Searching The Literature A Concise Manual

Transcription

1 WALAEUS LIIBRARY A Concise Manual

2 Flow diagram PICO Orientate Select components Formulate Search Strategy for each Component Combine Search Strategies Too many references Too few references Limit your search Extra component Majr/Ti(Ab) Filter Subheadings More synonyms Less components Other databases Embase Web Of Science PsycINFO CINAHL 2

3 Manual This document is a concise manual on searching the literature systematically. Some knowledge on and experience with searching is presumed. If you never searched PubMed before, you are advised to do the self study assignment for PubMed. This is available via the webpage of the Walaeus Library > Workshops en E-learningmodules. Manuals are available from Walaeus Library > Handleidingen. Tip : Open a Word document to keep a log of your search activities! 1. Formulate a search question. PICO: Component Patient/Population/Problem Terms Intervention Comparison/Control Outcome 3

4 or a Tripartite Question: Component Terms What is the... Of... In Orientation: Information Sources: Books, Dissertations: use the Catalog on the Walaeus Website Internet: Google (Scholar), Wikipedia, governmental sites, institutional sites etc. PointOfCare-tools: UpToDate (see database list on the Walaeus Website) Meta-search engines: TRIP, SumSearch (internet, database list on the Walaeus Website) Write down any source you used: title, year, page(s), Author(s), URL, date of retrieval in case of a website, etc.. In Citing Medicine 1 information on how to cite a particular source is presented. You can also use a reference management program like Reference Manager or EndNote to log all of your sources. Copy/paste synonyms which may be suitable search terms to your Word document Adapt your search question if necessary! 3. Pearl growing method / snowball method: Use the cited references from the internet sources and articles you already found Trace the original articles! Keep track of all references you use, either in your Word document or in a reference management database 4. Searching PubMed: a. Building a search strategy: Start PubMed via the Walaeus Website; this version is enriched with SFX links to get access to the full text collection if available Select the main components from your PICO to start your search with 4

5 Format search strategy for component x: "MeSH-term component x"[mesh] OR "synonym 1 component x"[all Fields] OR "synonym 2 component x"[all Fields] OR...OR "synonym n component x"[all Fields] Construct a search strategy for each component separately: 1. Use the MeSH database to find relevant MeSH-term(s) Tip: Check the list of MeSH terms added to relevant references on your subject (keyarticles) to find appropriate MeSH-terms for this particular subject. 2. Add free text search terms; terms you would expect to find in the titles and abstracts of the references you are looking for 3. Always add field codes to search terms: [MeSH] for Mesh-terms, [All Fields], [tw], [tiab] or [ti] for free text terms. Tip: the field code [tw] (text word) also searches the Author Keywords, i.e. the keywords the author added to the article. For an explanation about field codes click 4. Use the Boolean operator OR to combine synonyms 5. Copy the search strategy to your Word document 6. Test each search strategy separately (check for spelling mistakes, brackets, Boolean operator; do you get the number of references you would expect?) Combine the search strategies for the different components with the Boolean operator AND Note: put brackets around the separate search strategies Format combined search strategy: (Search strategy component 1) AND (Search strategy component 2) AND...AND (Search strategy component n) Check the retrieved references for relevancy. If the results are not relevant, try searching with a different combination of components or try the next steps to make the results more specific. b. Limiting the number of references You may limit the number of references by making your search more specific. Four methods will be described. You may use them separately or in combination. 1. Add an extra component 5

6 You can add an extra component from your PICO or add an component concerning the type of articles you are looking for (e.g RCT's) Build a search strategy for this new component, using both MeSH and free text Test it in PubMed Add the component to the combined search strategy; don't forget the brackets and use the operator AND Try the new search strategy and evaluate results. 2. Emphasize one or more components You can emphasize a component by using Major MeSH-terms. A reference in PubMed is tagged with about 15 MeSH-terms, of which about four are indicated as Major. Major MeSH-terms concern the main topics of the article. Instead of [Mesh] the field code [Majr] is being used. The field codes of the free-text terms have to be changed as well to either [Tiab] or [Ti]. Otherwise PubMed will still search the 'plain' MeSH terms for matching [All fields] or [tw]-free text terms and PubMed will try to map [All fields]-terms to plain MeSH terms *. * Entering your search terms between double quotes prevents PubMed from mapping to a Mesh. Check the Search Details to see how the query was translated. Replacing the field codes is easily done in your Word document: Copy the search strategy you want to adapt. Select the copy text by highlighting. Use the function Edit>Find and Replace (CTRL H) to change all of the [MeSH]- field codes into [Majr]-Field codes and all of the [All Field] or [tw]-field codes into [Tiab] of [Ti]-field codes. Try the new search strategy and evaluate results. 3. Use a filter PubMed offers ready made filters, the Clinical Queries. This option is presented on the opening page of PubMed. Clinical Queries are suitable for a limited search only (e.g. for a CAT). If you want to limit an extensive search for a Systematic Review or a Metaanalysis you should use more sensitive filters. The information specialists of the Walaeus Library may advise you on this topic. Additional Filters are presented on the left bar in the PubMed results window. As they are implemented by MeSH-terms only, the effect of using the Limits will often be the loss of all references that hadn't been indexed yet. (This doesn't apply to the Filters on Publication Dates and Languages) 4. Use subheadings Using subheadings is another way to combine components. Depending on the category of MeSH-term there is a selection of subheadings to choose from. Combining Major- MeSH terms with subheadings is also possible. Enter the MeSH-database. Select a MeSH-term Tick one or more subheadings. 6

7 Click Add to Search Builder Copy/paste the search strategy to your Word document and test it in PubMed NB: because you're not searching with free text, only indexed references will be retrieved. You can use this way of searching for an orientation on the subject. Subheadings can be used both to increase and to decrease the number of references. Increase the number of references by combining your MeSH/subheading search strategy with your combined search strategy, using the Boolean operator OR: Combinaton Mesh-term component 1/Subheading component 2[MeSH] OR ((search strategy component 1) AND (search strategy component 2)) Decrease the number of references by adding subheadings to one or more MeSH-terms in the search strategy. The field codes of the free-text terms have to be changed as well to either [Tiab] or [Ti]. Otherwise PubMed will still search the MeSH terms without subheadings for matching [All fields] or [tw]-free text terms and PubMed will try to map [All fields]-terms to MeSH terms without subheadings. Replacing the field codes is easily done in your Word document : Copy and select the search strategy you want to adapt. Use the function Edit>Find and Replace (CTRL H) to change all of the [All Field]-field codes into [Tiab] or [Ti]-field codes. Test the new search strategy and evaluate results. ("Combination MeSH-term component x/subheading component y"[mesh] OR "synonym 1 component x"[tiab] OR "synonym 2 component x"[tiab] OR...OR "synonym n component x"[tiab]) AND ("MeSH-term component y"[mesh] OR "synonym 1 component y"[all Fields] OR "synonym 2 component y"[all Fields] OR...OR "synonym n component y"[all Fields]) c. Check the search strategy with Boolean operators AND and NOT Are key articles present? Use the Boolean operator AND to check whether specific articles are present in your resulting set of references. First you have to identify those specific articles. There are three ways of doing this: 1. Use the Single Citation Matcher (link on the opening page of PubMed) 2. Type the PubMed ID of a specific reference/specific references (PMID) in the search box, separated by spaces 3. Type the title of a specific reference in the search box Combine keyarticle references, if more than one, with OR to create one set Trace the set number of the search you want to check in the Search History Type both set numbers in the search box of PubMed, preceded by a #. Use the operator AND to combine them, e.g. #3 AND #5 7

8 Click Search If all key references are present in the set, the result will be a set with exactly those references. If one or more references lack, check out why by checking their MeshTerms and free text terms. Add these terms to your search strategy, to also include those missing references. Which articles are lost? Narrowing your search will result in the loss of references. To find out which references you lose, you can use the Boolean operator NOT to compare sets. Do not use this operator in your search strategy, since you may lose relevant references. The left circle is set A. The right circle is set B. The coloured surface is A NOT B, i.e. the references that are present in set A but not in set B. Look up the number of the larger set in the Search History.e.g. #3 Trace the set number of the narrowed search, e.g. #7 Type both set numbers in the search bar, combined with NOT, e.g. #3 NOT #7. The new set contains references belonging to set #3, but not to #7 Consider whether the articles in this set would be relevant to your question or whether it is OK to leave them out. d. Increase the number of references: There are several ways to increase the number of references: Regarding key articles: Look up some key articles and use their MeSH-terms and free text terms to expand your search strategy Use the related citations button next to a key article Use the pearl growing method with the bibliography of a key article Perform a Cited Reference Search (Web Of Science only) with the key article. This shows more recent articles citing the key reference. Delete a component from your search strategy Use broader MeSH-terms Search other databases: See the Databanken en Catalogi list on the Walaeus Website 5. Document your search activities 8

9 Keep your search strategies in a Word document Copy/paste the history table to your Word document Save the best search strategy to a "MyNCBI" account and set up an Alert. ( updates at regular intervals) Use a Reference Management program like Reference Manager or EndNote. See the Walaeus Website/cursussen page for more information. 6. References 1. Patrias K. Citing medicine: the NLM style guide for authors, editors, and publishers [Internet]. 2nd ed. Wendling DL, technical editor. Bethesda (MD): National Library of Medicine (US); [updated 2011 Sep 15; cited 2013/28/01]. Available from: Appendix How to turn a PubMed search strategy into an Embase or Web-of-Science search strategy Building a good search strategy for PubMed may be time consuming. However if you subsequently search in Embase and Web Of Science for the same subject, you will save a lot of time. In order to do so, you have to convert your PubMed search strategy. This is easily done by using the Find and Replace function in Word. This appendix shows the main principles of translating a strategy. Consult the Walaeus Library whenever you need assistance. 1. Embase Copy / paste your PubMed search strategy to another part of your Word document Select this copy text by highlighting Select Edit > Find and Replace or use Ctrl- H Replace all of the [MeSH] field tags by a / (forward slash); answer NO to Do you want to replace the text in the whole document! Replace all of the [All Fields] field tags by.mp. (= multiple postings); answer NO to Do you want to replace the text in the whole document! Check for each term with a slash / whether this is also the correct Embase Subject Heading: Enter the term in the Embase search box (without the /) and click Search. If necessary, replace the term in your strategy by the correct Embase Subject Heading. Add exp in front of the term (with interspacing) to explode the Subject Heading To Focus Subject Headings (= make them "Major"), place an asterisk in front of the term, without interspacing. To perform a free text title search, replace.mp. by.ti. To perform a free text title and abstract search, replace.mp. by.ti,ab. N.B.: Concerning key-words: Embase has its own thesaurus. Both the Subject Headings and their hierarchy can be different from the PubMed MeSH-terms. Therefore it is necessary to check each Subject Heading separately in the Embase Thesaurus. By searching the Embase Thesaurus, you may find terms that can be added to your PubMed Search Strategy. Concerning the field codes: There are many more field codes than the ones mentioned, both in PubMed and Embase. If Embase doesn't have an equivalent for a PubMed Field 9

10 Code, a solution may be to choose.mp. in Embase. Information about the field codes in Embase you can find by clicking the tab Search Fields. Concerning quotes: Embase doesn't accept curly or smart quotes. You can select straight quotes in Word through Autocorrect Options. Remove the tick before "Straight quotes with smart quotes" both on the tab "Autoformat as you type" and on the tab "Autoformat". Example Simple search strategy in PubMed to find references on infections: "Infection"[Mesh] OR "infection"[all Fields] OR "infective"[all Fields] OR "infected"[all Fields] OR "infections"[all Fields] Converted to Embase: Exp "Infection"/ OR "infection".mp. OR "infective".mp. OR "infected".mp. OR "infections".mp. This is equal to: Exp "Infection"/ OR ("infection" OR "infective" OR "infected" OR "infections").mp. Emphasize by Focus term and Title search: Exp *"Infection"/ OR "infection".ti. OR "infective".ti. OR "infected".ti. OR "infections".ti. Note: On average you will retrieve more references from Embase than from PubMed with an equal search strategy. This is due to the fact that Embase adds far more keywords to each reference than PubMed. 2. Web of Science Copy / paste your PubMed search strategy to another part of your Word document Select this copy text by highlighting Select Edit > Find and Replace or use Ctrl- H Replace all of the field codes with blank (i.e. nothing); answer NO to Do you want to replace the text in the whole document! Remove redundant and duplicate terms and add terms from the Embase Thesaurus if so desired. For a subject search, put brackets around the whole search strategy. In front of the brackets add, without interspacing: TS= (TS= Topic Search) To perform a title word search, replace TS= by TI=; this may apply to all or one specific component of your search. Note: copy/paste the search strategy to the Advanced Search box of Web of Science. Concerning key-words: Web of Science doesn't use keywords, so you have to make an extensive free-text search strategy. Variants from PubMed and Embase can be useful. Concerning quotes: Web of Science doesn't accept curly or smart quotes. You can select straight quotes in Word through Autocorrect Options. Remove the tick before 10

11 "Straight quotes with smart quotes" both on the tab "Autoformat as you type" and on the tab "Autoformat". Example: Simple search strategy in PubMed to find references on infections: "Infection"[Mesh] OR "infection"[all Fields] OR "infective"[all Fields] OR "infected"[all Fields] OR "infections"[all Fields] Converted to Web of Science: TS=("Infection" OR "infective" OR "infected" OR "infections") Emphasize by performing a Title word search: TI=("Infection" OR "infective" OR "infected" OR "infections") Note: On average Web of Science yields less references on a subject than PubMed. This is partly explained by the absence of keywords and partly by the contents of Web Of Science, being not exclusively devoted to biomedical literature. Use of synonyms and spelliing variants therefore is crucial in Web of Science. 11