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UBC Urology Residents Library Skills Workshop 2010 Document Transcript

  • 1. Search Scholarship – UBC Urology Residents Dean Giustini, MLIS, MEd, November 2010 SEARCH SCHOLARSHIP WORKSHOP SERIES Welcome to your UBC Library tutorial on searching the literature. It is my pleasure to be working with you and Dr. Jennie Mickelson. My name is Dean Giustini and I work at the UBC Biomedical Branch Library in the Diamond Centre, teach at the UBC School of Library, Archival and Information Studies (SLAIS), and maintain a search-based wiki called HLWIKI Canada <http://hlwiki.ca>. This series of workshops is meant to provide an overview of searching the biomedical literature for you with an emphasis on urology topics. We will address three main areas in these sessions. WORKSHOP 1: Access & Search Skills A. How do I access the UBC Library’s Urology research guide? (This guide is a useful starting point.) First, go to: www.library.ubc.ca  Select ‘SUBJECT GUIDES’  Type in ‘UROLOGY’  Click SEARCH B. Access skills 1. How do I find a reference? 2. How do I search for articles appearing in a specific journal? 3. How do I save articles to my NCBI account? 4. How do I search for articles using the ISSN? 5. How can I refine / apply limits to my search? WORKSHOP 2: ADVANCED ACCESS SKILLS 6. How can MeSH terms refine my search? (e.g., make it precise?) 7. How can I combine searches? 8. How can I find what else an author has published? 9. How can I find the top authors for a given topic? WORKSHOP 3: BIBLIOGRAPHIC SOFTWARE, BIOMEDICAL DATABASES & GREY LITERATURE 10. How to use bibliographic management software (RefWorks) 11. How to access PubMed, MEDLINE & EMBASE via OvidSP interface Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 1
  • 2. The UBC Library subscribes to more than 65,000 online journals, books, pamphlets and government documents. We are moving further and further into the digital era for faculty and students. Our goal is to share ideas with you about how to find these materials efficiently. Note: when working off campus, you will need to change your computer’s settings to show you are affiliated with the University. To change your computer settings, remember your CWL and / or your UBC Library card numbers. To change the settings on your computer, see the instructions here: http://www.library.ubc.ca/home/proxyinfo/ 1-How to refresh and enhance your searching? A- Access Skills 1- How do I access UBC Library’s resources? First, go to: www.library.ubc.ca  UBC Library  Select ‘E-RESOURCES’  Then, Indexes & Databases Bookmark the UBC Library page for PubMed for easy access. PubMed.gov is maintained by the U.S. National Library of Medicine (NLM) and can be accessed for free BUT if you access it from the UBC Library information page, you will be able to see the UBC’s ‘link resolver’ to see all of our full text electronic subscriptions Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 2
  • 3. B- Search Skills 1. How do I find a reference? Let’s work with the following reference: Lerner MA, Ayalew M, Peine WJ, Sundaram CP. Does training on a virtual reality robotic simulator improve performance on the da Vinci surgical system? J Endourol. 2010 Mar;24(3):467-72. PMID: 20334558 There are several ways to retrieve an article’s fulltext BUT for now proceed to PubMed Tools. Scroll down to the Single Citation Matcher. Select a few elements of the above citation and type them into the appropriate boxes such as year, volume, issue, first page of article. Once you do so, click GO. Note: Every article in PubMed will be given a unique number or PMID by the librarians at the National Library of Medicine where MEDLINE is created. In the ‘brief record’ display in PubMed, all citations are given a PMID. Type the PMID number 20334558 into PubMed – this is an easy and helpful way to obtain the citation (and will save you time) To obtain the full text, click on the UBC eLink which takes you here: Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 3
  • 4. 2. How do I search for articles appearing in a specific journal? Go to PubMed. At the top of the page, use the ‘Search’ drop down menu, scroll down to “Journals” Type in “British Journal of Urology” and “Go” to retrieve a record that provides the ISSN. Click the box at right and from the dropdown menu above, select “Search box with “or”. This will create a second search box for the following: "Br J Urol"[Journal:__jrid1908]. Now, click on the button “Search PubMed”. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 4
  • 5. By clicking Search PubMed, you will retrieve all articles from the British Journal of Urology from volume 1, issue 1, or when PubMed began to index it. Notice the ISSN = 0007-1331. 3. How do I save articles to my NCBI account? At the top of the page, select “Save Search” and register for a My NCBI Account. When items are entered into PubMed that fit parameters of your saved searches, they will be emailed to you. Name the search Urology Journal search. Timesaver: Every journal has an identifying number called an International Standard Serial Number (ISSN). You can search that number instead of using the journal name. 4. How do I search for articles using the ISSN? In the PubMed ‘Journals Database’ type in the journal title to get the print (p) and electronic (e) international standard serials numbers (both numbers are needed to build a ‘journals set’ or filter). 1. American Journal of Kidney Disease / Indexed in Embase http://www.ajkd.org/ 2. American Journal of Surgery / pISSN: 0002-9610 / eISSN: 1879-1883 3. American Journal of Transplantation / pISSN: 1600-6135 / eISSN: 1600-6143 4. British Journal of Urology / ISSN: 0007-1331 5. Canadian Journal of Urology / ISSN: 1195-9479 6. Canadian Medical Association Journal (CMAJ) / pISSN: 0820-3946 / eISSN: 1488-2329 7. European Urology / pISSN: 0302-2838 / eISSN: 1873-7560 Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 5
  • 6. 8. Journal of the American Medical Association (JAMA) / pISSN: 0098-7484 / eISSN: 1538-3598 9. Journal of Clinical Oncology / pISSN: 0732-183X / eISSN: 1527-7755 10. Journal of Endourology / pISSN: 0892-7790 / eISSN: 1557-900X 11. Journal of Pediatric Urology / pISSN: 1477-5131 / eISSN: 1873-4898 12. Journal of Surgical Education / pISSN: 1931-7204 / eISSN: 1878-7452 13. Journal of the American College of Surgeons / pISSN: 1072-7515 / eISSN: 1879-1190 14. Journal of Urology / pISSN: 0022-5347 / eISSN: 1527-3792 15. Lancet / pISSN: 0140-6736 / eISSN: 1474-547X 16. Nature Reviews Urology / pISSN: 1759-4812 / eISSN: 1759-4820 17. Nephrology, Dialysis, Transplantation / pISSN: 0931-0509 / eISSN: 1460-2385 18. New England Journal of Medicine / pISSN: 0028-4793 / eISSN: 1533-4406 19. Prostate / pISSN: 0270-4137 / eISSN: 1097-0045 20. Transplantation / pISSN: 0041-1337 / eISSN: 1534-6080 21. Urology / indexed in EMBASE http://www.sciencedirect.com/science/journal/00904295 You can create a search across these journals by combining them into one ‘saved set’ using OR: 0002-9610 OR 1879-1883 OR 1600-6135 OR 1600-6143 OR 0007-1331 OR 1195-9479 OR 0820-3946 OR 1488-2329 OR 0302-2838 OR 1873-7560 OR 0098-7484 OR 1538-3598 OR 0732-183X OR 1527-7755 OR 0892-7790 OR 1557-900X OR 1477-5131 OR 1873-4898 OR 1931-7204 OR 1878-7452 OR 1072-7515 OR 1879-1190 OR 1527-3792 OR 1474-547X OR 1759-4812 OR 1759-4820 OR 0931-0509 OR 1460-2385 OR 0028-4793 OR 1533-4406OR 0270-4137 OR 1097-0045 OR 0041-1337 OR 1534-6080 This search retrieves about 41,000 articles. By saving this search in your MyNCBI, you can combine it with a topic or actual clinical question. At PubMed, login with your ID and password and click MyNCBI at the bottom right hand corner. Once into your account, find your saved search called ‘Urology journals’. 5. How do I save an article to my NCBI account? Once you create an account in MyNCBI, you can save articles to read later. Enter the article’s PMID (number only): 20334558 and click “Go”. This will bring up the ‘Da Vinci surgical’ article from earlier. In the “Send to” drop down menu, select “Collections”; the Pop-up box will ask whether you want to start a new collection or append this article to an existing one. It’s up to you. Why is this helpful? MyNCBI is a good strategy for saving articles you want to read later. Create a Collection called “Future Reading”. Your Collections and Searches stored in your my NCBI account are on the PubMed server so they can be accessed from any computer. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 6
  • 7. Summary of Search Scholarship I During this hour, you have learned how to: • Access PubMed from the UBC Library website http://www.library.ubc.ca • Use PubMed identifyinf numbers (PMIDs) to find specific citations or articles • Use a journal’s International Standard Serial Number (ISSN) to find specific journals • Find journals using the Journals Database in PubMed • Use Single Citation Matcher and open a MyNCBI account in PubMed • Save to Collections and Searches in MyNCBI • Create saved searches in MyNCBI in PubMed End of Session I Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 7
  • 8. 6. How do “limits” make my search more manageable? • Make sure you are logged in to MyNCBI • Enter your account by clicking the MyNCBI logo at the upper right hand corner. • Go to your Searches and select Urology Journals. • Run that search again by clicking on the title of the search. • Select the limits tab that is above the pink horizontal line. Note all the different restrictions you can put on a search. Select Published in the last ten years. From Type of Article, select randomized controlled trial. Then select “Go”. Note that any limits that are still operational will be visible as: 7. How can MeSH terms refine my search – to make it more precise? MeSH terms Every database has a thesaurus of terms that are used to organize references. In PubMed, these are called Medical Subject Headings (MeSH) and provide a thorough way to search for articles “about” certain topics. When searching by keywords, search tools find articles where keywords appear in the citation. BUT when searching with MeSH, articles have been indexed with those terms thereby making your retrieval more inclusive and sensitive. Let’s find the following article by entering its PMID: 16687642 This is what you should find: Smith M, Lennon MA, Brook AH, Robinson PG. A randomized controlled trial of outreach placement's effect on dental students' clinical confidence. J Dent Educ. 2006 May;70(5):566-70. Timesaver: See what MeSH terms are given to the article by changing the “Display”. The dropdown menu shows “Abstract” BUT change this to MeSH to see what ‘the tagged field’ display says. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 8
  • 9. Timesaver: The tagged format is how articles are entered into PubMed which will be IMPORTANT when we use RefWorks. For now, scroll down to see what MeSH terms are given to the article. The MeSH Terms for this article are: MH- Attitude of Health Personnel MH- Clinical Competence MH- Community Dentistry/*education MH- Dental Clinics MH- Education, Dental/*methods MH- General Practice, Dental MH- Great Britain MH- Humans MH- *Preceptorship MH- Schools, Dental MH- *Self Assessment (Psychology) MH- Students, Dental/*psychology 8. How can I combine searches? MeSH Terms give you further ideas to refine your search for similar articles. From the dropdown menu at the top of the page where you see “PubMed”, scroll down to MeSH. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 9
  • 10. Type in ‘self assessment’ as a MeSH Term and click on SEARCH Put a check mark next to the term that appears. From the drop down menu that appears, click on “Send to” and select “Search box with and”. This is Step I of creating a MeSH search in PubMed Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 10
  • 11. “Search PubMed”. Meanwhile, open up you’re MyNCBI account and open up your saved searches. Make sure you run your Journals search. Go to Advanced Search to see recently performed searches and combine your Journals search with the self-assessment MeSH search: Put your cursor over the number of the search – the number preceding the search Double click the search number; a search box should pop up with AND, OR & NOT Use “And” to send search to the search field. Do both searches. Then click “go”. How many articles have you retrieved? How can you make the search even more sensitive? 9. How can I find what else an author has published? Note the following article: Colthart I, Bagnall G, Evans A, Allbutt H, Haig A, Illing J, McKinstry B. The effectiveness of self-assessment on the identification of learner needs, learner activity, and impact on clinical practice: BEME Guide no. 10. Med Teach. 2008 Mar;30(2):124-45. Review PMID: 18464136 Let’s see what other articles the first author has published. Clear the search field. In the search field, type in Colthart I and select “Go”. How many articles have been authored by Colthart. You have added the following skills to your arsenal: searching for articles penned by a specific author, searching by a MeSH term, and combining searches from within the history tab. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 11
  • 12. Let’s develop a strategy to answer the following question: What articles have been published on the topic of “self assessment” in major journals in the last 5 years? • Create an “or” search using self assessment OR self-concept • Select MeSH Database and enter self assessment. Note the older term is self-concept Timesaving Tip: To run a good search on “self assessment”, both terms should be used • Find the term; put a check mark next to it; send it to the search box using “send to” with “or” • Clear the search. Note the search box with self assessment term remains (now add self concept) Find the term; put a check mark next to the term; send the term to the search box using the “send to” drop down menu with “or”. • From the search box that holds both terms ("Self Assessment (Psychology)"[Mesh] OR "Self Concept"[Mesh]), run the search • Go to “limits” tab • Under “Dates”, select “published in the last 5 years” • Under Subsets  Journal Groups  then select Core Clinical Journals Run the search again. Note the applied limits appear in a yellow bar at top of PubMed page Timesaving Tip: Whenever a search retrieves an inordinate number of articles, use limits to refine! 10. How can I find the top authors for a given topic? How can we deal with the following question: Who are the top authors (most references) on a topic (e.g., self assessment) in the main MHPE journals? • Go to previous search and select “Sort By” dropdown menu. Select “First Author”. This is a good starting place. You can also sort by “Last Author”. • Experiment with Google Scholar: http://scholar.google.com/ Enter the following search terms: (self-assessment OR self-concept) “medical education” 11. How do I report a simple search strategy in a manuscript? What about a more complex one? Example: “The literature on self-assessment in the past 5 years was searched using PubMed with the following search terms: xx, xx. XX articles were found, of which xx were directly relevant to our research.” Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 12
  • 13. Timesaver: PubMed tutorials are available on a number of topics under ‘Help’. For direct access, see: http://www.nlm.nih.gov/bsd/disted/pubmed.html Each tutorial cites the length of time it takes to view. These tutorials provide reinforcement for the exercises we have completed …. 2-How to use bibliographic management software (RefWorks) Tools such as RefWorks help to aggregate your citations into a personal library, and provide a way to create a bibliography. UBC provides access to RefWorks® FREE of charge to students and faculty. You need to register for RefWorks but can access it thereafter from any computer. Continue to use your subscription to RefWorks for a nominal annual fee after you leave UBC. Note: RefWorks is web-based and can be accessed from any web-connected computer. RW has an enabled Export feature that allows users to export citations from other databases. To use RefWorks at UBC Library, go to: www.library.ubc.ca  Then ‘E-RESOURCES - Indexes & Databases’  Bottom right Instructions to Use RefWorks • RefWorks is a common citation management tool, and completely web-based • It is accessible at UBC from any web-connected computer • You can create your own personal library of articles • import and store citations, format bibliographies and import citations • link to files e.g., PDFs, word documents, Excel spreadsheets “Sign up for an individual account” Interface overview • References: add references with pull-down menu • Search: search for citations by access point (i.e. author, descriptor, journal name) • Folders: view, edit or delete; Bibliographies: create bibliographies • Tools: download plugins e.g. RefGrabIt and Write-N-Cite Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 13
  • 14. Creating & organizing features: • Select Folders and choose Create … • Give your folder a name; rename or delete as necessary Importing references: • Search PubMed and select some citations • Choose Send to and select File MEDLINE • Save file as pubmed_result.txt (use “Send to” “File” option) • In RefWorks click on References …then Import • From Import Filter/Data Source pull-down menu, select “NLM Pubmed” • Create Folder you want to add references to import pubmed_result.txt file • Use RefGrab-It to capture webpage content. • Download plugin within RefWorks under “Tools” Searching your reference collections: • Your references are all searchable. Choose “Search” then, “Advanced. Ignore “Search Name” • Change your search field from “Descriptors” to “Anywhere” and choose folder to search • Type a keyword into the search box and click on “Search.” Annotating references, adding PDFs & other files: • Click on “Edit” to add comments, keywords, or attachments to a reference • Note the “Attachment” option. Note the “User” fields Creating footnotes & citations in papers: • Download Write-N-Cite How do I locate RefWorks Tutorials? Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 14
  • 15. RefWorks maintains a set of tutorials entitled “Direct Import from an Online Database Service”, “Importing Text Files”, Entering References Manually”, “Organizing your References” etc. They show three different ways to enter citations, how to organize references and how to create a bibliography. They are located here: https://www.refworks.com/Refworks/login.asp?WNCLang=false RefWorks Exercise: 1. Manually enter the following citations into your RefWorks account: • 1: Medina MS, Medina PJ, Wanzer DS, Wilson JE, Er N, Britton ML. Use of an audience response system (ARS) in a dual-campus classroom environment. Am J Pharm Educ. 2008 Apr 15;72(2):38. PMID: 18483604 • 2: Sobral DT. Student-selected courses in a medical school: scope and relationships. Med Teach. 2008;30(2):199-205. PMID: 18464147 • 3: Wang G, Tai B, Huang C, Bian Z, Shang Z, Wang Q, Song G. Establishing a multidisciplinary PBL curriculum in the School of Stomatology at Wuhan University. J Dent Educ. 2008 May;72(5):610-5. PMID: 18451085 2. Create a folder named ‘Medical Education’ 3. Put these citations into this new folder 4. Now, create a bibliography using the Word for Windows file type 4- How to access “grey” literature; As researchers, it is important to know about “grey literature” which is “any material that is not commercially-published or peer-reviewed. Typically, it is composed of technical reports, working papers, business documents, and conference proceedings”. (Matthews, Brian S. Gray Literature: Resources for locating unpublished research. C&RL News; March 2004 65(3).) Why is grey literature important? Research suggests that the percentage of conference proceedings published in peer reviewed journals ranges from 44% to 63%. (von Elm et al. More insight into the fate of biomedical meeting abstracts: a systematic review. BMC Med Res Method 2003, 3:12doi:10.1186/1471-2288-3-12.) Scherer RW, Langenberg P, von Elm E. Publication and access cycles run counter to one another and new research can be difficult to access. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 15
  • 16. “The Flow of Scientific Information” http://www.lib.uwaterloo.ca/usered/grad/researchskills/flow_of_info.html Here is a graphic showing “flow” of information in the Scientific Publication Cycle http://www.lib.washington.edu/subject/environment/imt220/pubcycle.jpg Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 16
  • 17. Initially, ideas are shared on the web or recorded in private notebooks, followed by observations and hypotheses which may remain in the “invisible college”. These start to filter up through dissemination via emails, memoirs, and informal meetings. Finally, the research is organized by indexes and databases such as PubMed. As research findings are more widely accepted, they become easier to access. Sources for grey or pre-published literature • Google Scholar: http://scholar.google.com Google Scholar has become one of the world’s largest free, open academic index and has an excellent cross-section of biomedical content. It is unclear how large it is, however. • Clinical Trials.Gov: http://ClinicalTrials.gov ~100,000 trials sponsored by the NIH, federal agencies and industry. Studies listed are conducted in 173 countries ClinicalTrials receives over 50 million page views per month 65,000 visitors daily. You can determine principal investigators and their contact information. • NLM Gateway: http://gateway.nlm.nih.gov/gw/Cmd?FAQ.x#Conference Some conference proceedings and abstracts can be retrieved from the NLM Gateway web site. • Scirus: http://www.scirus.com/ ~400 million scientific articles, researchers’ homepages, courseware, pre-prints and patents with an emphasis on European literature due to coverage of Elsevier journals. For a review of ‘grey literature’ searching, see http://hlwiki.slais.ubc.ca/index.php/Grey_literature Are you doing a systematic review? Please see your biomedical librarian for a consult Effective searching is a professional skill undertaken by librarians and information specialists. The aim of searching in the health sciences is to be as thorough as possible and to optimize recall with sufficient precision. Researchers doing systematic reviews (SRs) or meta-analysis should ensure that all relevant studies are found. The focus is on exhaustiveness and leaving no stone unturned. Reviews are useful tools for health professionals in view of the massive amount of biomedical information published worldwide as they are a useful distillation of evidence. http://hlwiki.slais.ubc.ca/index.php/Systematic_review_searching Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 17
  • 18. Glossary for Urology Residents Grey literature: is defined as ... "information produced on all levels of government, academics, business and industry in electronic and print formats not controlled by commercial publishing" ie. where publishing is not the primary activity of the producing body." (ICGL Luxembourg definition, 1997 - Expanded in New York, 2004) Institutional Repository: an institutional repository (IR) is a digital space to upload and maintain the research output and digital assets of knowledge-based institutions. As more research is born digital, institutions must identify and collect this information for archival purposes and to support further research. UBC Library has an IR called cIRcle. ‘Invisible College’: the term invisible college refers to the free exchange of ideas, expertise and information carried out with no authority or establishment institutional body governing the communication; in the digital age, this information is being shared by using online networks ISSN: a unique eight-digit number used to identify a print or electronic periodical publication. The ISSN system was adopted as an international standard ISO 3297 in 2007. The ISO subcommittee TC 46/SC 9 is responsible for the standard. MeSH Term: The Medical Subject Headings - MeSH thesaurus is a controlled vocabulary created by the National Library of Medicine (U.S.) for MEDLINE. MeSH terms are used to index, catalogue and retrieve biomedical information and documents from PubMed. Open access: Open access (OA) is the free and open access to scholarly research with no restrictions. OA is possible when researchers publish in OA journals, self-archive on personal websites or place their work in digital repositories. PubMed Central Canada (PMCC): aims to provide a freely accessible, Canada-based archive of biomedical and health research findings. It provides free download of full-text peer-reviewed biomedical papers in Canada's two official languages, English and French. PMCC provides access to a stable and permanent online digital archive of full-text, peer-reviewed articles and builds on PubMedCentral, the U.S. National Institutes of Health (NIH) digital archive of biomedical sciences journal literature and the PMC International (PMCI) network of e-repositories. RefWorks: is a web-based tool designed to help researchers gather, manage, store and share records from database searches and generate citations and bibliographies for manuscripts. Social media is often defined as "...the use of digital media (including internet and mobile) for collaborating with others to create user generated content and form self organizing communities. Blogs, forums, wikis, social networking sites, microblogging sites, social bookmarking sites, social voting sites, social review sites and virtual worlds are all examples of [social media]. So are social sites built around photos, audio, videos, presentations, music, and games...” Urology 2.0 refers to a second generation of urology practice using the benefits of social media. As a biomedical librarian, I would like to partner with a urology resident to write an article about this topic. Search Scholarship Series for Urology Residents / Giustini, Mickelson (handout adapted from Cleo Pappas (c) 2010 - with permission from author) 18