How to Export References from Zotero to Rayyan and Covidence

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-27

Quick Answer

• Export references from Zotero to Rayyan using RIS format for complete field preservation, including abstracts and keywords.
• Export references from Zotero to Covidence using RIS or XML format, with RIS being the most reliable for systematic review screening.
• Field mapping issues can cause data loss, so verify abstract and keyword transfer after import into either screening tool.

Understanding Reference Transfer Between Zotero and Screening Tools

Systematic reviews depend on accurate reference management from the initial search through screening and data extraction. Zotero serves as a common reference manager for organizing search results, while Rayyan and Covidence are web-based screening tools designed to streamline title and abstract screening. The transfer process between these platforms requires attention to file formats and field mapping to preserve the integrity of your reference data.

The National Library of Medicine provides access to authoritative biomedical research methods resources that describe systematic review workflows and the importance of transparent reporting throughout the review process. These resources emphasize that reference management is a foundational step in conducting reproducible research.

When you export references from Zotero, the software packages bibliographic data into standardized file formats. The three primary formats relevant to screening tools are RIS, XML, and CSV. Each format structures reference data differently, and the choice of format affects how completely your reference information transfers to Rayyan or Covidence.

RIS is a tagged format specifically designed for bibliographic citation exchange between reference management systems. It supports a wide range of field types including author names, titles, journal names, publication years, volumes, issues, pages, abstracts, and keywords. Most screening tools accept RIS files because the format preserves the structured nature of bibliographic data.

XML format provides a more flexible structure that can accommodate nested data elements. Zotero can export references in its native XML format, which some screening tools accept. However, the field mapping between Zotero XML and screening tool databases may not be as direct as RIS mapping.

CSV format presents reference data in a tabular structure with columns representing fields and rows representing individual references. While CSV is universally readable, it may not preserve all field types as effectively as RIS, particularly for complex data like multiple authors or nested keywords.

At a Glance: Export Format Comparison

The table above summarizes the practical considerations for each format. RIS is the recommended choice for both Rayyan and Covidence because it maintains the highest level of field fidelity during transfer. XML can work but may require additional troubleshooting. CSV serves as a fallback option when other formats fail, though you should expect some data loss.

Preparing Your Zotero Library for Export

Before exporting references, you need to ensure your Zotero library is organized and clean. Screening tools import whatever data you provide, so incomplete or inconsistent records in Zotero will result in incomplete records in Rayyan or Covidence.

Organizing References into Collections

Zotero allows you to organize references into collections, which function like folders. For systematic review purposes, create a dedicated collection for each search database or for the combined set of search results. This organization helps you track which references came from which source and makes the export process more manageable.

To create a collection, right-click on the Zotero library sidebar and select New Collection. Give the collection a descriptive name that matches your review protocol. Drag references into the collection or use the Add to Collection option from the reference context menu.

When you export references for screening, you can select a specific collection instead of exporting your entire library. This targeted approach reduces the risk of including irrelevant references and keeps your screening tool organized.

Checking Reference Completeness

Incomplete references create problems during screening because reviewers may not have enough information to make inclusion decisions. Before export, check that each reference includes the essential fields: author names, publication year, title, journal or source name, volume and issue where applicable, page numbers, DOI or URL, abstract, and keywords.

Zotero provides a way to identify missing fields through its column display options. Right-click on the column headers in the reference list and add columns for Abstract, DOI, and Keywords. Scan through your collection to identify references with missing critical fields.

For references missing abstracts, you have several options. You can locate the abstract through PubMed or the publisher website and add it manually to the Zotero record. The National Library of Medicine provides access to PubMed and other biomedical databases where you can retrieve abstract information for most published research.

Removing Duplicate References

Duplicate references waste screening time and can skew review results. Zotero includes a duplicate detection feature that identifies references with matching titles, DOIs, or other identifying information.

To check for duplicates, select the collection and click on the Duplicate Detection button in the Zotero toolbar. Review the suggested duplicates and merge them when appropriate. Merging combines the metadata from both records, preserving the most complete information.

The Committee on Publication Ethics core practices emphasize the importance of accurate data management throughout the research process. Removing duplicates before export aligns with these principles by ensuring your screening data is clean and reliable.

Exporting References from Zotero to RIS Format

RIS format is the most reliable choice for transferring references to both Rayyan and Covidence. The export process takes only a few steps but requires attention to the export settings.

Step-by-Step RIS Export Process

Open Zotero and select the collection you want to export. Click on File in the top menu, then select Export. A dialog box will appear asking you to choose the export format.

Select RIS from the format dropdown menu. The dialog box also offers options for what to include in the export. Check the box for Export Notes if you want to include any notes you have attached to references. For most systematic review workflows, you can leave this unchecked unless your review protocol requires notes to transfer.

Choose a location to save the exported file and give it a descriptive name that includes the collection name and export date. For example, "medline_search_20250115.ris" clearly identifies the source and date of the export.

Click OK to complete the export. Zotero will create a file with the .ris extension that contains all the references from your selected collection in RIS format.

Verifying the RIS File

After export, open the RIS file in a text editor to verify its contents. RIS files use a series of two-letter tags followed by a space and the field value. Common tags include AU for authors, TI for titles, PY for publication year, JO for journal name, AB for abstracts, and KW for keywords.

Check that the file contains the expected number of references and that key fields are present for each reference. If you notice missing abstracts or keywords, return to Zotero and correct the records before importing to your screening tool.

The EQUATOR Network provides reporting guidelines that emphasize transparent and complete reporting of research methods. Verifying your export file aligns with this principle by ensuring your screening data is complete before you begin the review process.

Exporting References from Zotero to XML Format

XML export from Zotero offers an alternative to RIS, particularly when you need to preserve Zotero-specific fields or when a screening tool has issues with RIS import.

Zotero RDF vs. Zotero XML

Zotero offers two XML-based export options: Zotero RDF and Zotero XML. Zotero RDF uses the Resource Description Framework to represent reference data in a structured format that preserves relationships between data elements. Zotero XML uses a simpler XML structure that mirrors the Zotero data model.

For screening tool import, Zotero RDF is generally more compatible because it follows a standardized structure that other systems can parse. Zotero XML may include Zotero-specific elements that screening tools do not recognize.

XML Export Process

Select your collection and click File > Export. Choose Zotero RDF from the format dropdown menu. Save the file with a descriptive name and click OK.

The resulting file will have an .rdf extension and contain XML-structured reference data. This format preserves the full range of Zotero fields, including custom fields and attachments information.

When to Use XML Instead of RIS

XML export becomes useful when you encounter persistent issues with RIS import into a screening tool. Some screening tools have limitations in their RIS parsers that cause certain field types to be dropped or misassigned. In these cases, XML may provide a workaround.

However, XML files are more complex and harder to verify manually than RIS files. If you use XML export, test the import with a small subset of references first to confirm that the screening tool correctly maps the fields before importing your full collection.

Exporting References from Zotero to CSV Format

CSV export from Zotero provides a tabular format that is useful for spreadsheet-based workflows and as a fallback when RIS and XML imports fail.

CSV Export Process

Select your collection and click File > Export. Choose CSV from the format dropdown menu. Zotero will prompt you to select which fields to include in the export.

The CSV export dialog allows you to check or uncheck specific fields. For screening purposes, include at minimum the following fields: Key, Title, Authors, Publication Year, Journal, Volume, Issue, Pages, DOI, Abstract, and Keywords.

Save the file with a descriptive name and click OK. The resulting CSV file will have a header row with field names and subsequent rows for each reference.

CSV Limitations for Screening Tools

CSV format has significant limitations for screening tool import. The tabular structure does not handle multiple authors or multiple keywords as elegantly as RIS. Some screening tools expect authors to be in a single column with a specific separator, while others expect separate columns.

Additionally, CSV files may lose the distinction between different reference types. A journal article and a book chapter may both appear as generic references in CSV format, losing the type information that screening tools use for filtering.

Use CSV export only when RIS and XML options are unavailable or when you need to manipulate reference data in a spreadsheet before import. For direct transfer to Rayyan or Covidence, RIS remains the preferred format.

Importing References into Rayyan

Rayyan is a web-based screening tool that supports collaborative title and abstract screening. Importing references from Zotero into Rayyan requires creating a review and uploading your exported file.

Creating a New Review in Rayyan

Log in to your Rayyan account and click on Create Review. Enter a title for your review that matches your systematic review protocol. You can also add a description and specify the review type.

Rayyan will ask you to name the review and optionally provide inclusion and exclusion criteria. These criteria help Rayyan organize your screening workflow, but you can add or modify them later.

Uploading References to Rayyan

After creating the review, Rayyan will prompt you to upload references. Click on the upload button and select your RIS file. Rayyan accepts RIS, XML, and CSV formats, but RIS provides the most reliable import.

Rayyan will process the file and display a summary of the imported references. Check that the reference count matches your Zotero collection count. If the counts differ, some references may have failed to import due to formatting issues.

Verifying Field Mapping in Rayyan

After import, review a sample of references in Rayyan to confirm that abstracts and keywords transferred correctly. Open several references and check that the title, authors, journal, year, abstract, and keywords are present and correctly assigned.

If you notice missing abstracts or keywords, the issue may be in the original Zotero records or in the RIS export. Return to Zotero, correct the records, and re-export before proceeding with screening.

Rayyan provides a duplicate detection feature that identifies potential duplicate references within your imported set. Run this check after import to catch any duplicates that Zotero missed.

Importing References into Covidence

Covidence is a web-based platform designed specifically for Cochrane systematic reviews and other review types. The import process differs slightly from Rayyan but follows the same general principles.

Creating a New Review in Covidence

Log in to your Covidence account and click on Create Review. Enter a title and specify the review type. Covidence will ask whether you are conducting a Cochrane review or another type of systematic review.

Covidence requires you to provide a review protocol or at least a description of your review scope. This information helps structure the screening workflow.

Uploading References to Covidence

Covidence provides an import screen where you can upload your RIS file. Click on the upload area and select your exported file. Covidence accepts RIS and XML formats.

After upload, Covidence will process the file and display the number of references imported. Verify that this count matches your Zotero collection.

Verifying Field Mapping in Covidence

Covidence maps RIS fields to its internal database structure. Check a sample of imported references to confirm that abstracts and keywords are present. Covidence displays reference details in a format similar to a bibliographic record.

If you encounter issues with field mapping in Covidence, the problem often relates to how Zotero exported specific field types. For example, some Zotero exports place keywords in a field that Covidence does not recognize. In these cases, you may need to adjust the Zotero export settings or clean the data in Zotero before re-exporting.

Troubleshooting Common Field Mapping Issues

Field mapping issues represent the most common problem when transferring references between Zotero and screening tools. Understanding these issues helps you prevent data loss and resolve problems quickly.

Missing Abstracts

Abstracts may fail to transfer when the original Zotero record lacks an abstract or when the export format does not include the abstract field. Check your Zotero records for missing abstracts before export.

If abstracts are present in Zotero but missing after import, the issue may be in the RIS export. Some Zotero versions have bugs that occasionally drop abstract fields during export. Re-exporting the file or trying a different format can resolve this issue.

Keyword Mapping Problems

Keywords transfer differently depending on the format and the screening tool. RIS format uses the KW tag for keywords, and most screening tools recognize this tag. However, some tools expect keywords in a specific format or limit the number of keywords per reference.

If keywords do not appear after import, check the original Zotero records to confirm keywords are present. Then verify that the RIS file contains KW tags. If the tags are present but the screening tool does not display them, the tool may have a limitation in keyword handling.

Author Name Formatting

Zotero stores author names in a structured format with separate fields for first name and last name. RIS format uses the AU tag with the format "Last Name, First Name." Most screening tools parse this format correctly.

However, some screening tools expect author names in a different order or format. If author names appear incorrectly after import, you may need to adjust the export settings or clean the author data in Zotero before export.

Special Characters and Encoding

References containing special characters, such as accented letters or Greek symbols, may display incorrectly after import if the encoding is not preserved. RIS files use UTF-8 encoding by default, which supports most special characters.

If you encounter encoding issues, check that your Zotero export uses UTF-8 encoding. Some older versions of Zotero may use a different encoding that causes character corruption during import.

Records and Measurements for Quality Control

Maintaining records of your export and import processes supports reproducibility and helps you identify issues when they arise. The National Institutes of Health data management and sharing policy emphasizes the importance of documenting data handling procedures throughout the research lifecycle.

Export Log

Create a simple log that records each export you perform. Include the date, the Zotero collection name, the export format, the file name, and the number of references exported. This log helps you track which versions of your reference data were used for which screening steps.

Import Verification Checklist

After importing references into Rayyan or Covidence, work through a verification checklist to confirm data integrity:

1. Reference count matches between Zotero and the screening tool
2. Sample of 10 references has complete title, author, and year information
3. Sample of 10 references has abstracts present
4. Sample of 10 references has keywords present
5. No obvious character encoding issues in titles or abstracts
6. Duplicate detection run and results reviewed

Document the results of this checklist in your review records. If any check fails, correct the issue before proceeding with screening.

Version Control for Reference Files

Keep copies of each exported file with clear version names. For example, "medline_search_v1_20250115.ris" and "medline_search_v2_20250120.ris" clearly indicate the version and date. This practice allows you to trace which file was imported into which screening tool.

Common Failure Patterns and Prevention

Understanding common failure patterns helps you prevent data loss and avoid wasting time troubleshooting import issues.

Pattern 1: Exporting the Entire Library Instead of a Collection

Exporting your entire Zotero library creates a large file that may exceed screening tool upload limits and includes irrelevant references. Always select a specific collection for export.

Prevention: Create a dedicated collection for each systematic review and export only that collection.

Pattern 2: Importing Before Verifying the Export File

Importing a file without checking its contents can result in silent data loss that you do not notice until later in the screening process. Always verify the export file before import.

Prevention: Open the RIS file in a text editor and check that abstracts and keywords are present for a sample of references.

Pattern 3: Ignoring Duplicate References

Duplicates in your screening tool waste time and can bias your review results. Run duplicate detection in both Zotero and your screening tool.

Prevention: Check for duplicates in Zotero before export and run duplicate detection in Rayyan or Covidence after import.

Pattern 4: Using CSV When RIS Is Available

CSV format loses data that RIS preserves. Using CSV when RIS is available creates unnecessary data loss.

Prevention: Always use RIS as your primary export format. Use XML as a fallback and CSV only when other options fail.

Pattern 5: Not Documenting the Transfer Process

Failing to document your export and import process makes it difficult to reproduce your methods or troubleshoot issues. Keep records of every transfer step.

Prevention: Maintain an export log and import verification checklist as described above.

Professional Escalation Criteria

Some issues require escalation beyond basic troubleshooting. Recognize when you need additional help or when a problem indicates a deeper issue with your reference data.

When to Seek Technical Support

If you have tried multiple export formats and verified your Zotero records are complete, but references still do not import correctly, contact the screening tool support team. Both Rayyan and Covidence provide support documentation and contact options for technical issues.

When to Consult Your Research Team

If field mapping issues affect a significant portion of your references, consult your research team before proceeding. The team may need to decide whether to manually correct affected records or adjust the review protocol.

When to Reconsider Your Reference Management Workflow

If you consistently encounter data loss during transfer, reconsider your reference management workflow. The issue may be in how references are entered into Zotero instead of in the export process. Review your data entry practices and consider implementing quality checks at the point of reference entry.

Safety and Regulatory Context

While reference transfer does not involve direct safety concerns, the integrity of your systematic review data has implications for research quality and publication ethics. The Committee on Publication Ethics core practices emphasize the importance of accurate data management and transparent reporting throughout the research process.

The National Institutes of Health data management and sharing policy requires researchers to plan for data management and sharing in their grant applications. This policy applies to the data generated during research, including the reference data used in systematic reviews. Documenting your reference transfer process supports compliance with these requirements.

The EQUATOR Network provides reporting guidelines that help researchers report their methods transparently. Following these guidelines when describing your systematic review methods, including how you managed references, supports the reproducibility of your work.

Frequently Asked Questions

Why do my abstracts disappear after importing into Rayyan?

Abstracts may disappear when the original Zotero record lacks an abstract or when the RIS export drops the abstract field. Check your Zotero records for missing abstracts before export. If abstracts are present in Zotero, try re-exporting the RIS file or use XML format as an alternative.

Can I import a Zotero collection directly into Covidence without exporting a file?

No, Covidence does not integrate directly with Zotero. You must export references from Zotero to a file format and then upload that file to Covidence. RIS format provides the most reliable transfer.

What is the difference between Zotero RDF and Zotero XML export?

Zotero RDF uses the Resource Description Framework to represent reference data in a standardized structure that other systems can parse. Zotero XML uses a simpler structure that mirrors the Zotero data model. Zotero RDF is generally more compatible with screening tools.

How do I preserve keywords when exporting from Zotero to Covidence?

Ensure your Zotero records have keywords in the Keywords field. When exporting to RIS format, keywords are included as KW tags. After import into Covidence, verify that keywords appear in the reference details. If keywords are missing, check the RIS file for KW tags and consider re-exporting.

Should I use CSV or RIS for exporting references to screening tools?

Use RIS format whenever possible. RIS preserves more field types and handles multiple authors and keywords more reliably than CSV. CSV should be used only as a fallback when RIS and XML options are unavailable.

How do I check for duplicate references before exporting from Zotero?

Use the Zotero duplicate detection feature by clicking the Duplicate Detection button in the toolbar. Review the suggested duplicates and merge them when appropriate. This reduces the number of duplicates that reach your screening tool.

What should I do if the reference count differs between Zotero and my screening tool?

Compare the reference count between your Zotero collection and the screening tool import summary. If counts differ, some references failed to import. Check the export file for formatting issues and try re-exporting. If the problem persists, contact the screening tool support team.

Can I export references from Zotero to Rayyan using XML format?

Yes, Rayyan accepts XML format for reference import. However, RIS format provides more reliable field mapping. Use XML only when RIS import fails or when you need to preserve Zotero-specific fields that RIS does not support.

Using the Evidence

Related Articles

• Meta-Analysis vs Systematic Review: What's the Difference?
• How to Cite Scientific Papers: A Guide to Citation Formats
• Data Management Software: A Guide to Choosing the Right Tools
• Scientific Literature Review Format: A Reproducible Structure for Researchers
• Sample Size Symbol and Notation: What You Need to Know

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.