Public Health 270B: Toxicology I, Spring 2013

Debbie Jan (djan@library.berkeley.edu)
Karen Andrews (andrews2@berkeley.edu)

Class Webpage: http://www.lib.berkeley.edu/PUBL/SPH/PH270B_S13.html

Location: 1 University Hall

Telephone: 642-2511

Library Hours: Monday-Thursday 9 am - 8 pm, Friday 9 am - 5 pm, Saturday-Sunday 1 - 5 pm

Library Reference Hours: Monday-Friday, 10-12 and 2-4 pm

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Contents:

• Before you start your research
• Understand your chemical/substance
• Find books/reports on your substance
• Search for published research literature
• Search for other literature
• Finding California, Federal, and Other Organizations
• Other resources of interest
• Other useful Public Health topical webpages
• Bibliographic Management Software Programs
• Upcoming Public Health Library Drop-In classes

Before you start your research:

1. Download the framework template.

2. Identify the research topic questions or problems being posed to you.

3. Gather your information.

4. Write down what you know about the topic.

• Chemical/substance identification and properties
  • What other names is the substance/chemical known as?
  • Are you looking at a family of chemicals or a specific chemical?
  • In what (e.g. fabrics, plastics, cosmetics, toys, etc.) and where (e.g. work, home, school, indoors, outdoors, etc.) is the substance being used?
• Identify what kind of exposure you're looking for:
  • Exposure population: infant, child, adolescent, adult, older adult
  • Location: occupational, home, school, etc.
  • Exposure level: chronic, acute, sub-chronic, etc.
  • Route: inhalation, oral, dermal, ocular, etc.
• Are there exposure limits?

5. What else do you need to know? What information are you missing to answer your research topic questions or problems?

   • What international, federal, state, or other organizations are interested in your topic and have already gathered information?
   • Identify the chemicals/substances or class of compounds you're looking for
   • What unique identifiers (CAS #) exist to help you ascertain that you have the right chemical?
   • What other chemicals are or can be used for the same purpose?

6. Break your topic into key concepts, listing each concept (with synonyms!)

7. Create search strings to help you formulate your search.

8. Start your research.

9. Add to or refine your topic key concepts and search strings as you search to incorporate the information you find while searching.

Understand your chemical/substance:

• Carcinogenic Potency Database Project (UC Berkeley)
  • "Provides easy access to the bioassay literature, with qualitative and quantitative analyses of both positive and negative experiments that have been published over the past 50 years in the general literature through 2001 and by the National Cancer Institute/National Toxicology Program through 2004. ... resource of the results of 6540 chronic, long-term animal cancer tests on 1547 chemicals."
• CHE Toxicant and Disease Database (Collaborative on Health and the Environment)
• Summarizes links between chemical contaminants and approximately 180 human diseases or conditions.
• Browse by disease category, disease, toxicant, or search by CAS RN or disease.
• ChemIDplus from the National Library of Medicine
  • Chemical dictionary file of compounds of biomedical and regulatory interest.
  • Records include names and synonyms, CAS Registry number, molecular formulas, and toxicity information.
  • Provides references to other databases including:
    • CCRIS (Chemical Carcinogenesis Research Information System) from the National Library of Medicine
      • National Cancer Institute data for over 9,000 chemicals is derived from studies cited in primary journals, current awareness tools, NCI reports, and other special sources.
      • Includes carcinogenicity, mutagenicity, tumor promotion, and tumor inhibition test results.
    • Developmental and Reproductive Toxicology Database (DART)
    • Citations on teratology and other aspects of developmental and reproductive toxicology.
    • Over 200,000 references to literature published since 1965.
    • Haz-Map (National Library of Medicine)
    • Haz-Map is an occupational health database linking jobs and hazardous tasks with occupational diseases and their symptoms
    • Hazardous Substances Data Bank (HSDB)
      • Toxicology of over 5,000 potentially hazardous chemicals.
      • Peer reviewed information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, and related areas.
    • Registry of Toxic Effects of Chemical Substances (RTECS) compiled by the National Institute for Occupational Safety and Health, US DHHS (via RightAnswer.com)
      NOTE: Access limited to UCB faculty, staff and students.
      • To get started, type your UCB e-mail address in the box. You can search by CAS # or name in the Integrated Index Search box.
      • Toxicity data extracted from scientific literature worldwide on more than 160,000 substances. Updated quarterly.
      • Includes mutagenicity, carcinogenicity, reproductive hazards, and acute and chronic toxicity on drugs, food additives, pesticides, fungicides, herbicides, solvents, diluents, chemical wastes, and substances used in industrial and household situations.
• Comparative Toxicogenomics Database (CTD) from the Mount Desert Island Biological Laboratory
  • Part of the TOXNET databases, CTD is supported by the National Institutes of Environmental Health Sciences, National Library of Medicine, and the National Center for Research Resources.
  • CTD incorporates data from PubMed, ChemIDplus, DrugBank, Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and more to show the association between chemicals, genes, and disease.
• eChemPortal from OECD
  • Provides physical chemical properties, environmental fate and behavior, ecotoxicity, and toxicity data.
  • Searches a number of databases including U.S. EPA ACToR, ECHA CHEM (REACH database), ESIS, INCHEM, and OECD Existing Chemicals Screening Information Data Sets (SIDS) Database. See the full list.
• GENE-TOX
  • Created by the U.S. Environmental Protection Agency, GENE-TOX contains genetic toxicology (mutagenicity) test data, resulting from expert peer review of the open scientific literature, on over 3,000 chemicals.
• Integrated Risk Information System (IRIS)
  • Information on human health effects that may result from exposure to various chemicals in the environment.
  • Includes oral reference doses (RfDs) and inhalation reference concentrations (RfCs) for chronic noncarcinogenic health effects and hazard identification, oral slope factors, and oral and inhalation unit risks for carcinogenic effects.
• Merck Index Online
  NOTE: Access limited to UCB faculty, staff and students.
  • Encyclopedia of chemicals, drugs, and biologicals.
  • Includes chemical, generic, and brand names; CAS registry numbers; physical data and literature references; structures and stereochemistry; toxicity information; and therapeutic uses.
• Micromedex Healthcare Series
  NOTE: Access limited to UCB faculty, staff and students.
  • To begin, click on MICROMEDEX 2.0. Then click on a Drug Identification.
  • Provides access to the REPRORISK System, which includes includes the REPROTEXT, REPROTOX, TERIS, and Shepard's Catalog of Teratogenic Agents databases.
  • Martindale: The Complete Drug Reference can also be searched via Tox & Drug Product Lookup.
• NPIC InfoBase Search (National Pesticide Information Center)
• Search for documents from the NPIC and EXTOXNET website, EPA Pesticide websites, the Federal Register, EPA Office of Pesticide Program E-Dockets from 2002 to present, print and electronic Code of Federal Regulations Title 40 - Pesticide Programs, and the Federal Food, Drug, and Cosmetic Act.
• Patty's Toxicology (5th edition)
  NOTE: Access limited to UCB faculty, staff and students.
  • Includes basic physical and chemical properties, production and use, exposure assessment, toxic effects, and occupational exposure limits of industrial chemicals.
• Plum (Public Library of Materials)
  • Free, open-access resource for finding out if a chemical is included in a selected set of scientific and regulatory authoritative lists (e.g. California Proposition 65 List, EC Endocrine Disrupter Priority List).
• Sax's Dangerous Properties of Industrial Materials
  NOTE: Access limited to UCB faculty, staff and students.
  • Includes toxicological, flammability, reactivity, and regulatory information for about 26,000 substances.
  • Toxicology data references reports of primary skin and eye irritation, mutation, reproductive, carcinogenic, and acute toxic dose data.
• Tox Town (National Library of Medicine)
• Interactive guide to commonly encountered toxic substances, your health, and the environment.
• "Towns" include Port, Town, City, Farm, and US-Mexico Border.
• Includes non-technical descriptions of chemicals.

Find books/reports on your substance:

• Electronic Books
• CRCnetBase
  NOTE: Access limited to UCB faculty, staff and students.
  • Thousands of titles on chemistry, environmental science, food science, and more.
• Knovel Library
  NOTE: Access limited to UCB faculty, staff and students.
  • Over 2,000 titles on biology, food science, nanotechnology and more. Selected titles include Environmental Contaminant Reference Databook; Food Chemical Risk Analysis; Patty's Industrial Hygiene and Patty's Toxicology; Sittig's Handbook of Toxic and Hazardous Chemicals and Carcinogens.
• National Academies Press Books
• The NAP publishes reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council. Over 4,000 NAP books are now available for free download in pdf format. Sign in required to download PDF book and chapters. Subject categories include agriculture, environment and environmental studies, food and nutrition, and health and medicine.
• Royal Society of Chemistry eBook Collection
  NOTE: Access limited to UCB faculty, staff and students.
  • Collection of over 1,000 biology, chemical science, medicinal drug discovery books published by the Royal Society of Chemistry.
• Springer eBooks
  NOTE: Access limited to UCB faculty, staff and students.
  • This collection of over 50,000 books includes most of the Springer scientific, technical and medical books published from 2005 to present.
• Wiley Online Library Ebook Collection
  NOTE: Access limited to UCB faculty, staff and students.
  • Includes 950 books with a 2011 publication date. The collection includes books in analytical chemistry, environmental chemistry, pharmaceutical & medicinal chemistry, food science, genetics, medicine, healthcare, and more. Access icons indicate which titles are included in our subscription.
• Environmental Health Criteria (International Programme on Chemical Safety, WHO)
  • "International, critical reviews on the effects of chemicals or combinations of chemicals and physical and biological agents on human health and the environment."
  • For those not available full text online the Public Health Library call number is: RA565.A1 E55
• IARC Monographs on the Evaluation of Carcinogenic Risks to Humans from the International Agency for Research on Cancer
  • Independent assessments by international experts of the carcinogenic risks to humans posed by a variety of agents, mixtures and exposures.
  • Index of all the monographs and supplements. A few recent monographs are available full text.
  • The full monographs have the Public Health Library call number: RC267.A1.I2
• MarketResearch Academic
  NOTE: Access limited to UCB faculty, staff and students.
  • Provides the full text of more than 600 market studies from three publications: Kalorama Information, Packaged Facts, and Specialists in Business Information.
  • Industries covered include: healthcare, demographics, consumer products, and more.
• NTP Study Reports from the National Toxicology Program, US DHHS
  • Includes long-term toxicology and carcinogenesis studies, short-term toxicity studies, developmental toxicity, reproductive assessment by continuous breeding, and other reports.
  • Full text reports include the Toxicity Studies and Toxicology and Carcinogenesis Studies.
• OEHHA Toxicity Criteria Database from Cal/EPA
  • Search by chemical name, CAS number, or select from a list to view cancer potency information, acute reference exposure levels, chronic reference exposure levels, California Public Health Goals, and Prop 65 NSRLs/MADLs.
• OHAT Evaluations and Workshops from the National Toxicology Program Office of Health Assessment and Translation
  • "This office conducts evaluations to assess the evidence that environmental chemicals, physical substances, or mixtures (collectively referred to as "substances") cause adverse health effects and provides opinions on whether these substances may be of concern given what is known about current human exposure levels."
• OskiCat (UCB catalog)
• Search on the chemical substance
• Other possible subjects: cancer, diet, endocrine toxicology, nanoparticles, nanostructured materials - health aspects, pesticides, reproductive toxicology
• Toxicological Profiles from the Agency for Toxic Substances and Disease Registry, CDC
• National Priorities List of hazardous substances.
• Profiles include health effects, chemical information, production, use and disposal, potential for human exposure, regulations, references, and more.
• Draft and final profile reports available.

Search for published research literature:

• PubMed for UCB
  • More than 22 million medical and health journal article citations back to the 1948.
  • To search:
    • Use the MeSH Database to find MeSH terms and appropriate subheadings (e.g. adverse effects, chemically induced, epidemiology, poisoning, toxicity, etc.)
      • Some possible useful MeSH terms - aerosols, adminstration - topical, food contamination, inhalation exposure, water pollutants, water pollution.
      • MeSH Subheadings: Definitions (Qualifiers)
    • To find citations that don't have MeSH terms:
      • Type in the search box: chemical substance "NOT medline[sb]"

        e.g. ("bisphenol a" OR bpa) NOT medline[sb]

      • Use the Limits tab to limit to publication date, publication type, species, language, gender, ages, etc.
  • Help using PubMed
    • PubMed Tips Sheet
    • PubMed Quick Guide (UCB Library)
    • PubMed Help for UC Berkeley
    • Selected chapters from NLM PubMed Help:
      • Combining search terms with Boolean operators (AND, OR, NOT)
      • Filtering your search
      • Saving and E-mailing Results and Searches
    • Selected NLM PubMed online tutorials:
      • Simple Subject Search (1 min.)
      • Searching with the MeSH Database (3 min.)
      • Applying Subheadings and Other Features of the MeSH Database (3 min.)
  • Use to access the full text of articles, Melvyl, and Request. Request allows you to easily request copies of articles from journals not available at UCB.
  • My NCBI
    • Allows you to permanently save citations, save searches, and automatically get sent e-mail alerts.
    • Save Search Results in Collections (3 min., YouTube)
    • Save Searches and Set E-mail Alerts (2 min., YouTube)

• BIOSIS Previews
  NOTE: Access limited to UCB faculty, staff and students.
  • Index to over 18 million citations from journals, reports, books, conference proceedings, and meeting abstracts back to 1926.
  • Topics include: biological research and medical research findings.
• Embase
  NOTE: Access limited to UCB faculty, staff and students.
  • Primary resource for conducting systematic reviews and researching evidence-based medicine
  • Indexes over 7,600 journals, including over 2,000 not in Medline, from over 90 countries; also indexes conference abstracts from over 2,000 conferences.
  • Broad biomedical scope with strong coverage in drug, pharmaceutical, and toxicological research, including economic evaluations.
• Environmental Sciences and Pollution Management
  NOTE: Access limited to UCB faculty, staff and students.
  • Index to over 3.8 million citations from journals, reports, books, conference proceedings, and government publications back to 1967.
  • Topics include: diet, pesticides, risk assessment, toxicology, and more.
• Global Health
  NOTE: Access limited to UCB faculty, staff and students.
  • Indexes over 5,000 journals, books, reports, conference proceedings, patents, theses, and electronic only publications.
  • Topics include: environmental and occupational health, food safety and hygiene, nutrition, public health, toxicology, and more.
• NIOSHTIC-2
  • Contains over 48,000 occupational safety and health information resource citations. Some citations date back to 1971. Some links to full-text. Includes some NIOSH Mining Safety & Health Research Laboratories publications back to the 1930's.
• SciFinder Scholar (Chemical Abstracts)
  NOTE: Access limited to UC faculty, staff and students.
  • In order to access SciFinder Scholar, users must register on the web.
  • Access SciFinder Scholar (once registered)
  • Search SciFinder for chemistry literature by topic, author, Registry Numbers, patent numbers from 1907 to the present. More than 70 million chemical substances may be searched by chemical name, chemical structure, Registry Numbers, and formula.
  • Some limits you might want to use are applied to the search results. In the Analysis tab, click on Categorize then click on different catagory headings. Pay special attention to Physical chemistry, Biology, Environmental chemistry, Biotechnology, Analytical chemistry.
• TOXLINE
  • Index to over 4 million citations covering the biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals. Includes PubMed and DART citations. Can search by CAS numbers.
• Web of Science
  NOTE: Access limited to UCB faculty, staff and students.
  • Includes Science Citation Index Expanded (1900-present), Social Sciences Citation Index (1900-present), and Arts and Humanities Citation Index (1975-present). Links to cited articles and times cited are provided for retrieved articles.

Search for other literature

• Newspapers
NOTE: Although not scholarly, newspapers can be useful for getting information on new, hot topics.
• San Francisco Chronicle (1985 to present)
  NOTE: Access limited to UCB faculty, staff and students.
• San Francisco Chronicle (1865-1922)
  NOTE: Access limited to UCB faculty, staff and students.
• New York Times (1980 to present)
  NOTE: Access limited to UCB faculty, staff and students.
• New York Times (1851 to 2009)
  NOTE: Access limited to UCB faculty, staff and students.
• Wall Street Journal (1984 to present)
  NOTE: Access limited to UCB faculty, staff and students.
• Wall Street Journal (1889-1995)
  NOTE: Access limited to UCB faculty, staff and students.
• PapersFirst (OCLC; 1993 to present)
  NOTE: Access limited to UCB faculty, staff and students.
  • PapersFirst is an index of papers presented at conferences worldwide. It covers a broad range of disciplines.
• Proceedings (OCLC; 1993 to present)
  NOTE: Access limited to UCB faculty, staff and students.
  • Proceedings is an index of worldwide symposia, meetings, and conference proceedings. Each record contains a list of the papers presented at that conference.
• Science.gov
• "Science.gov searches over 55 databases and over 2100 selected websites from 13 federal agencies."

Finding California, Federal, and Other Organizations

• California Agencies and Resources
  • California Department of Conservation
  • California Environmental Protection Agency
    • Office of Environmental Health Hazard Assessment
• Federal Agencies and Resources
  • Environmental Protection Agency (EPA)
  • Food and Drug Administration (FDA)
  • National Institute of Mental Health. Health Topics
• International Health Resources
  • Health Canada
  • World Health Organization (WHO)
    • Food Safety
    • International Programme on Chemical Safety
• Other Associations, Organizations, and Resources
  • Environmental Working Group
  • Green Science Policy Institute

Other resources of interest

• How to Search for Literature More Effectively (Public Health Library)
• Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment (National Academy Press, 2007)
  • RA1224.3 .N378 2007 Public Health Library
• Chemical composition of everyday products (Greenwood Press, 2005)
  • QD75.22 .T64 2005 Reference, Chemistry Library
• The Dose Makes the Poison: A Plain-Language Guide to Toxicology (Wiley, 2011)
  • RA1213 .O88 2011 Public Health Library
• Evaluating Chemical and Other Agent Exposures for Reproductive and Developmental Toxicity (National Academy Press, 2001)
  • RA1221.E9 2001 Public Health Library
• General, Applied and Systems Toxicology (Wiley, 2013)
• Toxicity Testing for Assessment of Environmental Agents: Interim Report (National Academy Press, 2006)
  • QH54.15.T68.T68 2006 Public Health Library
• Toxicological risk assessment of chemicals : a practical guide (Informa Healthcare, 2008)
  • RA1190.N54 2008 Public Health Library
• Toxicology and Epigenetics (Wiley, 2012)
• ToxLearn (U.S. National Library of Medicine's Toxicology and Environmental Health Information Program and the U.S. Society of Toxicology)
  • ToxLearn is a free online educational tool providing an introduction to fundamental toxicological principles and concepts. Broken into 3 modules available on the web or in pdf, it is written for the general public, first level undergraduate toxicology students, and users of NLM's toxicology databases. Currently only Module 1 is available.

Other useful Public Health topical webpages:

• Environmental Resources
• Indexes and Databases
• Toxicology/Occupational Health Resources

Bibliographic Management Software Programs

• RefWorks - Web-based bibliographic management program licensed for UCB students
  • Login into RefWorks - Click on "Sign up for an Individual Account" to create a log-in name and password.
  • You can also use RefMobile on your smart phone, cell phone, or PDA
• EndNote X6 - Software you install on your computer
  • Purchase an EndNote license from the Scholars Workstation at the Cal Student Store for $84.95
  • This is an immediate electronic download price. Special orders, which take a few weeks, may be placed for software on a media disk and are an additional $10 charge. Purchases must be made in person at the student store.
  • Purchase the software from the Cal Student Store JourneyEd or EndNote website.
  • EndNote Web - 2 year free subscription available with your purchase of EndNote X6 or freely available if you register up from within a Web of Knowledge database (e.g., BIOSIS, Global Health, Web of Science).
  • Request a 30 day trial of EndNote X6.
• Comparison chart
• Vancouver convention: Uniform Requirements for Manuscripts Submitted to Biomedical Journals from ICMJE.

Upcoming Public Health Library Drop-In classes

• PubMed/My NCBI - Tuesday, February 12th, 10-11:30, in the Marian Koshland Bioscience and Natural Resources Library Training Room, 2101 Valley Life Sciences Building
• Advanced EndNote X6 - Tuesday, March 12th, 10-11:30, in the Marian Koshland Bioscience and Natural Resources Library Training Room, 2101 Valley Life Sciences Building

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