Occupational and Environmental Health Searching for Information - PDF document

Occupational and Environmental Health Searching for Information Evans Whitaker, MD, MLIS UCSF Library evans.whitaker@ucsf.edu Disclosures I have no disclosures to report Goals Build a search from a question using new PubMed. Along the way I will introduce some tools librarians use to help with search development and getting the full text of articles

Objectives By the end of this session you will:  Be more familiar with the structure of PubMed  Will see new PubMed in action  See how to create a thorough search starting with a question  Hear how to you may generalize the approach used in PubMed to other databases  Be introduced to some tools which will help you develop your search, save your work, and find full text of articles Legacy to New 5 New PubMed

New PubMed appeared about a year ago as PubMed Labs Now linked from a larger banner in “legacy” PubMed It will become default interface in the next few months Legacy PubMed will be “retired” by end of 2020… Terminology PubMed MEDLINE Controlled vocabulary MeSH or Emtree Keywords = Problem, Patient, Population P = Intervention or Exposure I Ask PICO = Comparison group C Acquire 5 A’s of EBM Appraise = Outcome O Apply Assess

Controlled vocabulary Most databases have a dictionary or glossary of preferred terms. If a search uses these words, the database will look for synonyms at the same time it looks for the preferred term: Example from MeSH in PubMed: Occupational Medicine  Entry Terms (= synonyms) Medicine, Occupational ○ Medicine, Industrial ○ Industrial Medicine ○ MEDLINE vs. PubMed PubMed 30.5M Publishers supply information MEDLINE 26.5M Searching for information for biomedicine Searches for information are usually of two types:  Quick search for a few good things for patient care or verification  Thorough search for detailed information for research or publication Thorough literature reviews, especially those for systematic reviews, search in more than one database. Cochrane handbook states that at a bare minimum PubMed and Embase should be included.

A question to work with… Courtesy of Dr. Blanc Is carbon disulfide associated with adverse reproductive outcomes?  How many concepts?  What are they? 2, CS2 and adverse reproductive outcomes  How would you use PICO on this? P - may not need to define I (OR E) - CS2  What issues do you see with this C – not defined search? O – adverse reproductive Fully defining adverse reproductive outcomes will be outcomes challenging 13 Presentation Title Problems with this search…  The adverse reproductive outcomes will be hard to full characterize  Switch to new PubMed to explore So what did we do there?  We developed a question , this might have come from a patient, from research we want to do, or the topic for an invited paper…  We parsed the question into concepts. We might have used PICO to help  We found controlled vocabulary (MeSH), thought of synonyms/ keywords to describe each concept  We used Boolean operators ( AND, OR , rarely NOT) to assemble the search and added parentheses and quotation marks as needed.  We tuned up the search based on results. A good search should find a list of “known” good articles)  We saved our work 15

This approach will work for any database!  Databases each have their own controlled vocabulary (e.g., Embase uses Emtree)  Databases in which you would look for information related to biomedicine have extensive overlap. Each database will contribute a few things to the good results. Tools to help  Yale MeSH Analyzer can take up to 20 PMIDs and create a table showing MeSH, author keywords, title and abstract to help find the terminology in common between articles you like  Unpaywall, Kopernio and OA Button help find full text of articles for you  MyNCBI saves your searches, keeps you updated, can send tables of contents of selected journals to you, and can save collections of articles  Embase and other databases have functionality similar to MyNCBI Tools to help  That was a whirlwind tour  If you have questions about the content or need clarification feel free to email me at evans.whitaker@ucsf.edu

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MeSH is ______ (pick all correct answers) A controlled vocabulary of preferred subject terms used in PubMed. 1. A means to remove leaves from brewed tea. 2. Stands for Medical Subject Headings. 3. Used by all databases. 4. Includes a list of “Entry terms” for each MeSH 5. Entry terms are synonyms for MeSH 6. PubMed and MEDLINE are the same thing. 1. True 1. 2. False 2. Once you have run a search what tool built into PubMed will help you understand how PubMed interpreted your search? 1. Details 1. 2. MeSH database 2. 3. MyNCBI 3. 4. Advanced 4. 24 Presentation Title

UCSF Occupational and Environmental Health Conference – Library presentation 5-7 March 2020 Hi everyone, I am Evans Whitaker from UCSF Library. If you have questions after taking a look at this please contact me at evans.whitaker@ucsf.edu We have 40 minutes to talk about how to search the scientific literature for the information you need to help take care of your patients, teach students, do your research, and write your papers. As you know, and as I have found out while preparing this talk, the information for your field of Occupational and Environmental Health is widely spread throughout the biomedical literature and not conveniently located in a few key journals. I expect there is a great deal of diversity in the group. Some of you have access to multiple databases and extensive full-text journal article access, others will be limited to PubMed and Google Scholar for searching and whatever full text to which you, your practice/medical group, or your hospital/medical system purchase. I have tried to make this presentation relevant to this broader spectrum of information seekers. Today we will focus on: 1. New PubMed , we can imagine two kinds of searches… a. A search for a few good things, I suspect you all are already good at this… b. A thorough search as if for a systematic review or to become well-versed in a particular topic or as background for conducting your own research. c. I will try to emphasize principles you can apply to the search of any database. 2. Tools : a. Use of MyNCBI and other database-associated personal accounts to save your work and receive updates b. Google Scholar can be used in that same way. c. Other useful tools I will mention include Unpaywall, Kopernio, OA Button to help find legal full-text. We do not recommend or condone the use of SciHub. PICO as a framework for creating questions. Yale MeSH Analyzer to help with finding terms to use in your search. d. A reference manager (like EndNote or Zotero) to store, organize, remove duplicates and add citations and a reference list to document you are writing. e. Evernote or OneNote adds a second way to quickly store useful information you find that reference managers do not do as well with (images or tables from an article, parts of a website, etc. I want you to leave this session today ready to try out the new PubMed and with an approach to the process that carries you from identifying a question to storing and organizing the information you found in a reference manager. Background and introduction which applies to old and new PubMed. PubMed is made of two parts. MEDLINE (26.5 M) is 86% of PubMed and is well organized and easier in which to search.“The part of PubMed not in MEDLINE” (4 M) is where new material is housed until indexed (which can take days to years depending on the journal). See graphic next page to explain. Have questions about this handout or the presentation? evans.whitaker@ucsf.edu 1