# In order to be able to use the Skim command line utilities, you might have to need to copy them to your /usr/bin/ folder
sudo cp -p /Applications/Skim.app/Contents/SharedSupport/skimpdf /usr/bin/ 
sudo cp -p /Applications/Skim.app/Contents/SharedSupport/skimnotes /usr/bin/ 
sudo cp -p /Applications/Skim.app/Contents/SharedSupport/displayline /usr/bin/ 

# Use skimnotes to extract annotations:
skimnotes get Almeida2013.pdf Almeida2013.txt   # extract annotation into text format
skimnotes get Almeida2013.pdf Almeida2013.skim  # extract annotation into skim format