Organizing and Annotating Your PDFs

Specific software is needed to organize and annotate PDF files across devices.

Commonly used programs

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Citation Managers that automate PDF ingest and organization

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Workflows

Once you have chosen software to annotate your PDFs, you will need a workflow for organizing and tracking them across your programs and devices. Here are some examples:
1. Organizing
  • Identify one place to store your PDFs
  • Organize your files by developing a file structure and create a scheme for file naming
  • Rename files and move them to the appropriate folder
2. Citation + Reading + Storage
  • Zotero manages your citations and offers free options for working in groups
  • Zotpad free iOS app for Zotero
  • Use Zotpad with your favorite iPad reader for reading and annotating, one example is Good Reader.
  • For storage, Zotero syncs with a variety of cloud storage options.
3. Citation + Reading + Storage + Sharing

Your Workflow

Your workflow in dealing with the PDF version of journal articles and other documents probably resembles this one:
  • Identify - Locate already saved or newly discovered PDFs
  • Organize - Name the file and save the file within your file structure
  • Read (and annotate) your document
  • Use/Share - Cite it in a paper or share it with others
  • Find or relocate
Dealing with existing PDFs
  • Decide how to deal with paper
  • It's OK to toss documents you won't need again
  • Consider hiring a helper
File Names Most default PDF file names are not useful. Rename them in a consistent schema. Tips for renaming:
  • Uniqueness
  • Consistency
  • A quick scan should tell you about the contents of the file
  • Names should allow files to display in a useful order
Examples of file names:
  • SmithM 1998.pdf
  • AHAgrant Smith 1998.pdf
  • SmithM 1998 NEJM heart AHAgrant.pdf
File Structure
  • Choose a scheme that works well for you.
  • Consider reusing a strategy from your e-mail.
  • If you use search to find your files, then your file structure may not need to be as elaborate.
Storage Options
  • Pick one place to save all of your related files
  • Consider what works for long-term back-up of important documents
  • Is it just for you? Use your hard drive with a separate back-up or a cloud solution
  • Sharing with others? Consider cloud storage options.
  • One solution might be a citation manager

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Get More Help

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