Once you OCR all your paper (FineReader is not bad),
and full-text index your PDFs (Beagle for Linux, MOSS for Windows),
you'll still have a problem with narrowing down a keyword search.
Try Amplify http://www.hapax.com/amplify.php on the title/abstract/methods page of each document
and maybe you'll get useful metadata.
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Once you OCR all your paper (FineReader is not bad), and full-text index your PDFs (Beagle for Linux, MOSS for Windows), you'll still have a problem with narrowing down a keyword search. Try Amplify http://www.hapax.com/amplify.php on the title/abstract/methods page of each document and maybe you'll get useful metadata.