That's a common and manageable challenge! Zotero is excellent for this. The process involves two main steps:

• Importing all references from your various files into a single Zotero collection.


• Deduplicating the imported references.

Part 1: Importing All References into Zotero

The good news is that Zotero is designed to handle multiple file formats and large imports.

A. Preparation (Highly Recommended)

• Organize Your Files: Gather all your reference files (e.g., .ris, .bib, .nbib, .xml, .csv, etc., and any PDFs) into a single dedicated folder on your computer. This will make the import process much smoother.


• Create a New Zotero Collection: In Zotero, it's a good idea to create a temporary collection specifically for this import. This keeps your main library clean while you process the new batch.


• In Zotero, click the "New Collection" icon (the yellow folder with a green plus sign) in the top left.


• Name it something like "Import Batch [Date]" or "References to Deduplicate."

B. Importing Methods

Zotero can typically handle files from various databases (PubMed, Scopus, Web of Science, Embase, Google Scholar, etc.) as long as they are in a standard format.

Method 1: Drag & Drop (Easiest for most files)

This is often the quickest way if you have a mix of standard formats.

• Open Zotero and navigate to the new collection you created ("Import Batch [Date]").


• Open your folder containing all the reference files.


• Select all the reference files (e.g., Ctrl+A on Windows, Cmd+A on Mac) from your folder.


• Drag them directly into the central pane of your Zotero collection.


• Monitor the progress: Zotero will process each file. For 3000 references, this might take a few minutes. You'll see a progress bar.

• It will automatically detect the file type (RIS, BibTeX, etc.) and import the data.


• If you drag in PDFs, it will attempt to extract metadata and create an item for each PDF, attaching the PDF to it.


• It will attempt to link PDFs to existing items if it finds a match.

Method 2: File > Import (More control, good for problematic files)

If drag-and-drop doesn't work perfectly for some files, or if you prefer a more guided approach:

• Open Zotero and navigate to your "Import Batch [Date]" collection.


• Go to File > Import... in the Zotero menu bar.


• Choose "A file (BibTeX, RIS, Zotero RDF, etc.)" and click "Next."


• Navigate to your folder and select one or more reference files (you can select multiple files of the same type at once, or repeat this process for different file types).


• Tip: If you have many files of different types, it's often easier to do them in batches by type, or use Method 1.


• Check "Copy files to the Zotero storage folder" (recommended for PDFs or if your files are scattered). For pure reference data files (RIS, BibTeX), this option is less critical but doesn't hurt.


• Click "Next" and then "Finish."


• Repeat for any remaining files.

C. Tips for a Smooth Import

• Be Patient: 3000 references is a substantial amount. Zotero might take a while to import and process, especially if there are many PDFs. Don't close Zotero until it's finished.


• Error Handling: If Zotero encounters a corrupted or unsupported file, it will usually skip it and give you an error message. You might need to inspect those specific files or try different import methods for them.


• PDFs: If you have a separate folder of PDFs and you've already imported the reference data (RIS/BibTeX), you can drag the PDFs into the Zotero collection. Zotero will try to match them to existing items or create new items from their metadata.

Part 2: Deduplicating Your References

Once all 3000 references are imported, you'll inevitably have many duplicates. Zotero has a powerful built-in feature for this.

• Go to "Duplicate Items" in the Left Pane:


• In the left-hand column of Zotero, click on the "Duplicate Items" entry.


• Zotero will analyze your library and display groups of items it believes are duplicates in the center pane.


• Review and Merge Duplicates:


• For each group of duplicates, Zotero will show you the records side-by-side or stacked.


• Crucially, Zotero doesn't automatically merge them. You need to review each group.


• Review the records: Look at the titles, authors, publication year, journal, DOI, abstract, and attachments (PDFs, snapshots).


• Select the "Master" Record: Zotero tries to highlight the "best" record (often the one with the most complete metadata or attachments), but you can manually select which fields you want to keep from each record.


• Look for the record that has the most complete information: e.g., correct journal name, full author list, abstract, DOI, and attached PDF.


• Click on the radio buttons next to each field to choose which version of the field (e.g., title, authors, abstract) you want to retain in the merged item.


• Click "Merge X Items": Once you're satisfied with your selection, click the "Merge X Items" button at the bottom right.


• Attachments: Zotero is usually smart about attachments. If both duplicate items have PDFs, it will merge them so that both PDFs are attached to the single, merged item.


• Iterative Process:


• For 3000 references with "many duplicates," this will be an ongoing task.


• Start with the obvious duplicates, then move to less obvious ones.


• As you merge, Zotero will update the "Duplicate Items" list.


• It's a good idea to work through them in batches. Don't feel pressured to do all 3000 at once. You can close Zotero and come back to it.

D. Tips for Effective Deduplication

• Prioritize Completeness: Always aim to keep the record that has the most complete and accurate metadata (DOI, abstract, full author list, correct journal/publication details).


• Check for False Positives: Zotero is very good, but sometimes it might flag two different articles as duplicates because they have very similar titles or authors (e.g., a conference paper and a journal version that are distinct enough for your purposes, or two different review articles by the same lead author in the same year). Do not merge these. Simply select them and click "Unmerge" or delete one if it's truly not needed.


• Check for False Negatives (Missed Duplicates): Zotero might miss some duplicates, especially if the metadata is inconsistent (e.g., different spellings of authors, slightly different titles, or missing DOIs).


• Sorting: After you've done the main deduplication, you can try sorting your main collection by "Title," "Author," or "Year" to manually spot any remaining duplicates that are close but weren't flagged.


• Advanced Search: For persistent issues, you might use Zotero's advanced search (the magnifying glass icon) to look for partial titles or author names.

In summary:

• Organize your files and create a new Zotero collection.


• Drag and drop all reference files into that collection.


• Go to "Duplicate Items" and systematically review and merge the identified duplicates, prioritizing the most complete record.