Cochrane training: 2 Identifying search terms. Julie Glanville Associate Director, YHEC May 2016

Transcription

1 Cochrane training: 2 Identifying search terms Julie Glanville Associate Director, YHEC May 2016

2 Today s Agenda How do we typically identify search terms discussion How might word frequency analysis tools help us? Can MeSH finders help us? How can we identify phrases? How can we identify word adjacency? Questions and discussion

3 How do we typically identify search terms Our review team approaches us with a new SR topic How do we currently identify the search terms we will use? What are the strengths and weaknesses of these approaches? Group discussion

4 How might word frequency analysis tools help us?

5 Simple text analysis tools Word frequency analysis of database records PubMed PubReMiner GoPubMed EndNote Voyant

6 PubMed PubReMiner Prepare your choices before running the search Choose which fields to search (Fieldtype option) e.g. title only or title/abstract Choose dates (FromDate and ToDate) Choose which columns to display (options on far right) Choose abstract limit (top) number of abstracts On completion of the search you can then modify it by incorporating more terms Choose which columns to display (right) Choose default operator (middle) Choose whether to merge similar words (middle) Choose minimal count (e.g. words must appear at least x times) (middle)

7 PubMed PubReMiner Results are shown in columns Numart= number of records in which word has occurred Count = number of times a word has occurred in all records * Indicates words with this stem (i.e. truncation) Outputs: can save results to a text file Can choose which columns to export Run search in PubMed Click on Goto PubMed with Query (button at top of screen)

8 GoPubMed Similar approach to PubReMiner but with some key differences No analysis of title/abstract words Example topic: fdg-pet AND "colon cancer After search click on Statistics This shows the frequency of various things such as authors, journals and MeSH

9 GoPubMed,2 Facilities to analyse MeSH are really nice Click on a term and it shows lots of useful information

10 What about databases other than MEDLINE? Many of the free interfaces interact directly with PubMed What can we do if we want to analyse subject indexing, say, for Embase or PsycINFO? We can do word frequency analysis using EndNote Voyant Other statistical software

11 EndNote, 1 EndNote offers simple frequency analysis: You can see which terms might be useful for strategy development All records are indexed as they are loaded into EndNote: The Keywords field is indexed automatically to create a Term List Term Lists can be used to create an index Additional Term Lists can be defined and populated e.g. title, title/abstract Ideal for analysing Embase records Frequency of terms in the title, title/abstract, EMTREE

12 EndNote, 2 Before loading records into EndNote decide how to treat the information coming in to Keywords field: You can break up subject index terms by changing the term delimiters: E.g. Pseudomonas infection/dt [Drug Therapy] can be parsed differently: Separate words - Pseudomonas Infection dt drug therapy Two phrases - Pseudomonas Infection dt [drug therapy] If you want to do frequency analysis of other fields or combinations of fields you can do this once the records are loaded

13 EndNote, 3 Keywords field To set the term delimiters you can use the following sequence (EndNote X7.5) in a new empty EndNote library: Tools, Define term lists, Keywords (Change) Delimiters select the / symbol to cut the subheading from the EMTREE heading Update list OK Load your file of Embase records

14 EndNote, 4 Create the frequency analysis of the EMTREE terms : Tools, Subject bibliography Keywords, OK Select all, OK Choose display format by selecting Layout Terms, Subject terms only Change number of lines between entries e.g. remove suffix ^p^p Change display order to frequency by selecting By term count descending Select OK To print listing, select Print To save the listing select Save

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16 EndNote, 5 Create the frequency analysis of the Title and Abstract terms combined: Tools, Subject bibliography Select Title and also Abstract fields from the list (using control key to select multiple fields) At the bottom of the screen Deselect List each author separately Click on the delimiter option entitled In other fields Click OK The term list will display

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18 Endnote, 6 To save or print out the title and abstract frequency analysis Select all, OK Choose display format by selecting Layout Terms, Subject terms only Change number of lines between entries e.g. remove suffix ^p^p Change display order to frequency by selecting By term count decending Select OK To print listing, select Print To save the listing select Save

19 Endnote, 7: Title and abstract frequency count

20 EndNote: pros and cons Pros Easy and quick to create frequency counts Built into a package you might be using to manage your search results Cons Not very visual Cannot do phrase analysis of title and abstract Cannot do more sophisticated analyses such as word collocation Cannot implement stopwords

21 Using other packages for word frequency Many packages need the records in plain text format It is also best to select only the fields you want to analyse so that The files process more quickly The output is not cluttered with unwanted words e.g. from the address fields To get clean data Either download just the selected fields from your database of choice (e.g. in OvidSP select text file output and then selected fields e.g. sh Or, download records to EndNote and export only fields of interest from EndNote into a file Then depending on what you want to analyse you have files of subject headings title/abstract title/abstract + subject headings That you can upload into software directly, or cut and paste

22 Voyant Tools Can upload a text file or cut and paste the contents of a text file into Voyant It provides various views on the text Example Subject headings from 499 biofilms AND wounds records

23 Text Analyzer Paste in records e.g. subject headings from batch of records and it will offer an analysis

24 Can MeSH finders help us?

25 MeSH on Demand Paste in text e.g. from protocol or a batch of relevant records The software identifies MeSH Terms in the text Returns a list of MeSH Terms relevant to the text Note: check which version of MeSH it is using may not always be the most current Note: has a size limit (10,000 characters) Example: Comparison of self-administered survey questionnaire responses collected using mobile apps versus other methods (Cochrane protocol)

26 MeSH on Demand, 2 Example results: Cochrane protocol

27 Go PubMed Select Bioinformatics tools (book icon) Paste in example text, e.g. protocol It produces a concept cloud MeSH terms [M] Other concepts [G] e.g. biosynthetic process in this example Bioinformatics tools

28 Word cloud analysis of the protocol text; showing MeSH terms that relate to the concepts in the text [M]

29 Yale Add in a string of PMIDs Identifies MeSH terms Creates a MeSH analysis grid showing which headings have been used Best for using with a batch of known relevant studies

30 How can we identify phrases? Voyant we have seen already Text Analyzer we have seen already VOSviewer TERMINE

31 VOSviewer Can be run online (needs Java) but best to download software VOSviewer creates maps of themes within documents Network visualisation Density visualisation Example: biofilms and wounds search Possible to zoom into areas of interest Scroll over the map and zoom in For phrases click on the Items list

32 TERMINE 2 MB file size Can paste in records, document text e.g. protocol, or parts of records Analysis of EMTREE headings from a batch of 498 Embase records Blue items are phrases any frequency Red items are phrases with frequency of at least 4

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34 TERMINE Table representation of phrases appearing with frequency of 4 or more NOTE: additional pre-processing (tidying) could be undertaken e.g. taking out the * for the focused headings

35 How can we identify word adjacency? Text analyzer words separated by other words Voyant Key word in context Voyant Collocator Listing of collocated terms Diagram of collocated terms corpus=5efc743cc58dd036d0f38c6a35210b85&panel s=cirrus,reader,trends,summary,contexts

36 Voyant: collocates Biofouling collocated with a range of terms

37 Voyant: links Shows the words which are closely linked with biofouling

38 Voyant: KWIC

39 Questions/Discussion

40 Homework Use your most current review question to test out exploratory searches in these resources Compare and contrast PubReminer and GoPubMed Compare and contrast Termine and TextAnalyser Compare and contrast MeSHOnDemand and GoPubMed for MeSH identification Prepare a table with key strengths and weaknesses of each resource Which do you prefer? Which might you use?

41 Thank You Telephone: Website: Providing Consultancy & Research in Health Economics