Retrieving the references in a publication automatically

Both Scopus and Web of Knowledge contain all the information that you need and have APIs that can be used to automate access:

• http://info.sciencedirect.com/scopus/scopus-in-detail/tools/api
• http://wokinfo.com/products_tools/products/related/webservices/

I have never used them personally, but I hope this kind of information can be accessed using them. Each site indexes articles with their own unique key, so you can use those instead of DOIs if you only need them as unique keys.

Neither of them is free; you can probably access them through your university's subscription though. Be sure to check the usage limits.

It's backwards from your proposed approach, but you could also use Google Scholar. It (apparently) has no API yet. Thus, someone created a python module to parse its output. http://www.icir.org/christian/scholar.html

Google Scholar only gives you the articles that cite the given article. So you can build the links that are to the article, rather than from it.

Edit Google Scholar Citation Visualisation Tool seems to be based on this approach. However, the bookmarklet doesn't seem to work (for me in Chrome) when I browse Google Scholar as shown in the video on that page.