Why search in PubMed?
How to search in PubMed?
You can search in PubMed with free text (see Automatic Term Mapping and Searching via Tags). You can also search using MeSH terms, the thesaurus keywords (see Searching via MeSH terms). However, a good search action requires a combination of the two (see Searching via free text and MeSH terms).
In PubMed the following Boolean operators can be used to set up your search query:
- AND: all terms should appear. In a standard search query AND is automatically placed between search terms.
- OR: one of the terms should appear.
- NOT: this term should not appear.
Use double quotation marks in PubMed to search for an exact word or word combination, e.g. “cardiovascular disease”. The use of round brackets changes the order in which the AND, OR and NOT combinations are carried out. The latter is also called ‘nesting’.
When entering a search term – without tags and quotation marks – both free text and MeSH terms, keywords from the controlled thesaurus, are automatically searched on.
Via Details – which you can view from the Advanced Search – you can see how PubMed translates your search term(s) via Automatic Term Mapping using operators and tags.
With tags, you yourself indicate the fields in which your search term should appear. The tags or field codes are placed between square brackets and follow the search term, e.g. hypotension[All fields]. The tag [All fields] is automatically added (e.g. via Automatic Term Mapping). Be aware that in relation to this tag, the search term may also appear in the author name or affiliation (but never in the full text). However, if you use the tag [TIAB], you limit the search results to those in which the search terms only appear in Title, Abstract and/or Author Keywords.
An overview of the tags or field codes in PubMed is available here.
In MEDLINE keywords, the so-called MeSH or Medical Subject Headings, are assigned per article.
MeSH terms are searchable via the MeSH-database.
You will find a number of building blocks for your search query on the detail page of a MeSH term:
- Subheading: index term that explains an aspect of a MeSH term.
- Major Topic: MeSH term indexed as main subject.
- Location of the term in the tree structure, with indication of MeSH terms higher and lower in the hierarchy. In a standard search query all underlying terms are included, but here you have the choice to switch off this option if it would be relevant.
TIP: Key articles can provide MeSH terms that are useful for further search queries.
The advantage of searching on MeSH terms has the advantage that the article deals with the subject (regardless of how the author described the subject). Moreover, it also leads you to articles without an abstract. It is recommended to combine this search action with free text, so that articles that have not (yet) been assigned keywords appear in your search query. It may be useful to add the tag [TIAB] to your search term(s) for that second search action, so that the search terms only appear in fields relevant to the content i.e. Title, Abstract and/or Author Keywords.
You can develop a search strategy using the Advanced Search Builder.
Via the Add terms to the query box option, you can add tags of field codes to your search term(s).
In the Query box you can build your search strategy based on different search terms and Boolean operators.
The previously entered search terms are saved under History. You can combine terms from History with (a) new search term(s).
Search results can be refined by filtering in the left column on: Text Availability, Article Attribute, Article Type, Publication Date and Journal Category.
Additional filters or options of a standard filter can be added via ‘Additional Filters’. After adding, you still need to activate the filter via the check box in front of the filter.
Tip: after logging in via MyNCBI, you can see and adjust your personal filters at the top of the left column. For example, you can add a frequently used search block (that applies to your research domain), so you can always activate it while searching in PubMed.
- Use a Truncation operator i.e. asterisk (*) to allow variability for several characters in your search query. You can use this operatore to substitute 0 or more characters and you can use it in one word or multiple words. For example: the search query “vaccin* schedul*” will find terms such as “vaccine schedule”, “vaccine scheduling”, “vaccination schedules”, etc. You can also use the truncation operator multiple times in a word, e.g. organi*ation* for organisation and organizations. Note that you must use at least 4 characters before you can add the truncation operator, e.g. colo* will be applied correctly, but col* will not.
- Use the proximity operator “search term”[field:~N] to indicate that your search terms have to occur at a certain distance (cf. number n) in title and/or abstract. Indicate the maximum number of words. The words will be searched in any order.
- Please note: the proximity operator cannot be used in combination with truncation (the asterix *). It can be used in combination with a boolean operator
- Example 1: searching “test bias”[title/abstract:~4] will show results for ‘test bias’ and for ‘test for publication bias’.
- Example 2: “standard care”[tiab:~2] AND “hip pain”[tiab:~2] will show results where ‘standard care’ as well as ‘standard of care’ will occur in one article with ‘hip pain’ or ‘pain in hip’
- In PubMed you can easily consult related articles via Similar Article, on the right side of a detail page of a record.
- And it is also definitely worth searching in Embase, the European equivalent of PubMed. Both PubMed and Embase have a number of unique references on most subjects, since you search the MEDLINE database through both of them. For more information, click here.
- When you search via an author name, enter the surname first and then one or more initials.
- If you are searching for an article and you know the title, copy and paste it into the Single Citation Matcher on the PubMed homepage.
With PubCrawler and MyNCBI you can stay up to date with new articles on your subject. You will need to create an account for both services, but its use is free. It works best if you formulate a specific search query, so that you are not overloaded. The results can be seen on the websites, but can also be sent to your email address. It is easy to create Alerts via MyNCBI while searching in PubMed. In PubCrawler you can also receive updates of articles related to one specific article.
Link with EndNote
If you want to import one or more references to your personal EndNote library, select them in the list of search results.
Then select Send to > Citation manager.
An nbib file is created which you can open when your EndNote is opened. Articles are then automatically imported into your EndNote library.
Tip: when using EndNote via Athena, you also need to have PubMed opened via a browser on Athena to enable direct import.
The maximum number of references you can import to you EndNote library in one step is 10000.
Subsequently click on the Import File button in EndNote. Select the txt file and choose PubMed (NLM) as Import Option.
Additional information/courses organised by the KCGG
Watch the tutorial or contact the KCGG if you have any questions about PubMed.
You will find a list of the planned PubMed courses here. If there is no course in the near future or you are interested in a customised course, please contact the KCGG.