Tip #46: Exporting Records from Clinicaltrials.gov into EndNote

Many thanks to Ben Harnke, MLIS from the Strauss Health Sciences Library, University of Colorado (ben.harnke@cuanschutz.edu) for this week's tip!

 

Overview

The following are instructions to export records from clincicaltrials.gov (Trials) to EndNote, with the ultimate goal of sending the records to a screening software, namely Covidence.

The new Trials website (https://www.clinicaltrials.gov/) will only export in JSON (Java Script format) and Comma Separated Values (CSV) formats. We will be using the CSV export format, the format for spreadsheets. These instructions are simply slight modifications to the Clarivate instructions for importing tab-delimited files (spreadsheets) into EndNote.

Before proceeding with the following instructions, first decide whether it is necessary to export directly from clinicaltrials.gov to begin with. Cochrane CENTRAL contains records from Trials and is more user friendly. CENTRAL is limited to "randomized and quasi-randomized controlled trials" with daily harvests from Trials in addition to several other sources. Reasons to export directly from clinicaltrials.gov might include:

• No access to CENTRAL.
• The need to export Trials fields not included in the CENTRAL record.
• Controlling which EndNote fields will hold which Trials' field information (important for exporting to screening software, see below)
• The need for non-RCT study designs

If you will eventually be sending the Trials records into Covidence via EndNote, be aware that the only fields available for screening in Covidence are Title, Author, Journal Title (volume, issue, etc.) Year, Abstract and DOI. This means that any fields exported from Trials that are required for screening will need to be routed to one of those EndNote fields. Luckily, it is possible to route more than one Trials field to a single EndNote field. For example, the EndNote "Abstract" field can hold information from multiple Trials' fields

When Exporting from Trials, the chosen export fields (bold) become column headers in the spreadsheet:

We will simply be changing those column headers to match the EndNote field that that column information should land in. For example, the "Brief Summary" column header from Trials can be changed to "Abstract" to send that information to the Abstract field in EndNote. Again, you can change multiple column headers to "Abstract" to make that information available for screening in Covidence.

Steps to Import

1. Run search in clinicaltrials.gov, select records and fields to export and then export in CSV format.
2. Open the spreadsheet with Excel, then re-save the file as a "Text (Tab delimited) (*.txt)" file.
3. Open the text file with Word.
4. In Word display markup by clicking the paragraph symbol (¶) in the Word File > Paragraph tool bar.

 

1. We will be using the EndNote reference type "Journal Article" to hold the Trials' information. To indicate that, in the first line of the text file, against the left margin, manually type:

*Journal Article¶

The paragraph mark is a literal return.

2. Manually change each field exported from Trials (the column headers) to the corresponding field in EndNote that will hold that information. For example, the Trials' field "NCT Number" can be changed to "DOI" or "Brief Summary" might logically be changed to "Abstract".

Original View (Column headings only):

NCT Number     Study Title     Brief Summary     Interventions     Study Design     Completion Date

Converted Text File View:

*Journal Article¶
DOI  →  Title    →    Abstract →    Abstract →     Abstract → Year¶

You can see that the original column headings from Trials were manually changed to the EndNote landing fields for the "Journal Article" reference type. Specifically, "NCT Number" to "DOI"; "Study Title" to "Title"; "Brief Summary" to "Abstract"; "Interventions" to "Abstract" and so on.

The information for each column heading is separated by a tab (→) with the line ending with a literal return indicated by the paragraph mark.
 

Regarding the rest of the text, each reference must end with a single paragraph mark (shouldn't have to do this manually). There should be no paragraph marks or line breaks within a reference, if so delete them. Do not "line wrap" in the original Excel file, simply let the lines run on. Here is an example of a complete text file for the first two records of an export:

3. Resave the text file, and then import into EndNote: In EndNote: File > Import > File > choose file; Import Option: Tab Delimited > Import
4. All records should import into EndNote

 

Special thanks to Ellie Svoboda for testing these instructions and providing valuable feedback.