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Zotero

Zotero is a free and open-source software (FOSS) for management of references, citations and research documents. The Zotero desktop application has cross-platform support for Windows, macOS and Linux.

Personal Experience

Originally I used Mendeley by Elsevier because is provided a built in pdf annotation tool and could be synced with a mobile app. I experienced ongoing issues with duplicate citations and pdfs and loss of annotations. Mendeley also deprecated their mobile app. I switched to Zotero when they announced their own pdf annotation function (Beta).

Tools & Software Integrations

  • Zotero Connectors - Connectors are available for most popular web browers. These allow you to save documents and webpages to Zotero as you browse.
  • Barcode Scanning - Apps can be used to add books to Zotero using a mobile phone. iPhone users can achieve this using iPhone Shortcut. Android users can instead use a free barcode scanner and link it to the Zotero API as outlined here.
  • Zotero PDF Reader and New Note Editor (Beta) - Zotero recently announced a new built-in PDF reader and annotation function. This functionality is cureently in Beta and requires download of the latest development build. NOTE: Annotations are stored in the Zotero database, not in the PDF file. In order to view highlights and annotations in external PDF readers, or export them with ZotFile, the annotations first need to be saved to the PDF. This prevents further editing of those annotations and highlights in Zotero at present.

Zotero provide a list of plugins in their support pages. Plugins I typically use are as follows:

  • Mdnotes for Zotero by Argentina Ortega Sáinz. A Zotero plugin to export item metadata and notes as markdown files. I use this plugin to convert quotes and annotations from PDFs into markdown once they have been extracted with the ZotFile plugin. The resulting markdown can then be pasted into Obsidian and includes links back to the PDFs in Zotero. NOTE: Installation instructions recommend prior installation of the ZotFile and Better Bibtex plugins as dependencies.
  • Night for Zotero by Thomas F. K. Jorna. Night for Zotero enables ability to switch between light and dark themes for the UI along with the ability to change the theme of compatible pdfs in the Zotero document reader.
  • Zotero Citation Counts Manager by Erik Schnetter. The tool can retrieve citation counts from a number of sources including Crossref, Inspire HEP, and Semantic Scholar. Google Scholar is not supported because automated access is against its terms of service. Zotero doesn't currently have any special field for the number of citations, so they are stored in the 'Extra' field.
  • Zotero DOI Manager by Brenton M. Wiernik. The add-on can auto-fetch DOI names for journal articles using the CrossRef API, as well as look up shortDOI names using http://shortdoi.org. The add-on additionally verifies that stored DOIs are valid and marks invalid DOIs.
  • ZotFile by Joscha Legewie. Zotfile is a Zotero plugin to manage your attachments: automatically rename, move, and attach PDFs (or other files) to Zotero items, sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad, Android tablet, etc.) and extract annotations from PDF files. I typically use this to extract quotes and annotations from PDFs. NOTE: While the Zotero PDF reader and annotation function is in BETA and annotations made with Zotero's reader need to be saved to the PDF before they can be extracted.

Resources

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Notes and Troubleshooting

Citing Book Chapters or Essays

Source: https://library.tiu.edu/zotero/booksection

  1. Save the full book into Zotero.
  2. Make a copy of the book record by right clicking on the book, then choose 'Duplicate Item'.
  3. Change the Item Type from 'Book' to 'Book Section'.
  4. Click 'ok' to accept the information that will be lost.
  5. Add the title of the chapter under 'Title'.
  6. Click the down arrow by the author(s) of the book and change them to be 'editor'.
  7. Add the author of the chapter by clicking the '+' sign to the right of the author's name and make sure it is set to 'author'.
  8. Add the page numbers for the chapter.

Save Zotero Annotations and Export to Markdown

Annotations created in Zotero are stored in the Zotero database, not in the PDF file. In order to view highlights and annotations in external PDF readers, or export them with ZotFile, the annotations first need to be saved to the PDF. However, this prevents further editing of those annotations and highlights in Zotero at present.

To export highlights and annotations from Zotero while retaining the ability to edit them in Zotero use the following work around:

  1. Ensure you have the Zotfile and MDNotes plugins for Zotero installed.
  2. Open the required PDF in from the main Zotero library view.
  3. Click File > Store Annotation in File to ensure the annotations are baked into the PDF document. This will lock your annotations from editing in Zotero.

  4. Close and restart Zotero.

    NOTE: This step is important. If you don't restart Zotero the ZotFile plugin may not recognise that annotations are now available to be extracted.

  5. Find the PDF in the main library view and select Manage Attachments > Extract Annotations. A new file containing the annotations will appear under the PDFs parent item.

  6. Right click on the new extracted annotations file and select MDNotes > Export to Markdown.
  7. Select he location to output the markdown file to and click 'OK'.
  8. The annotations will be exported as a markdown file and a copy will appear in Zotero alongside the PDF beneath their parent item.
  9. The markdown can then be imported into Obsidian.
  10. If you need to unclock your annotations for editing in Zotero, open the PDF, click File > Import Annotations.

NOTE: Annotations can be stored and reimported in Zotero as often as required.