For turning a bibliography into RIS format, I wrote a tool based on a whole pile of regex commands bundled into sed files wrapped in an AppleScript app:
Code4Lib article: http://journal.code4lib.org/articles/6286
Let me know if you've got questions about using/adapting it. Both of those links also list other tools I found trying to do similar things.
From: Code for Libraries [mailto:[log in to unmask]] On Behalf Of Eric Lease Morgan
Sent: Friday, 19 June 2015 5:04 a.m.
To: [log in to unmask]
Subject: Re: [CODE4LIB] Desiring Advice for Converting OCR Text into Metadata and/or a Database
On Jun 18, 2015, at 12:02 PM, Matt Sherman <[log in to unmask]> wrote:
> I am working with colleague on a side project which involves some
> scanned bibliographies and making them more web searchable/sortable/browse-able.
> While I am quite familiar with the metadata and organization aspects
> we need, but I am at a bit of a loss on how to automate the process of
> putting the bibliography in a more structured format so that we can
> avoid going through hundreds of pages by hand. I am pretty sure
> regular expressions are needed, but I have not had an instance where I
> need to automate extracting data from one file type (PDF OCR or text
> extracted to Word doc) and place it into another (either a database or
> an XML file) with some enrichment. I would appreciate any suggestions
> for approaches or tools to look into. Thanks for any help/thoughts people can give.
If I understand your question correctly, then you have two problems to address: 1) converting PDF, Word, etc. files into plain text, and 2) marking up the result (which is a bibliography) into structure data. Correct?
If so, then if your PDF documents have already been OCRed, or if you have other files, then you can probably feed them to TIKA to quickly and easily extract the underlying plain text.  I wrote a brain-dead shell script to run TIKA in server mode and then convert Word (.docx) files. 
When it comes to marking up the result into structured data, well, good luck. I think such an application is something Library Land sought for a long time. “Can you say Holy Grail?"
 Tika - https://tika.apache.org
 brain-dead script - https://gist.github.com/ericleasemorgan/c4e34ffad96c0221f1ff
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