Searching PubMed

Research methodology - Course files - Internet and PubMed/Medline - GQuery - PubMed - MEDLINE

Searching PubMed

http://www.ncbi.nlm.nih.gov/pubmed/

Identify the key concepts (terms) for your search (e.g., anemia pregnancy).
- Alternative terms, check MeSH terms (e.g., contraception - contraceptives; contraception, postcoital - contraceptives, postcoital).
Enter the terms in the search box
- Language: American English or British English (e.g., anemia or anaemia). Searches will retrieve the same citations regardless of whether the American or British spelling is used for MeSH or entry terms.
- Stopwords are not indexed and PubMed will ignore them. NB: AND, OR, NOT are recognized as Boolean operators (see below).
- Searching for a phrase: enclose the phrase in double quotes (e.g., "making pregnancy safer"). Many phrases are recognized as a MeSH concept, e.g., fever of unknown origin (details: "fever of unknown origin"[MeSH Terms] OR ("fever"[All Fields] AND "unknown"[All Fields] AND "origin"[All Fields]) OR "fever of unknown origin"[All Fields]); enclosing the phrase in double quotes ("fever of unknown origin") will give a different result (details: "fever of unknown origin"[All Fields]).
- Truncation: to find all terms that begin with a given text string, enter the truncated term/word followed by an asterisk (*), e.g. flavor*.
Boolean operators
- AND, OR, NOT. In PubMed, Boolean operators must be entered in uppercase letters.
- The default Boolean operator between two terms is AND (anemia pregnancy = anemia AND pregnancy).
- If search terms are recognized as MeSH terms (e.g., hemolytic anemia), adding AND between these terms will produce a different result: hemolytic anemia ("haemolytic anaemia"[All Fields] OR "anemia, hemolytic"[MeSH Terms] OR ("anemia"[All Fields] AND "hemolytic"[All Fields]) OR "hemolytic anemia"[All Fields] OR ("hemolytic"[All Fields] AND "anemia"[All Fields]) ≠ hemolytic AND anemia (hemolytic[All Fields] AND ("anaemia"[All Fields] OR "anemia"[MeSH Terms] OR "anemia"[All Fields]).
- Use parentheses to "nest" concepts: e.g., common cold AND (vitamin c OR zinc).
Search results
- Automatic term mapping
  - When you click Search, PubMed will look for a match in several lists: MeSH terms, journal titles, author names, all fields...
  - Search field descriptions and tags
- To see how PubMed interpreted your search, look at Search details (image).
- Search results are displayed by default in a summary format: author, title, and source information. Documents can be viewed in different formats (summary-text, abstract, MEDLINE, etc.). If you are not using a reference manager, summary (text) display is very useful for citation of the article according to the NLM style: simply copy and paste the reference, e.g., Myers L. Postpartum plasma exchange in a woman with suspected thrombotic thrombocytopenic purpura (TTP) vs. hemolysis, elevated liver enzymes, and low platelet syndrome (HELLP): a case study. Nephrol Nurs J. 2010 Jul-Aug;37(4):399-402.
- Click the title of the article to see the abstract (“no abstract available” is indicated on citation’s without an abstract). The abstract display may provide links to electronic copies of the journal article.
- Sort results by author, journal, article title, or publication date.
- Send to clipboard: click on Send to, then select clipboard from the Choose destination menu and click Add to clipboard.
Filters
- Article types: e.g., search for anemia pregnancy clinical trials.
- Text availability: e.g., search for anemia pregnancy free full-text articles.
- Publication dates.
- Species.
- Languages: e.g., search for anemia pregnancy articles in English language.
- Sex.
- Subjects.
- Journal categories.
- Ages.
- Search fields.
Features
- Previewing the number of search results
- Clipboard
  - Saving items in the clipboard
    - Select the citations you want to save, or select none to save all of the items in your clipboard.
    - Select file from the Send to menu, choose Format and Sort by, click Create file.
    - Change the name of the file to something more meaningful.
    - Use an appropriate file extension (e.g., doc).
    - Save the file to a location on your computer.
  - Removing items from the clipboard
    - Check the citations you want to delete, click "Remove selected items".
- Details (image)
  - Query translation box: actual search strategy and syntax used to run the search.
  - URL: if you want to save the current strategy for later use, click on the URL button, then use your Web browser's bookmark or favorites feature to save this URL.
  - Translation: shows how each term was translated.
  - User query: shows the search as you entered it in the query box.
More resources
- Journals database
  - Search by topic, journal title or abbreviation, ISSN, or browse by subject terms (e.g., Obstetrics[st]).
- MeSH database: allows to
  - Locate and select MeSH terms (headings, subheadings, publication types); supplementary concept terms (substance names) and pharmacological action terms.
  - See the definition and other helpful information for a MeSH term (e.g., Anemia, Diamond-Blackfan).
  - Build a PubMed search strategy: e,g, "Urinary Tract Infections/therapy"[Mesh] AND "Pregnancy"[Mesh].
  - Display MeSH terms in the hierarchy: e.g., Pregnancy.
  - Limit MeSH terms to a major concept for a search (major topic heading): e.g., "Pre-Eclampsia"[Majr].
  - Attach subheadings for a search: e.g., "Contraceptives, Oral, Combined/contraindications"[Mesh].
  - See also Use MeSH to Build a Better PubMed Query.
- Single citation matcher: enter the bibliographic information you have, click Go (e.g., Ndowa F[author]).
- Special queries
  - Clinical queries
    - Clinical study category: e.g., ovarian cancer therapy.
    - Systematic reviews: e.g., malaria in pregnancy.
    - Medical genetics searches: e.g., Huntington disease genetic counseling.
  - Cancer
  - Research reporting guidelines and initiatives
  - TOXNET
Advanced search
- Advanced search builder.
- Combine searches using PubMed search history.
My NCBI
- To use My NCBI you need to register and sign in when you want to use My NCBI features.
- My NCBI saves searches and results and features an option to automatically update and e-mail search results from your saved searches. My NCBI includes additional features for highlighting search terms, storing an e-mail address, filtering search results and setting LinkOut, document delivery service and outside tool preferences.
Reference manager: Zotero, a free Firefox extension, allows to capture, import and archive citations directly from PubMed. Several different citation styles are available. Microsoft Word and OpenOffice plugins allow to add in-text citations and footnotes in addition to bibliographies.

Sources