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UBC Radiology Residents 2012

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An early draft of our session on Tuesday July 3rd, 2012 for the new UBC radiology residents.

An early draft of our session on Tuesday July 3rd, 2012 for the new UBC radiology residents.

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    UBC Radiology Residents 2012 UBC Radiology Residents 2012 Document Transcript

    • Search Scholarship – UBC Radiology Residents rdDean Giustini, MLIS, MEd, July 3 2012 SEARCH SCHOLARSHIP– UBC RADIOLOGY RESIDENTS 2012Welcome to your UBC Library tutorial on searching the literature. It is my pleasure to beworking with you. My name is Dean Giustini and I work at the UBC Biomedical Branch Libraryon the 2nd floor of the Diamond Centre, teach at UBC’s School of Library, Archival andInformation Studies (SLAIS), and maintain a technologies wiki called HLWIKI <http://hlwiki.ca>.Ifyou wish to develop your search skills, this can be a helpful starting point.This introduction to search scholarship for radiology residents is meant to provide an overviewof searching the biomedical literature with an emphasis on your discipline.WORKSHOP 1: ACCESS & SEARCH SKILLSA. How do I access UBC Library’sRadiology research guide?–auseful starting point for your searchingFirst, go to: www.library.ubc.caSelect ‘RESEARCH GUIDES’Type in ‘RADIOLOGY’Click SEARCHOR go to: http://toby.library.ubc.ca/subjects/subjpage1.cfm?id=282B. Access & Search Skills 1. How do I find a radiology reference in Medline? 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 searches?WORKSHOP 2: ADVANCED SEARCH SKILLS 6. Howcan MeSH terms refine my search? (e.g., make it more precise?) 7. How can I combine searches? And use Boolean operators? 8. How can I find what else an author has published? find the top authors in a given area?WORKSHOP 3: BIBLIOGRAPHIC SOFTWARE, BIOMEDICAL DATABASES & GREY LITERATURE 9. How to use bibliographic management software (RefWorks) 10. How to access biomedical databases (PubMed, MEDLINE&EMBASE via OvidSP) Search Scholarship for Radiology Residents 2012/ Giustini-1
    • The UBC Library subscribes to more than 75,000 online journals, books, pamphlets and governmentdocuments. We are moving further and faster into the digital era for faculty and students than ever in2011. Our goal today is to share ideas with you about how to find these materials. Note:When off campuschange your computer’s settings to show you are affiliated with UBC. To change settings, remember your CWL and UBC Library card. To try the myVPN or EZproxy, see the instructions:http://www.library.ubc.ca/home/proxyinfo/1-How to refresh and enhance your searching?A- Access Skills1- How do I access UBC Library’s resources?First, go to: www.library.ubc.caUBC Library Select ‘E-RESOURCES’  Then, Indexes & DatabasesBookmark the UBC Library page for PubMedPubMed.gov is maintained by the U.S. National Library of Medicine (NLM) and is freely-accessible BUT ifyou access it from the UBC Library information page, you will see UBC’s ‘link resolver’ for our full textcollections. This is what the link resolver looks like… Search Scholarship for Radiology Residents 2012/ Giustini-2
    • B- Search Skills1. How do I find a reference?Let’s work with the following reference: Lungren MP, Horvath JJ, Welling RD, Azene EM, Starikovsky A, Bashir MR,Mollura DJ, Maxfield C. Global health training in radiology residency programs.AcadRadiol. 2011 Jun;18(6):782-91. PMID:21458308There are several ways to retrieve the fulltext of articlesBUTfirst go toPubMed Tools.Scroll down andclick on the Single Citation Matcher. Select some unique elements of the citation and type them intothe box such as year, volume, issue and first page of article. THEN, click GO.Note:Every article in PubMedhas a unique number or PMIDassigned by the librarians at the NationalLibrary of Medicine where MEDLINE is created. In the ‘brief record’, citations aregiven a PMID. Type thePMID 21458308 into the search box. This is a quick way to get the citation (and saves time)To obtain full-text, click on the UBC Citation Linker which takes you here: Search Scholarship for Radiology Residents 2012/ Giustini-3
    • 2. How do I search for articles appearing in a specific journal?Go toPubMed. At the top of the page, use the ‘Search’ drop down menu, scroll down to “Journals”Typein “British Journal of Radiology” and “Go” to retrieve a record that provides the ISSN. Click the boxat left and from the dropdown menu above, select “Add to search builder”. This will paste into thesearch box the following: "Br J Radiol"[Journal]. Now, click on the button “Search PubMed”. Search Scholarship for Radiology Residents 2012/ Giustini-4
    • By clicking onSearch PubMed, you retrieve all articles from the British Journal of Radiology from vol 1,iss 1 or when PubMed began to index it. You retrieve about ~14000 articles. Note the ISSN 0007-1285.3. How do I save articles to myNCBI?At PubMed, select “Save Search” and register for My NCBI. When items are entered into PubMed thatfit the parameters of your search, they will be emailed to you. Give your search a name. 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. Search Scholarship for Radiology Residents 2012/ Giustini-5
    • 4. How do I search for articles in specific ‘high-impact’ radiology journals?In PubMed’s ‘Journals Database’ type in the journal title to get the print (p)and electronic (e)?SSNs:1. Academic radiology / ISSN:1076-6332 (Print) ; 1878-4046 (Electronic)2. AJNR - American journal of neuroradiology / 0195-6108 (Print) 1936-959X (Electronic)3. AJR - American journal of roentgenology / 0361-803X (Print) ; 1546-3141 (Electronic)4. British journal of radiology / ISSN:0007-1285 (Print) 1748-880X (Electronic)5. Canadian Association of Radiologists journal / 0846-5371 (Print) 0846-5371 (Linking)6. Emergency radiology / ISSN:1070-3004 (Print) 1438-1435 (Electronic)7. European radiology / ISSN:0938-7994 (Print) 1432-1084 (Electronic)8. Investigative Radiology / 0020-9996 (Print) 1536-0210 (Electronic)9. Journal of the American Medical Association(JAMA) / pISSN: 0098-7484 / eISSN: 1538-359810. JMRI - Journal of magnetic resonance imaging/ 1053-1807 (Print) 1522-2586 (Electronic)11. Lancet/ 0140-6736 (Print) 1474-547X (Electronic)12. New England journal of medicine0028-4793 (Print) 1533-4406 (Electronic)13. Nuclear medicine and biology / 0969-8051 (Print) 1872-9614 (Electronic)14. Radiographics / ISSN:0271-5333 (Print) ; 1527-1323 (Electronic) ; 0271-5333 (Linking)15. Radiology / ISSN:0033-8419 (Print) ; 1527-1315 (Electronic) ; 0033-8419 (Linking) Create a search across Fifteen (15) High Impact Radiology Journalsin one ‘saved search set’ using OR1076-6332 OR 1878-4046 OR 0007-1285 OR 1748-880X OR 0846-5371 OR 1070-3004 OR 0938-7994 OR1432-1084OR 0098-7484 OR 1538-3598 OR 0140-6736 OR 1474-547XOR 0028-4793 OR 1533-4406OR0271-5333 OR 1527-1323OR 0033-8419 OR 1527-1315OR1872-9614OR0969-8051OR1053-1807OR1522-2586 OR 0020-9996OR 1536-0210OR0195-6108 OR1936-959XOR 0361-803X OR 1546-3141This search retrieves just over ~356,000 articles+. With this search saved, you can now combine it with atopic or actual clinical question. Go toPubMed login with your ID and password and click on My NCBI atthe bottom right hand corner. To begin, find your saved search called ‘Radiology journals’.5. How do I save an article to my NCBI?After you have created an account in My NCBI, you can save articles in your account. Enter the followingPMID (number only): 20334558. Select “Go”.This will bring up the ‘Da Vinci surgical’ article from earlier. Search Scholarship for Radiology Residents 2012/ Giustini-6
    • From the “Send to” drop down menu, select “Collections”. You will get a Pop-up box that asks whetheryou want to start a new collection or append this article to an existing one. Save the article or cancel it.Why is this helpful? This is a good strategy for saving articles you want to read later. Create a Collectioncalled “Future Reading”.Your Collections and Searches stored in your my NCBI account are on thePubMed server so they can be accessed from any computer.Summary of Search Scholarship IDuring this hour, you have learned to: Find the ‘RADIOLOGY’ Subject Guide at the UBC Library website http://www.library.ubc.ca Access PubMed from the UBC Library website http://www.library.ubc.ca Use PubMed identifying 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 MyNCBIaccount inPubMed Save to Collections and Searches in MyNCBI Create saved searches in MyNCBI in PubMedEnd of Session I Search Scholarship for Radiology Residents 2012/ Giustini-7
    • Search Scholarship for Radiology Residents 2012/ Giustini-8
    • 6. How do “limits” make my search more manageable? Make sure you are logged in to My NCBI. Enter your account by clicking the My NCBI logo at the upper right hand corner. Go to your Searches and select Radiology Journals. Run that search again by clicking on the title of the search. Select the limits tab that is above the pink horizontal line.Notethe many different restrictions you can put on a search. Select Published in the last ten years. FromType of Article, select randomized controlled trial. Then select “Go”. Note that the limits that areoperational appear in yellow above the entries. You should retrieve ~[blank] articles.7. How can MeSH terms refine my search – to make it more precise?MeSH termsEvery database has a thesaurus of terms that are used to organize references. In PubMed, these arecalled Medical Subject Headings (MeSH) and provide a way to search for articles “about” topics. Whensearching by keyword, any search tool will find items where keywords are found in the citation. BUT ifyou use MeSH, articles are indexed with those terms thereby making retrieval more sensitive.Let’s find the following article by entering its PMID: 21436101This is what you should come up: Chammas MC, Moon HJ, Kim EK. Why do we have so many controversies in thyroid nodule Doppler US?Radiology. 2011 Apr;259(1):304.Timesaver: What MeSH terms are associated with this article? Next to “Display”, see the dropdownmenu for “Abstract” or “MEDLINE”or click the + sign by Publication Types, MeSH Terms Search Scholarship for Radiology Residents 2012/ Giustini-9
    • Timesaver:The MEDLINE tagged format is used to enter articles in PubMed –IMPORTANT informationwhen you try to import into RefWorks. For now, look atthe MeSH terms given to this article: MH - Aged MH - Aged, 80 and over MH - Biopsy, Fine-Needle MH - Chi-Square Distribution MH - Female MH - Humans MH - Male MH - Logistic Models MH - Middle Aged MH - Neovascularization, Pathologic – *ultrasonography MH - Predictive Value of Tests MH - ROC Curve MH - Retrospective Studies MH - Thyroid Neoplasms/*ultrasonography MH - Thyroid Nodule/*ultrasonograph MH - Ultrasonography, Doppler Search Scholarship for Radiology Residents 2012/ Giustini-10
    • 8. How can I combine searches?MeSH Terms give you further ideas to refine your search for similar articles. From the dropdown menuat the top of the page where you see “PubMed”, scroll down to MeSH.Type in ‘self assessment’ as a MeSH Term and click on SEARCH Search Scholarship for Radiology Residents 2012/ Giustini-11
    • Put a check mark next to the term that appears. From the drop down menu that appears, click on “Sendto” and select “Search box with and”. This is Step I of creating a MeSH search in PubMed“Search PubMed”. Meanwhile, open up yourMyNCBI account and your saved searches. Make sure yourun your Journals search. Go to Advanced Search to see recently performed searches and combine yourJournals search with the self-assessment MeSHsearch: 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?Notethe following article: Forster BB, Cresswell M. Musculoskeletal ultrasound: changing times, changing practice? Br J Sports Med. 2010 Dec;44(16):1136-7.Let’s see what other radiology articles that the first author has published. Who is it? In the search field,type in Forster BB and select “Go”. How many articles have been authored by Forster Bruce?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 for Radiology Residents 2012/ Giustini-12
    • Let’s develop a strategy to answer the following question: What articles have been published on thetopic of “MENTORING” and “RADIOLOGY” in major journals in the last 5 years? Create a search set using“MENTORING” OR “MENTOR” Select MeSH database and enter mentoring. Note theMeSHis MENTORSTimesaving Tip:To run a good search on “MENTORING”, both terms should be used Find MeSHterm; 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 MENTORS term remainsFind 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("MENTORING" OR "MENTORS"[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 JournalsRun the search again. Note the applied limits appear in a yellow bar at top of PubMed pageTimesaving 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 inthe main radiology 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 search terms to describe what you would like to search: _____________________________11. How do I report my search strategy in a manuscript?Example: “The literature on mentors and mentoring 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 the issues at hand.” Search Scholarship for Radiology Residents 2012/ Giustini-13
    • Timesaving Tip: PubMed tutorials are available on a number of topics under ‘Help’. For direct access,see: http://www.nlm.nih.gov/bsd/disted/pubmed.htmlEach tutorial cites the length of time it takes to view. These tutorials provide reinforcement for theexercises we have completed ….2-How to use bibliographic management software (RefWorks 2.0)Tools such as RefWorks 2.0 (new in July 2011)help toaggregateyour citations into a personal library, andprovide a way to create a bibliography. UBC Libraryprovides access to RefWorks®FREE of charge tostudents 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 anenabled Export feature that allows users to export citations from other databases. To use RefWorks atUBC Library, go to: www.library.ubc.caThen ‘E-RESOURCES - Indexes & Databases’ Bottom rightInstructions to Use RefWorks common citation management tool, widely-used and web-based; create a personal library of articles import and store citations, format bibliographies and import citations link to files e.g., PDFs, word documents, Excel spreadsheets add new citations by importing or manual entering; share citations for collaborative projects Go to: http://bit.ly/4r9wVA and “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 Folders Bibliographies: create bibliographies Tools: download plugins e.g. RefGrabIt and Write-N-Cite Search Scholarship for Radiology Residents 2012/ Giustini-14
    • Creating & organizing features: Select Folders and choose Create … Give your folder a name; rename or delete as necessaryImporting 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” fieldsCreating footnotes & citations in papers:Download Write-N-Cite Search Scholarship for Radiology Residents 2012/ Giustini-15
    • How do I locate the RefWorks 2.0 Tutorial?RefWorks maintains a tutorial with simple videos and handouts:locatedhere:http://www.refworks-cos.com/refworks/tutorials/basic.htmlRefWorks Exercise:1. Enter the following citations into your RefWorks account: 1: De Langhe E, Lories R, Maenaut K, De Vlam K. The kaleidoscopic presentationof the spondyloarthritis concept in a female patient. Joint Bone Spine. 2011 Jun 22. 2: Sobral DT.Student-selected courses in a medical school: scope and relationships.Med Teach. 2008;30(2):199-205. PMID: 18464147 3: Timpone VM, Lattin GE Jr, Lewis RB, Azuar K, Tubay M, Jesinger RA. Abdominal twists and turns: part I, gastrointestinal tract torsions with pathologiccorrelation. AJR Am J Roentgenol. 2011 Jul;197(1):86-96.PMID: 21701015.2. Create a folder named ‘Radiology test’3. Put these citations into this new folder4. Now, create a bibliography using the Word for Windows file type Search Scholarship for Radiology Residents 2012/ Giustini-16
    • 4- How to access “grey” literature;As researchers, we need to concern ourselves with what is known as “grey literature” or “materials notformally or commercially published … especially conference proceedings”. (Matthews, Brian S. GrayLiterature: Resources for locating unpublished research. C&RL News; March 2004 65(3).)Why is grey literature important? Research suggests that of all conference proceedings, the percentage published inpeer reviewed journals ranges from 44% to 63%. (von Elm et al. More insight into the fate of biomedical meetingabstracts: a systematic review. BMC Medical Research Methodology 2003.) Scherer RW, Langenberg P, von Elm E.Publication and access cycles run counter to one another and new research can be difficult to access.View“The Flow of Scientific Information” http://www.lib.uwaterloo.ca/usered/grad/researchskills/flow_of_info.html Search Scholarship for Radiology Residents 2012/ Giustini-17
    • Initially, ideas areshared on the web or recorded in private notebooks, followed by observations andhypotheses while they remain in the “invisible college”. They start to filter up through dissemination viaemails, memoirs, and informal meetings. Finally, the research is organized by indexes and databasessuch as PubMed. As research findings are more widely accepted, they becomemore easyto access.Here is a graphic showing “flow” of information in the Scientific Publication Cyclehttp://www.lib.washington.edu/subject/environment/imt220/pubcycle.jpg Note that information easilyfound in indexes appears parallel to the latter quartile of the time cycle.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. Search Scholarship for Radiology Residents 2012/ Giustini-18
    • 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 mainly by librarians and information specialists but, as a radiology resident, you can certainly acquire good basic searching skills. The aim of searching is to be as thorough as possible and to optimize recall with sufficient precision. All 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_searchingOther Radiology Resources – eBooks & eBook Collections Adam: Grainger & Allisons Diagnostic Radiology, 5th ed (2008)–online Basic Radiology, 2e– online Gangi Imaging in percutaneous musculoskeletal interventions (2009)– online Grainger & Allison diagnostic radiology (2001) or MD Consult– online2008 Merrills Atlas of radiographic positions (2003)– print Mettler: Essentials of Radiology, 2nd ed (2005) - online Muellers Radiologic diagnosis of chest diseases (2001) – print CT- and MR-guided interventions in radiology (2009)- online Radiography essentials for limited practice (2006) – print Magnetic resonance imaging in orthopedic sports medicine- online Search Scholarship for Radiology Residents 2012/ Giustini-19
    • Glossary for Radiology ResidentsInstitutional Repository: an institutional repository (IR) is a digital space to upload your research andknowledge-based assets. As more research is born digital, institutions must identify and collect thisinformation for archival purposes and to support further research. UBC Library has an IR called cIRcle.‘InvisibleCollege’: the term invisible college refers to the free exchange of ideas, expertise andinformation carried out with no authority or establishment institutional body governing thecommunication; in the digital age, this information is being shared by using online networksISSN: a unique eight-digit number used to identify a print or electronic publication. The ISSN system hasbeen an international standard ISO 3297 since 2007.MeSH Term: The Medical Subject Headings - MeSH thesaurus is a controlled vocabulary created by theNational Library of Medicine (U.S.) for MEDLINE. MeSH terms are used to index, catalogue and retrievebiomedical 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 theirwork in digital repositories.PubMed Central Canada (PMCC):is a freely-accessible Canada-based archive of biomedical research. Itprovides downloads of full-text biomedical papers in English and French. PMCC provides access to anonline archive of peer-reviewed articles and builds on PubMedCentral, the U.S. National Institutes ofHealth (NIH) digital archive of biomedical journal literature.Radiology or ‘imaging informatics’: Imaging Informatics – also known as radiology informaticsor medical imaging informatics – is a subspecialty of biomedical informatics that aims to improve the efficiency, accuracy, usability and reliability of medical imaging services in healthcare. It is the study of how information about and contained within medical images is retrieved, analyzed, enhanced and exchanged.Radiology 2.0refers to a second generation of radiology practice applying the benefits of social media.As a medical librarian, I’d like to partner with a radiology resident to write about this topic. Moein A, Malekmohammadi M. Introduction to the next generation of radiology in the web 2.0 world. Proceedings of the International Federation for Medical and Biological Engineering (IFMBE). 2010;459-462.RefWorks: is a web-based tool designed to help researchers gather, manage, store and share recordsfrom database searches and generate citations and bibliographies for manuscripts.Social media is defined as "...the use of digital media (including internet and mobile) for collaboratingwith 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 reviewsites and virtual worlds are all examples of [social media].” Search Scholarship for Radiology Residents 2012/ Giustini-20