, MedlinePlus and many others
 Several hundred million searches of PubMed each year
 Articles from several thousand journals indexed monthly

Research and Development
 Biomedical informatics and communications

Relatively new focus (within Specialized Information
Services): Disaster information
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Mission
Collect, Organize, Preserve, & Disseminate Health-related Information
Free & Open Source
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Technologies (and Data)
are Changing!
Photo courtesy of Cesar Bandera, Ph.D. New Jersey Institute of Technology
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NLM’s challenges
Need to identify and compile authoritative, trustworthy
information
Information needs to meet the needs of the users
Users need to have access when and where they need it
Users need easy access, e.g., during emergencies
Information evolves
Ways to deliver and access the information evolve
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NLM’s Efforts:
Include collecting, organizing, preserving,
and disseminating
current and emerging information
in
toxicology, exposure science,
risk assessment, and risk management
Plus: Offer tools and training
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http://sis.nlm.nih.gov
The Specialized Information Services Division (SIS)
of the NLM is responsible for information resources
and services in:
• Toxicology and Environmental health
• Chemistry
• HIV/AIDS, and Specialized topics in minority
and other special populations health
• Disaster information
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http://sis.nlm.nih.gov/enviro.html
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Suggested starting point to
http://sis.nlm.nih.gov/enviro.html
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TOXNET ® (TOXicology Data NETwork) is:
A suite of databases covering toxicology, hazardous
chemicals, environmental health and related areas.
Accessible free of charge at http://toxnet.nlm.nih.gov
Linked to PubMed®, NLM's free web interface to the
world's biomedical literature, and to additional sources
of toxicological information.
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TOXNET's web interface:
Is designed as an easy way to search databases of
varying formats and content
Can be used to locate toxicology data, literature
references, and toxic release information on particular
chemicals
Can be used to search to identify chemicals associated
with specific effects.
Offers a variety of ways to display and sort information.
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Toxicology Data Network (TOXNET): Examples
 Haz-Map –
A relational database of hazardous chemicals and occupational
diseases. It shows which agents (chemical or biological) cause each of the 235
occupational diseases, based on current scientific evidence. Can find the diseases
that are linked to each agent and the agents that are linked to each disease. Other
linked tables in the database are industrial processes, non-occupational activities,
jobs, industries, hazardous job tasks, and signs & symptoms.
 Hazardous Substances Data Bank – Comprehensive overviews of information
on substances (toxicity, safety and handling, environmental fate, and more).
Scientifically peer-reviewed.
 TOXLINE - Extensive array of references to literature on biochemical,
pharmacological, physiological, and toxicological effects of drugs and other
chemicals.
 ChemIDplus - Numerous chemical synonyms, structures, regulatory list
information, and links to other databases containing information about the
chemicals.
 New in 2011: Comparative Toxicogenomics Database
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http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB
HSDB® (Hazardous Substances Data Bank)
Focus is on toxicology, and includes almost 6,000 substances.
In addition to toxicology information, provides
emergency handling procedures, industrial hygiene, environmental
fate, human exposure, detection methods, and regulatory
requirements.
The information is fully referenced and is peer-reviewed by a
Scientific Review Panel.
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TOXLINE®
Bibliographic database providing comprehensive coverage of the
biochemical, pharmacological, physiological, and toxicological effects
of drugs and other chemicals from 1965 to the present.
Contains several million citations, almost all with abstracts and/or
index terms and CAS Registry Numbers.
Can search +/- PubMed content.
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TOXLINE®
(Toxicology Bibliographic Info)
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ChemIDplus®
ChemIDplus contains several hundred thousand chemical records,
most of which include chemical structures.
ChemIDplus is searchable by Name, Synonym, CAS Registry
Number, Molecular Formula, Classification Code, Locator Code,
Structure, and/or Physical properties.
Enhanced structure display is available in ChemIDplus Advanced.
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An important recent effort:
Access to the Comparative Toxicogenomics
Database (CTD, http://ctdbase.org) via TOXNET.
CTD includes extensive sets of curated information
(next slide).
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Please note the numerous tabs
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Basics tab
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Interactions tab
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Genes tab
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Diseases tab
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ChemComps tab
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Pathways tab
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References tab
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Links tab
Add Haz-Map?
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A CTD Primer
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Selected publications about the CTD
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Additional NLM Resources
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ITER (International Toxicity Estimates for Risk)
Data in support of human health risk assessments. It is compiled by
Toxicology Excellence for Risk Assessment (TERA) and contains over
650 chemical records.
Comparison of international risk assessment information in a side-byside format and explains differences in risk values derived by different
organizations.
Focuses on hazard identification and dose-response assessment, is
extracted from each agency’s assessment, and contains links to the
source documentation.
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Household Products Database®
Information on the potential health effects of chemicals contained in
thousands of products used inside and around the home.
Browse a product category, such as 'Pesticides' or 'Personal Care,' by
alphabetical listing of brand names.
Products can also be searched by type, manufacturer, product
ingredient/chemical name, and by health effects.
Ingredients as reported in the manufacturer's Safety Data Sheet
(MSDS), and includes other information such as handling, disposal,
and health effects.
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NLM is developing an enhanced version of its
ALTBIB® Web portal.
Will provide better access to information on in
silico, in vitro, and improved (refined) animal
testing methods, along with information on the
testing strategies incorporating these methods
and other approaches.
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Selected links to information on environmental health,
toxicology, disasters, chemicals, drugs, & special populations
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Selected Summary: TOXNET
•
•
•
•
•
Haz-Map – A relational database of hazardous chemicals and occupational
diseases. It shows which agents (chemical or biological) cause each of the 235
occupational diseases, based on current scientific evidence. Can find the
diseases that are linked to each agent and the agents that are linked to each
disease. Other linked tables in the database are industrial processes, nonoccupational activities, jobs, industries, hazardous job tasks, and signs &
symptoms.
Hazardous Substances Data Bank – Comprehensive overviews of
information on substances (toxicity, safety and handling, environmental fate,
and more). Scientifically peer-reviewed.
TOXLINE - Extensive array of references to literature on biochemical,
pharmacological, physiological, and toxicological effects.
ChemIDplus - Numerous chemical synonyms, structures, regulatory list
information, and links to other databases containing information.
Comparative Toxicogenomics Database – Curated data describing crossspecies chemical–gene/protein interactions and chemical– and gene–disease
relationships.
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PubMed
http://pubmed.gov
PubMed includes over 21 million citations from MEDLINE, life
science journals, and online books.
Citations may include links to full-text articles from PubMed Central
or publisher web sites.
My NCBI – store searches; automatic updates
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MedlinePlus Includes Poisoning, Toxicology, and
Environmental Health Information
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2011-2012 News
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How to stay informed
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Goals of of Presentation

Introduction to NLM databases & tools
of likely interest to you
Next:
 Haz-Map review process
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From Dr. Brown’s Presentation:
“Like Editing a Textbook”

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The editor chooses which information to include or
exclude.
The editor requires that all references are up to date and
from the peer-reviewed literature.
The editor ensures that all chapters are written clearly,
topics are covered in a consistent manner, and indexing
is accurate.
After completion, the editor submits the new edition to a
publisher for final layout design and copy editing.
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From Dr. Brown’s Presentation: Haz-Map Review
Environment Since 2000 (NLM) and 2006 (DOL)

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Reviewed monthly in teleconferences with DOL and
Paragon professional staff.
New chemical profiles reviewed by Ann Gravatt, who has
worked for many years on NLM’s HSDB, and Paragon’s
Bernie Kokenge, PhD (chemistry).
Mike Hazard, PhD (chemistry) and author of
ChemIDplus, reviewed information in Haz-Map when it
was first published in 2002.
Bert Hakkinen, PhD (toxicology) has reviewed Haz-Map
topics in his work at NLM since 2008.
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From Dr. Brown’s Presentation:
Conclusions


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Haz-Map is a peer-reviewed and scientifically rigorous
database of toxic chemicals and preventable
occupational diseases.
Diseases are included only if there is sufficiently robust
evidence that occupational exposure can cause the
diseases, and therefore, that the diseases can be
prevented by good occupational hygiene practices.
It is up to future mapmakers to build a better map and to
fill in the details as more complete knowledge is
discovered.
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Committee on Review of the Department of Labor’s Site
Exposure Matrix (SEM) Database
Questions for Jay Brown:
1. What are your criteria for determining causality? For
cancer outcomes? For non-cancer outcomes?
(examples, strong versus convincing, IARC categories?)
Dr. Brown: (From long response) “In general: Is there
consensus in occupational medicine textbooks that this
occupational disease is caused by these hazardous agents?
Can the disease be prevented by good occupational hygiene
practices? Occupational cancer: Is it a Group 1 carcinogen
in the “Occupation” chapter in Schottenfeld & Fraumeni's
Cancer Epidemiology and Prevention, 3rd Edition?...”
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2. What are the criteria for determining that there is
no causal link to an occupational exposure or more
research is needed? What is difference between
blue, yellow, and red highlighted diseases from
your handout?
Dr. Brown: (From long response) “Is there a causal
relationship as defined in the response to question #1?
The handout of occupational diseases in Haz-Map
shows that there is little basis for debate for most of
these diseases. There is a consensus in occupational
medicine textbooks that these are established
occupational diseases. I highlighted the ones that I
thought were debatable…There is a rule in Haz-Map for
handling occupational cancers. See my response to
question #1 above.”
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3. How do you select new chemicals or diseases to
review?
Dr. Brown: (From long response) “All chemicals in the
NIOSH Pocket Guide, all chemicals that cause
occupational asthma, all chemicals that cause allergic
contact dermatitis, all chemicals sent to me by Bernie
Kokenge from the SEM database, all diseases in the
SHE(O) list of Mullan and Murthy, all diseases in
occupational medicine textbooks…
Dr. Hakkinen: Keep watch for possible new information
to note to Dr. Brown. Also have other interactions with
Dr. Brown.
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4. How often do you update diseases and chemicals?
How do you select those to update? If a decision is
made not to link a chemical with a disease, when is the
decision re-examined?
Dr. Brown: (From long response) “The first chemicals
added to Haz-Map have the lowest ID numbers. So,
lower ID number is one criteria used to find chemicals
that need reviewing based on newer resources
available. Chemicals and diseases are continuously
reviewed as questions are asked and new chemicals
added are compared to chemicals already in the
database. Periodically, all journal articles in selected
journals are reviewed…”
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5. When using individual studies for information,
how do you assess the study’s quality (study type,
bias, sample size, etc)?
Dr. Brown: “See the study of Parkinson’s disease by
Firestone et al., in which a number of potential
weaknesses of case control studies are addressed:
confirmation of diagnosis, interview bias, and recall
bias…”
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6. How do you use animal and epidemiological data and
how is it included or weighted into causal decisions?
Dr. Brown: “For occupational cancers, I follow IARC in the
way it synthesizes animal and epidemiological data. For
acute occupational diseases, animal data is sufficient if the
routes of entry correspond… In Haz-Map, there is a
distinction between adverse effects (includes animal
toxicology and human poisonings by ingestion cases) and
occupational diseases (cases of workers made ill after
inhalation or skin absorption). Therefore, chemicals are
linked to the diseases "Asphyxiation, chemical" and
"Hemolytic anemia" only if occupational cases (and not just
ingestion cases) have been reported. Likewise, all chronic
occupational diseases in Haz-Map are based on reports of
occupational cases.”
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7. What are your criteria for picking resources? The
reference list is long and varied, with many different
purposes and methodology.
Dr. Brown: “The best and most up-to-date resources are
selected. Accuracy is improved by cross referencing.
Cross referencing also enables one to compare
resources and to get different perspectives… Is there
concurrence? Is there a body of knowledge that
supports the agent-disease link?”
Dr. Hakkinen: Keep watch for possible new information
to note to Dr. Brown. Also have other interactions with
Dr. Brown.
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8. Who reviews your data entry and data extraction
and who verifies the information as accurate?
Dr. Brown: “Much of the data entry for the first draft is
cutting and pasting from ChemIDplus, HSDB, and other
Internet resources. Difficult lists are based on the work
of experts, e.g., Malo & Chan-Yeung for occupational
asthma and IARC for cancer. Ann Gravatt reviews new
chemicals. Principles I used for data extraction were
published in my journal article, which was one of the
handouts. Preliminary work is first published on my
website and presented at monthly conferences.”
Dr. Hakkinen: Keep watch for possible changes and
enhancements to note to Dr. Brown.
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9. How is new information in new textbook
additions identified?
Dr. Brown: “I read new chapters and material written by
new authors. I check all references already in Haz-Map
to see if any changes have been made.”
Dr. Hakkinen: Keep watch for possible new information
to note to Dr. Brown.
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10. What do you submit to NLM, do they review/verify
the content? If so, what is the process?
Dr. Brown: “Ann Gravatt reviews all chemicals (synonyms,
CAS #s, formulas, and OELs). She sends corrections to
me, and I make changes to my copy of Haz-Map. Haz-Map
is published with new chemicals and her corrections.”
Dr. Hakkinen: Entire content not reviewed/verified within
NLM. Focus has been on selected chemicals and
opportunities to add additional chemicals, e.g.,
isocyanates, and new information sources, e.g., the
Comparative Toxicogenomics Database.
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11. What is NLM’s Role in Haz-Map?
Dr. Brown: “Haz-Map is like an electronic textbook. NLM
is the publisher.”
Dr. Hakkinen: NLM also provides access to
Comparative Toxicogenomics Database, Household
Products Database, ITER, etc.
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We welcome your comments, suggestions, and
possible collaborations
Pertti J. Hakkinen, Ph.D.
Senior Toxicologist, and Toxicology and
Environmental Health Science Advisor
National Library of Medicine
National Institutes of Health
Bethesda, Maryland USA
pertti.hakkinen@nih.gov
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