PubMed Guide. A. Searching

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1 TSRI, 400-S PubMed Guide A. Searching 1. Keyword searching: What is really going on when you search for a term like stem cells? can use Boolean (AND, OR, NOT) type in: shingles AND stem cells 2. Term Mapping: automatically checks MeSH Terms and phrases index Scroll down the results page to see Search details box on right to see what PubMed is really searching Click on See more to go to the Search Details screen Created by amurrell Last updated August 2, 2013

2 Phrase searching with quotation marks bypasses Term Mapping (also truncation will bypass Term Mapping). stem cells AND neuron* 3. Using Advanced Search Search Builder: To change the field to search in, click on the All Fields pull down and choose the field you wish to search. Combine terms using AND OR or Not from the pull down box. To add another term, click the plus sign to the right of the last row

3 Show index list: Use the Show index list link to see what terms are indexed in each field. Choose a field ( MeSH Terms is a good one to explore). Type in a word (or the beginning of a word). Click the Show index list link. The index is displayed 200 items at a time. Scroll down to see 200 entries. Click the Previous 200 link to go backward in the index, and Next 200 to go forward 200 terms in the index. Tips MeSH In the MeSH Terms field, the main term is followed by all applicable subheadings using the / and the subheading. E.g., protein c/analysis (975) Symbols (such as /) and even a space, come first, then numbers, then letters. E.g., if you are looking for protein c deficiency you need to scroll past all the subheadings (since they use / ) in MeSH Terms field, and past the symbols and numbers. Title For the Title field, words and some phrases are indexed, but not full titles. This field does NOT use the automatic MeSH Term Mapping. Author Author names are indexed and possible names will appear as you time. Full names are indexed when available, from

4 4. Combining searches/ Using History The history displays at the bottom of the Advanced Search page. To add to the Builder with AND, simply click the Add next to the search. If you wish to use another Boolean term (OR, NOT) or to Delete, Show or Save, click on the number, and select form the pop up box. Click Search or Add to History at the top. 5. Searching with field codes Can search specific fields (author [au], title [ti], abstract [ab], [MeSH Terms], etc.) Turns off automatic term mapping. Can combine field codes and keyword searching Type in the search box: stem cells [tiab] AND neurology - 4 -

5 6. Using the MeSH database to locate MeSH Terms MeSH (Medical Subject Heading) is controlled vocabulary terms selected by indexers to represent a topic Can search the MeSH database to find the best terms for your topic The record provides: o the definition of term, o subheadings used with that term, o entry terms (if used in PubMed will automatically include the MeSH Term), o previous indexing terms, o and the tree structure for term (where it falls in categories and in relation to other Terms). To use the term in a PubMed search, click Add to search builder Or modify the term by selecting subheadings (optional) And choose whether you wish Major Topics only, or whether or not to include terms that fall under the Term in the MeSH tree (also called Explode) - 5 -

6 Entry terms are the trigger terms that will cause the automatic term mapping to return a MeSH Term. So if a user typers in cancer or tumors PubMed will return Neoplasms [MeSH]. See also references are related terms or terms used previously to describe this topic. Sometimes they will have dates. It s a good idea to compare dates and check if you need to run searches using the see also terms to get a comprehensive search. Finally the position the term holds in the MeSH tree is given, beginning at All MeSH Categories. Often a term appears under several branches, so you may see several hierarchies displayed. 7. Subheadings Used to further refine a MeSH term. When selecting multiple subheadings combine them with OR. There are currently x of subheadings an indexer can use to refine the topic of a paper. When a MeSH record is displayed, only the subheadings which have at least one paper indexed by that termand subheading combination (i.e., Neoplasms/blood) will be displayed

7 8. Setting Filters (the old Limits) You can refine your search by selecting Filters. The default Filters display on the left.. Filters are not active to begin. To activate a Filter, just click on it. The Filter is now blue and has a check by it. Filters remain active unless you click clear near the Filter type, or click Clear all at the top or bottom. There are several ways to see more Filters, the key is that you need to select them to display in the main window and then select them AGAIN to be active

8 Still need to click Clinical Trial to make it active There are also additional categories of Filters available. Click on Show additional filters - 8 -

9 9. Related Citations/Data This feature allows you to see citations to articles that are related to the chosen article. PubMed uses a formula based on cited references and words in the title to select related citations. A Related citations link appears below the citation in the default (Summary) display format. Or a list of related citations appears to the right in the Abstract display format. Hint: You can get to other NCBI databases from here

10 B. Finding full text [SFX button] When you find a citation to an article you want to get, click down to the individual record level. You should see the button to the right of the citation NOTE: The Publisher s button does not mean it is FREE or that we have access, just that the publisher has full text, but may require a fee or a password. Click on the SFX@TSRI button. This will open a new window with a menu of choices First the title and source (citation) are given Then, if full text is available there will be a link And if not in print in the catalog you can order from ILLiad We also have a link to see who cited it in Web of Science

11 C. RSS feeds After performing a search or displaying results from a prior search, click on the RSS feed from beside the search box. Select number of items (up to 100) to display. Type in a feed name. Click Create RSS Either click on the xml button that appears, and this will launch your reader, Or right click on the XML button and select Copy Link Location. NOTE: See the blog or RSS reader for further assistance

12 D. Downloading to EndNote or Reference Manager First open the EndNote library. Go to PubMed and perform your search. Next, Mark the citation(s) you wish to save to EndNote. Click on the arrow next to the Send to: link. Select Citation Manager (option only allows up to 200 at a time) If you select File then select MEDLINE for Format. Click Create File. For Firefox users: Firefox has an add-on that will prompt you to Open with choose the EndNote program. Then select PubMed from the list that opens. For IE users: A File Download window may appear (if it does not recognize the nbib format). Click Save. Select a location (recommend the desktop). In the File name box type the name of the file (or use the default citations.nbib ). Click Save

13 If you had to save the file, use the Manual Import procedure: In EndNote: Open the EndNote library you wish to add the records to. Select File >Import. Locate the file. PC: click Choose file select the file in the box that opens. click Open. MAC: find the file in the Finder window. Next select the PubMed (NLM) filter from the pull down list of Import Options. If the filter has not already been used it will not show in the list. Select Other filters to search for PubMed (NLM) Choose to delete duplicate records from Duplicates pull down list. Click Import. EndNote PC EndNote MAC Change to Pubmed.enf In Reference Manager, use the Manual Import procedure: Select the Database (Library) to import into. Select the PubMed.cap filter using the button, choose the filter from the window that opens Find the file using the next... button after Text file: Click Import An EndNote window or Reference Manager tab with just the imported records should appear

14 E. Single Citation Matcher If you know some information about a given article (journal, volume, year, author, title), Single Citation Matcher provides an easy way to find the citation and then use the features of PubMed (like SFX to find full text or to download to EndNote). Select Single Citation Matcher from the center list of PubMed Tools on the initial PubMed screen, Or at the bottom of the Advanced Search screen. You do not need to enter all the information, usually journal, volume, and first page; or journal, year, title words. Too much information can sometimes yield no results. As you enter the journal name, a list of options will appear (do not use abbreviations). Choose the correct title from the list. NOTE: If the journal has a leading article (The, A, etc.) you must select the title from the list or the journal name will not be found. Finish entering the information. Click Go to Search