How to import articles from reference managers into ATLAS.ti

Who this article is for

This article is for researchers, students, instructors, and research teams who use reference managers such as Mendeley, Zotero, EndNote, or similar tools and want to bring journal articles or literature review materials into ATLAS.ti.

What is reference manager import?

Reference manager import allows you to bring article information and related article files from a reference manager into ATLAS.ti Desktop.

This is useful if you have already collected literature in a reference manager and want to continue organizing those articles in ATLAS.ti.

Reference manager import can help bring in:

• article documents
• abstracts when the full document is not available
• notes from the reference manager
• URLs
• document groups based on reference information

ATLAS.ti Desktop can create document groups based on metadata such as first author, co-author, publication type, language, source, periodical, year, volume, issue, edition, and publisher

Before you begin

Before importing reference manager data into ATLAS.ti Desktop:

1. Open your reference manager.

2. Create a focused collection or folder containing the articles you want to import.

   Remove articles that are not relevant to the project.

   Export the selected references as:

   • EndNote XML, or
   • BibTeX
3. Make sure the linked PDF files are still stored in the location referenced by the exported file.

For best results, create a focused collection in your reference manager before importing articles into ATLAS.ti. The reference manager exports only the bibliographic data; PDF files are not copied to a separate folder and must remain in the locations specified in the XML or BibTeX file.

Can I import reference manager data into ATLAS.ti Web?

Reference manager import is not currently available in ATLAS.ti Web. Use ATLAS.ti Desktop if you need to import a reference manager export file directly.

However, ATLAS.ti Web still supports literature review workflows in two ways:

• manually adding supported article files, such as PDFs or Word documents
• using Paper Search to search for and import papers directly into an ATLAS.ti Web project

Add articles manually in ATLAS.ti Web

Use this option if you already have article files saved on your computer.

Step 1: Open your Web project

1. Log in to ATLAS.ti Web.
2. Open the project where you want to add your articles.

Step 2: Open the Document Manager

1. Click the Documents icon in the left-hand menu.
2. Open the Document Manager.

Step 3: Add article files

1. Click Add Document.
2. Select the article file from your computer.
3. Complete the import process.

Supported text formats include .docx and .pdf.

Step 4: Add citation information manually

After importing the article:

1. Open the Document Manager.
2. Select the article.
3. Open Details.
4. Add the citation or bibliographic reference in the document comment field.

The literature review workflow article recommends renaming articles clearly using author name, publication year, and title, and pasting the bibliographic reference into the document comment area.

Use Paper Search in ATLAS.ti Web

Use this option if you want to search for articles directly from ATLAS.ti Web instead of importing them from a reference manager.

Paper Search allows users to search and import research papers into ATLAS.ti Web.

1.    Open Paper Search inside ATLAS.ti Web.

2.   Search using keywords related to your research question.

3.   Filter results by publication type or publication date if needed.

4.   Review abstracts and summaries to identify relevant papers.

5.   Click Import PDF to add selected articles directly into your project.

How to import reference manager data in ATLAS.ti Desktop

ATLAS.ti Desktop includes ATLAS.ti Windows and ATLAS.ti Mac. Both versions support importing reference manager data for literature review workflows.

Step 1: Export references from your reference manager

Before importing into ATLAS.ti, export your selected reference manager collection.

1. Open your reference manager.

   Select the folder or collection containing the articles you want to import.

   Export the selected references as:

   • EndNote XML, or
   • BibTeX
2. Save the exported file somewhere easy to find.
3. Confirm that the associated PDF files remain accessible from the exported reference file.

ATLAS.ti Desktop can import EndNote XML and BibTeX files.

Step 2: Open the reference manager import option

• In ATLAS.ti Windows

1. Open your ATLAS.ti project.
2. Go to the Import & Export tab.
3. Click Reference Manager.

• In ATLAS.ti Mac

1. Open your ATLAS.ti project.
2. From the main menu, select Document > Import > Reference Manager Data.

Step 3: Choose document group options

During import, ATLAS.ti can create document groups based on information from the reference manager file.

Available grouping options may include:

• first authors
• co-authors
• publication type
• language
• source
• periodical
• year
• volume
• issue
• edition
• publisher

These groups can help organize imported articles automatically.

Step 4: Choose the document name format

ATLAS.ti uses the document name from the reference manager by default.

For easier sorting and organization, you can choose to add:

• first author
• publication year

Step 5: Choose what to import if the full document is unavailable

If the full article file is not available, ATLAS.ti can import the abstract as a document.

Step 6: Select the exported reference manager file

• In ATLAS.ti Windows

1. Make your import selections.
2. Click the file loader icon.
3. Select the XML or BibTeX file exported from your reference manager.
4. Complete the import process.

• In ATLAS.ti Mac

1. Make your import selections.
2. Click Choose File.
3. Select the XML or BibTeX file exported from your reference manager.
4. Complete the import process.

Step 7: Inspect the imported documents

After import, open the Document Manager to review the imported articles.

• In ATLAS.ti Windows and Mac

1. Open the Document Manager.
2. Review the imported documents.
3. Check whether document names are sorted as expected.
4. Review automatically created document groups.
5. Open selected articles to confirm that the content imported correctly.

What to do if your reference manager exports a different format

ATLAS.ti Desktop currently imports EndNote XML and BibTeX files for reference manager workflows.

If your reference manager does not export one of these formats:

1. Check whether the reference manager offers an EndNote XML or BibTeX export option.
2. Export again using one of those supported formats if available.
3. If needed, use another reference manager to convert the references into a supported format.
4. Import the supported EndNote XML or BibTeX file into ATLAS.ti Desktop.

When your reference manager exports in an unsupported format, you may need to use another reference manager as a workaround before importing into ATLAS.ti.

Common issues and mistakes

• Trying to import reference manager data into ATLAS.ti Web
  • Reference manager import is currently available in ATLAS.ti Desktop only. In ATLAS.ti Web, add supported article files manually or use Paper Search.
• Exporting the wrong file format
  • Use EndNote XML or BibTeX for reference manager import into ATLAS.ti Desktop.
• Moving PDF files after exporting the reference file
  • If the exported XML or BibTeX file points to PDF file locations, keep the PDFs in those locations until the import is complete. Otherwise, ATLAS.ti may not be able to locate the full documents.
• Importing too many articles at once
  • For literature review workflows, import a focused collection of relevant articles instead of an entire reference library.
• Forgetting to inspect imported documents
  • After import, open the Document Manager and review the imported documents, comments, groups, and content.
• Expecting abstracts to behave like full articles
  • If the full article is not available, ATLAS.ti may import only the abstract. Review imported documents before continuing your work.

When to contact support

Contact ATLAS.ti Support if:

• the reference manager import option is missing in Desktop
• your EndNote XML or BibTeX file does not import
• imported documents are missing
• linked PDFs are not imported
• document groups are not created as expected
• notes or comments do not appear as expected
• Paper Search does not import selected PDFs in Web
• imported articles behave differently from the documentation

When contacting support, include:

• your platform: Web, Windows, or Mac
• your ATLAS.ti version if using Desktop
• the reference manager used
• the export format used
• screenshots or error messages
• a short description of what you expected and what happened instead