It would be simplest to store references to articles as an ID number which can be looked up elsewhere. Here are some possibilities in order of preference:
(*) I doubt that there are articles with both a DOI *and* a handle, but if you encounter one, use the DOI. There is a text query interface to look up DOI at CrossRef: http://www.crossref.org/SimpleTextQuery/
For most articles earlier than 1997 there almost certainly won’t be a DOI. Try JSTOR and use their SICI-based link but the best way for those that can’t be readily assigned an identifier is to enter the complete citation.
(**) There aren’t many articles with Pubmed ID that lack a DOI, but it’s possible for pre-1998 pubs.
(***) Jim & Hilmar looking into interface to help do this
(****) Requires ISSN for construction, won’t work for book sections