Resources of APIs for automated paper citation aggregation
The name for the type of research related to your question is referred to as: Bibliometrics or Scientometrics. 

That being said, the answer to your question is not simple since it depends on a few factors. You could be lucky and have a service such as this available that has a lot of the data available for you:
http://www.scimagojr.com/journalsearch.php?q=22078&amp;tip=sid&amp;clean=0

There is also a whole host of tools that can help you parse the files without using an API:
https://www.mat.unical.it/ianni/wiki/ScholarHIndexCalculator
https://sites.google.com/site/hjamali/scientometric-portal

In my case they did not provide all the information I required and ultimately I had to write a few tools of my own. The problem with this approach is that most papers are only available in PDF and requires PDF text extraction. Plenty of frameworks available to assist with that, but the structure of the document needs to be customised for each source of information since they are not all the same. Long story short, the following API's helped me a lot.

A list of scholarly APIs that can assist:
http://libguides.mit.edu/apis

Text extraction for individual files:
http://sourceforge.net/projects/itextsharp/
https://pdfbox.apache.org/