Hardcore PubMeding (advanced PubMed searching)

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Revision as of 11:13, 2 June 2007 by Jakob Suckale (talk | contribs) (small corrections)
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PubMed [1] at http://www.pubmed.org is maybe the best search machine for articles in biology. It is run by the NCBI [2], USA, and gives you the possibility to search a gigantic archive of life science literature.

But searching is not easy. Type almost any single term and you will get thousands of hits which you will never be able to browse let alone read. So, to find your preferred needle in the haystack you will need to learn how wring the best out of PubMed.

Below you find some tips how to become a hardcore PubMeder. Please add your own tricks if you miss them on this page.

MeSH - standardised keywords

The NCBI provides you with standardised search vocabulary. This is advantageous because the right MeSH term (medical subject heading) will find all articles using various synonyms of the term. For example, a brute text search for translation will not return publications using the synonym protein synthesis. The PubMed team annotates all incoming articles with their standardised and hierarchical search terms. You can find out about them by searching the MeSH database [3]. After you have found appropriate terms use them for searching. Type, for example:

protein biosynthesis[mh] stem cells[mh] This returns all publications that have protein biosynthesis (translation) AND stem cells as MeSH terms. PubMed automatically assumes AND as boolean. You can specify OR if required, but connectors have to be capitalised otherwise they are not recognised!
protein biosynthesis[mj] stem cells[mj] Replace the tag [mh] with [mj] to get back only publications that have the term in question as a major (mj) topic. This will significantly reduce the search hits.
  • Note that it is not advisable to put quotes around the search term, like this "stem cells"[mh], since it interferes with the word stemming functions of PubMed. Word stemming is the automatic forwarding of related terms to the main MeSH entry. For example the singular stem cell and the synonym progenitor cell(s) are automatically redirected to the main entry stem cells.
  • Also note that short and long tag names lead to the same results. Instead of [mh] and [mj] you can expand to [MeSH] and [majr] or even [MeSH Terms] and [MeSH Major Topic].
  • Capitalisation is not important for either the search tags or the search terms. stem cells[mh] and Stem Cells[MH] return the same hits.

Besides [mh] and [mj] here are some common PubMed search fields:

[au] author name; e.g. "smith g"[au]
[ti] article title; e.g. stem cells[ti] - note that even without quotes stem cells is considered a phrase
[ta] journal title; e.g. nature[ta]; who know why this field name was chosen
[dp] date of publication; e.g. 2006[dp] or 2006/01[dp] for January 2006; format is YYYY/MM/DD[dp]; month and day are optional

can also be used in different ways: e.g. "last 10 days"[dp] or "last 2 months"[dp] (quotes are required)
or 1998:1999[dp] for all publications in these two years

See this PubMed help page for a complete list.

My NCBI - personalising PubMed

PubMed offers you the possibility to save your searches for reuse and automatic email alerts. You need to register for this option. My NCBI also allows you to set up filters, define document delivery options, and set user preferences. You will find the link on the left of PubMed main search page [4]

Related Articles function

PubMed includes a very useful function to suggest related articles to the one(s) you just retrieved by a search. The feature relates articles by comparing their words [5]. You will find them on the right of the abstract page. Often this will help you to find article not spotted by your search but of interest to you.

Further reading