PubMed molecular bioscience search notes

• See PubMed's own tutorial for step-by-step search instructions. The following notes highlight a few features and use molecular bioscience examples.
• Link to PubMed through the University of Adelaide customised interface link http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=iauualib or through the library catalogue, or the Molecular biosciences databases page. The interface has a convenient Uni of Adelaide online journals link.
• PubMed includes articles indexed for Medline as well as more recent in process and publisher-supplied articles awaiting indexing.

Topic search

1. Click Details after you have run a search to see how PubMed has treated your terms.

2. Combine terms with Boolean operators AND, OR, NOT and use brackets to group ORed terms.
   AND, OR, NOT must be in upper case.

3. Search both MeSH terms and your own text words.

4. MeSH
   PubMed assigns standard subject terms (MeSH or Medical subject headings) to most articles. Look in the MeSH database for possible MeSH terms. MeSH have advantages. For example, if you search the MeSH vertebrates, you can:
   • explode vertebrates and automatically search for narrower terms, the organism groups listed under vertebrates in the MeSH database
   • choose subheadings such as immunology or genetics to search only those aspects
   • restrict search to major topic headings, so that vertebrates is searched as the main point of an article.
   Note:
   • PubMed will automatically explode a MeSH such as vertebrates. It will also search vertebrates as a text word in titles, abstracts, etc as long as you don't search it as vertebrates[mh].
   • Ideally, you want to search variations as well e.g. vertebrate, vertebrata by truncating (e.g. vertebrat*). However, truncation prevents MeSH explosions. To overcome this, enter it as, for example, vertebrates OR vertebrat*.
   • Don't put quotes around a MeSH. Quotes also prevent MeSH explosions.

5. Text words
   Many molecular bioscience topics don't have appropriate MeSH, so use your own search terms as well. They will be searched in ti, abstract and other text word fields.
   • Try a range of synonyms. Gather extra terms from abstracts and titles.
   • Truncate with an asterisk *
   • If necessary, you can restrict searches to fields using [ti], [tiab] etc
   • Quotes " " can be used for phrases e.g. "oxygen sensing"
     Truncated phrases e.g. oxygen sens* don't need quotes.
     PubMed may search less common phrases as ANDed terms rather than phrases.
   • Try acronyms, with all forms of likely punctuation, Roman or Arabic numerals, English names for Greek letters. Acronyms may have more than one meaning.

6. If necessary, broaden your search with alternative search terms or refine it with limits.
   • Get suggestions for extra terms from titles, abstracts and MeSH of useful articles. Use History to see search statement numbers and recombine them e.g. #1 AND #7.
   • Limit to review articles through Limits then Publication types.
   • Limit to English through Limits then Languages.

Journal title search

• Distinctively named journals e.g. j biol chem can be entered directly, as Medline abbreviations or as full titles. PubMed will recognise them as journals.
• Journals with less distinctive names should be entered with the title abbreviation [ta] field name as a qualifier e.g. Cell[ta] or through the Journals Database. Otherwise, PubMed will search them as topics.
• To verify a citation, use the Single citation matcher.

Author search

• Author names with one or two initials can be entered directly, since PubMed recognises them as authors e.g. o'brien j, o'brien jj.
• Qualify with [au] author names without initials e.g. o'brien[au]
• To get only a single initial, search in quotes and qualify with [au] e.g. "o'brien j"[au]

Linking to data from sequence databases etc

• Link from a PubMed article to its relevant entries in sequence databases etc via Links next to each reference. Where data are available, the Links menu will show Protein, Nucleotide etc.
• Display database links for all articles through Display.

Getting the full text of journals

• At the abstract display of an article citation, click Uni of Adelaide Online button to link to the electronic full text.
• If PubMed does not have a full text link, check the Library catalogue since the Library may still have access to the journal electronically or in print.

Saving results

• Change Display to Medline format if importing to EndNote.
• Use Send to File.
• In EndNote, use the PubMed(NLM)filter.

Saving a strategy and creating an email alert

• Click Save search
• Sign in (or register a new account).
• Enter the requested details.
• To edit or remove the saved search, click My NCBI at the top of the screen.