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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. 1) NLM Databases, and 2) NLM Review Process for Haz-Map.

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1) NLM Databases, and 2) NLM Review Process for Haz-Map

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  1. Pertti (Bert) Hakkinen, Ph.D.Senior Toxicologist and Toxicology and Environmental Health Science AdvisorFriday, March 16, 2012IOM, Committee on Review of the Department of Labor’s Site Exposure Matrix (SEM) Database 1) NLM Databases, and 2) NLM Review Process for Haz-Map

  2. 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 InformaticsUniformed Services University of the Health Sciences (USUHS)

  3. Disclaimer:The views expressed are thepersonal opinion of the speakeranddo not necessarily reflect the opinions of NLM, NIH, or other parts of the U.S. Government.

  4. Goals of Presentation Introduction to NLM databases & tools of likely interest to you Haz-Map review process

  5. U.S. National Library of Medicine (NLM) NLM’s Mission: Collect, organize, and disseminate health-related 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

  6. Mission Collect, Organize, Preserve, & Disseminate Health-related Information Free & Open Source

  7. Technologies (and Data) are Changing! Photo courtesy of Cesar Bandera, Ph.D. New Jersey Institute of Technology

  8. 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

  9. 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

  10. 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

  11. http://sis.nlm.nih.gov/enviro.html

  12. Suggested starting point to http://sis.nlm.nih.gov/enviro.html

  13. 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.

  14. 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.

  15. Toxicology Data Network (TOXNET): Examples • Haz-Map– Arelational 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 ToxicogenomicsDatabase

  16. 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.

  17. 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.

  18. TOXLINE® (Toxicology Bibliographic Info)

  19. 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.

  20. 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).

  21. Please note the numerous tabs

  22. Basics tab

  23. Interactions tab

  24. Genes tab

  25. Diseases tab

  26. ChemComps tab

  27. Pathways tab

  28. References tab

  29. Links tab Add Haz-Map?

  30. A CTD Primer

  31. Selected publications about the CTD

  32. Additional NLM Resources

  33. 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-by-side 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.

  34. 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.

  35. 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.

  36. Selected links to information on environmental health, toxicology, disasters, chemicals, drugs, & special populations

  37. 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, 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. • ChemIDplus- Numerous chemical synonyms, structures, regulatory list information, and links to other databases containing information. • Comparative Toxicogenomics Database– Curated data describing cross-species chemical–gene/protein interactions and chemical– and gene–disease relationships.

  38. 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

  39. MedlinePlus Includes Poisoning, Toxicology, and Environmental Health Information

  40. 2011-2012 News

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