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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 1 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) National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 2 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 3 Goals of Presentation Introduction to NLM databases & tools of likely interest to you Haz-Map review process National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 4 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 5 Mission Collect, Organize, Preserve, & Disseminate Health-related Information Free & Open Source National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 6 Technologies (and Data) are Changing! Photo courtesy of Cesar Bandera, Ph.D. New Jersey Institute of Technology National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 7 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 10 http://sis.nlm.nih.gov/enviro.html National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 11 Suggested starting point to http://sis.nlm.nih.gov/enviro.html National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 12 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 15 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 18 TOXLINE® (Toxicology Bibliographic Info) National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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). National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 21 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 22 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 23 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 24 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 25 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 26 Please note the numerous tabs National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 27 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 28 Basics tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 29 Interactions tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 30 Genes tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 31 Diseases tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 32 ChemComps tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 33 Pathways tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 34 References tab National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 35 Links tab Add Haz-Map? National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 36 A CTD Primer National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 37 Selected publications about the CTD National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 38 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 39 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 40 Additional NLM Resources National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 41 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 42 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 43 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 44 Selected links to information on environmental health, toxicology, disasters, chemicals, drugs, & special populations National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 45 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 46 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 47 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 48 MedlinePlus Includes Poisoning, Toxicology, and Environmental Health Information National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 49 2011-2012 News National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 50 How to stay informed National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 51 Goals of of Presentation Introduction to NLM databases & tools of likely interest to you Next: Haz-Map review process National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 52 From Dr. Brown’s Presentation: “Like Editing a Textbook” 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES From Dr. Brown’s Presentation: Haz-Map Review Environment Since 2000 (NLM) and 2006 (DOL) 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES From Dr. Brown’s Presentation: Conclusions 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 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?...” National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 56 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.” National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 57 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 58 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…” National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 59 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…” National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 60 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.” National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 61 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 62 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 63 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 64 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 65 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. National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES 66 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 National Library of Medicine NATIONAL INSTITUTES OF HEALTH ◊ U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES