5.3 Reference managment

5.3.1 Mendeley

It is a reference manager and academic collaboration network.

5.3.1.1 Organize pdf files

By default, Mendeley will create links to the pdf files. In case the file is modified, the link will break. This approach is also not useful in case you work with more than one machine.

When installing Mendeley in another machine, it will save all the pdf’s at ~/.local/share/data/Mendeley Ltd./Mendeley Desktop/.

I prefer to use the File Organizer option to save the papers at a path of my choice (e.g. /home/me/Papers). This way the papers will renamed, with a pre-specified format, and saved at the specified path.

5.3.2 Zotero

Zotero Preferences

zotfile and betterbibtex

General

  • Uncheck Automatically take snapshots when creating items from web pages: To not include unnecessary small notes about the web page.

Sync

  • Uncheck Sync full-text content: To not sync pdf, images, videos. I prefer to use a cloud server to save those heavier files.

Advanced

  • Files and Folders: setup a custom Linked Attachment Base Directory path, where the pdf files will be linked. You can link this folder with a cloud server.

Better bibtex

  • Setup Citation key format (e.g. [auth:lower][year][shorttitle1_1:lower]): To define the citation key based on author last name, year and first work of paper title.

Zotfile Preferences

General Settings

  • Setup custom Source Folder for Attaching New Files: Where new files could be used to add new citations.

  • Setup custom Location Files: Where documents will be saved, same as Linked Attachment Base Directory.

  • Check Use subfolder defined by and set it to /%c: To create files order by subfolder with the same structure as in Zotero.