SYTEMATIC LITERATURE SEARCHES A Guide (for EndNote X3 Users using library resources at UConn) Michelle R. Warren, Syntheses of HIV & AIDS Research Project, University of Connecticut Monday, 13 June 2011 1. Get familiar with your databases a. PubMed: Search Tutorials i. Biomedical in nature ii. Encompasses MEDLINE, AIDSearch, and others iii. Indexing terms are called MeSH terms: Articles are systematically indexed in databases based on their topics; two problems are that not all articles are indexed and new additions to a database are not indexed immediately b. Ebscohost databases (e.g., PsycINFO, ERIC, CINAHL): Read explanations of how to construct a search under Searching i. You can search multiple databases at once (will eliminate some duplicates between databases) Caution: different Ebscohost databases use different thesauruses and terminology if you are trying to do a search using indexing terms c. Scopus: Basic Search Tutorial d. Read this article to help understand the differences between some of the main databases of scholarly works: Falagas ME, Pitsouni EI, Malietzis GA, Pappas G. Comparison of PubMed, Scopus, Web of Science and Google Scholar: Strengths and weaknesses. FASEB J. 2008;28:338-342. 2. Conducting your search a. Will always be more or less the same in each database, but make sure assumptions are correct (e.g., truncation styles, indexing terms) before carrying out the search b. Use all variants of a word (e.g., HIV or human immunodeficiency virus ; sex or intercourse) c. Do a couple practice searches and d. REMEMBER: typically a search only finds matches in an article s title, abstract, or keywords. If the search option is full-text it will only search the full-text of articles that the database can access, which is NOT all of the articles retrieved in a single search (even if your institution grants you access to them). e. Go broad or go home: In order to make sure your search is inclusive enough, be as broad as you can possibly be without returning an overwhelming number of search results. Using Endnote to Organize Literature Searches Page 1 of 6
3. Export search to EndNote a. PubMed i. Once you punch in your search, and your results are displayed, click the Send to: button on the top right-hand side of the screen. In the drop down menu, click File, and then change the format to MEDLINE. Click Create File ii. A text file will be downloaded to your computer. Make sure you know where it is storing the file (e.g., Desktop, Downloads) iii. In EndNote, create a new library (or use one that you ve already created for this literature search). 1. To import your search from PubMed, you need to either click the Import button (blue circle with a downwards-pointing arrow) or go to File and Import 2. In the Import Data field, choose the text file that you downloaded from PubMed. Change Import Option to PubMed (NLM) and make sure that Discard Duplicates is enabled. Click Import 3. Your library should now be populated with all of the studies that your search retrieved from PubMed. Using Endnote to Organize Literature Searches Page 2 of 6
b. Ebscohost databases i. Once you punch in your search, and your results are displayed, click the Alert/Save/Share button on the top right-hand side of the screen. In the drop down menu, click Email a link to download exported results (up to N). [Note: N should be the number of your search results. Also, Ebscohost will only email up to 5,000 results. If your search yields >5,000 citations, then construct 2 smaller searches and export separately] ii. Type in your email (use an account such as gmail that can accommodate very large files), and make sure that you check off for the citations to be in EndNote, ProCite, or Reference Manager format before sending. Note: it can take up to 45 minutes for the file to reach you. iii. Once you ve received the email, download the attached file to your desktop. It will be a zipped file unzip it. iv. Open EndNote, and either create a new library or use the same library that you ve been importing other searches into for this project. 1. To import your search, you need to either click the Import button (blue circle with a downwards-pointing arrow) or go to File and Import 2. In the Import Data field, choose the file that you just downloaded onto your desktop. Change Import Option to Reference Manager (RIS) make sure that Discard Duplicates is enabled. Click Import (see image in the PubMed example on the previous page) 3. Your library should now be populated with all of the studies that your search retrieved from the Ebscohost databases. 4. Using EndNote, Eliminate Duplicates (will eliminate most, but not necessarily all) a. When importing your searches, oftentimes EndNote will automatically prompt to ask if you would like to eliminate duplicates. b. Otherwise, go to References and Find Duplicates. EndNote will bring up matched citations, and you will have to either go through them individually and decide whether or not they are truly duplicates, or (not recommended) get rid of them all at once. Using Endnote to Organize Literature Searches Page 3 of 6
5. Export to Excel: a. First, make an excel file. You will want it to have the following columns: Full Citation, Abstract, PDF, Inclusion Status. I have prepared a template excel file that you can use and re-title on the basis of your project. b. In EndNote, make sure your studies are sorted in a particular manner, e.g., by Author, by year of publication. It doesn t matter exactly how they are ordered, as long as it remains consistently sorted in this way throughout the exportation process. c. Select all of the studies in the library d. Either click the Export button (blue circle with upwards-pointing arrow) or go to File Export. Note, You will repeat this process twice. e. For the first export, make sure that you are saving the file as a Text File, and that JAMA is selected as the Output Style (this will result in a list of AMA-style references). Also make sure that the box next to Export Selected References is marked. f. Open the resulting text file. Select All, and then copy into the Full Citation column of your Excel file. There should be one citation per row. g. For the next exportation from EndNote, we are going to want to get the Abstracts for each of the citations. In order to do this, we are going to need to build a Custom Filter. h. In EndNote, go to Edit Output Styles New Style i. In the left column, click Templates under Bibliography and type in AB: Abstract. i. Close out of the viewer and save as Abstract when prompted. ii. Now, as before, highlight all of your references (making sure that it s sorted in the same way as before) and click Export. Make sure that you re saving the file this time as a Rich Text Format Using Endnote to Organize Literature Searches Page 4 of 6
(.rtf), and under Output Style find the Abstract filter that you just created. Make sure that Export Selected References is marked. iii. Open the resulting word document, and FIND and REPLACE all ^p in the document with nothing. This will get rid of all hard returns in the document since many abstracts are formatted in EndNote with breaks between sentences. iv. Now, to ensure that there are only hard breaks between abstracts, and not within, FIND all AB: (with format set as bold) and replace with ^pab: (with format set as bold). v. Select all and then copy into the Abstract column of your Excel file. Make sure that there are as many cells filled with Ab: [Abstract text] as there are citations. If there are too many entries in one of the columns, scroll up through the list and look for anomalies. See if some abstracts or citations were split out over multiple cells. If some do split over multiple cells, copy the text from the lowermost cell and paste at the end of the text in the cell above. Delete the lowermost cell and allow the column to shift up. Using Endnote to Organize Literature Searches Page 5 of 6
6. Identify Included/Excluded Studies a. Now that you have both the full citations and corresponding abstracts in excel, go through once and eliminate those that OBVIOUSLY do not qualify for inclusion. If a title even makes you hesitate, do not get rid of it. Also do not delete these exclusions. Rather, cut out the cells and copy into another worksheet within the excel file. We want to have a record of every decision made. b. Now with the smaller list, go through and eliminate or include each study, writing a brief justification next to it (also can simultaneously record which pdfs you ve obtained and which are missing/illed) c. BEST FOR INCLUSION/EXCLUSION DECISIONS TO BE DONE BY 2 PEOPLE! i. Have each person complete the first step (initial exclusions) individually, and then merge lists and eliminate only those that both chose to exclude. ii. Split the resultant, smaller list in two parts. Have each person find abstracts, pdfs and make further judgments for his/her part, and then trade lists to review each other s judgments. (This may be done by different people than the first step) iii. Come together and agree on a final list to start coding with. iv. Assign unique IDs 7. Save your EndNote File! If you ever have to update your search, or import more citations to go through, you can quickly and efficiently eliminate overlaps between your original and updated search. a. Before importing your new search, right-click on My Groups and Create Group. Label the group after the date of your original search, the database used, or whatever label best suits you. Select all of the citations in your EndNote library and drag them into this group. b. Import your new search as you did before (see Step 3 above), making sure to discard all duplicates. c. All of the Unfiled references are the unique additions from your update. Select just these Unfiled references and export to Excel as you did before (see Step 5, above). Using Endnote to Organize Literature Searches Page 6 of 6