Connecting clinical trials to research articles

We can search PubMed database by specifying clinical trial id(s) and retrieve all the relevant journal articles. The NLM (The world’s largest medical library, the U.S. National Library of Medicine is part of the National Institutes of Health) extract those trail IDs and placed them into PubMed secondary id field.

How to  query single trial id??

Example: To search for journal articles related to a clinical trial id say NCT00000419, use PubMed’s application protocol interface (API) called e-Utils, which can be accessed through URL

Now, specify clinical trial id in the eutils api as shown below:[si]

All the journal articles related to the clinical trial id will be displayed as shown below:

In the above url, query string [SI] refers to Secondary ID which can be used to search for articles. This field contains accession numbers of various databases (molecular sequence data, gene expression or chemical compounds etc.)

How to  query multiple trial id’s ?

Here,we have taken a large number of clinical trial numbers in one file and the results were taken into another file which contains pubmed articles of respective trials.

Input file contains multiple NCT numbers which can be used as a query in PubMed API(e-utility) search field. Sample input file looks as below:

Below Perl language script will search for each clinical trial id specified in the input file against PubMed database using PubMed(API) E-Utils.

Output file: Output file contains PMIDs (pubmed records) of respective clinical trials.

In this way, we can retrieve journal articles related to any clinical trial(s) by using PubMed(API) E-Utils.  

All the files (input, script and results) we have used in the above example are available on GitHub and can be downloadable from

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