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As a seasoned journalist I had to deal with a lot of PDF documents, powerpoint presentations, infographics and interview audio files. So I ma going to share my experience here.
Mendeley is the best tool in the industry to help you with organizing your research (in the form of PDF documents), I believe it is essential to be able to do them manually as well. Something they teach you a lot at J-schools.
My format is the following:
TIP: Each PDF has a section of properties, make sure you fill the tags section with all the terms that will help you look for the files in the future.
Strongly recommend: To create an excel sheet of all your PDF and folder structure that will serve as a reference point and help you to replace missing files before you are done with your research, thesis etc. Print this sheet to keep a hard copy
Backup a copy of your files on a weekly basis to Dropbox or Evernote.