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Hindawi are a large CC-BY publisher based in Egypt, their XML corpus can be retreived from http://www.hindawi.com/corpus/
We have a bunch of well documented APIs, and support content negotation on our articels to return markdown. Our main rest api is built on top of fluidinfo. We have also just launced lens.elifesciences.org, and the front end and XML -> JSON converter can be found here and here. We are also experimenting with workflow systems in Amazon, you can find that proejct here.
Search the fulltext content of all PLOS articles, including search in specific sections (e.g. financial disclosure or materials_and_methods). The web interface is here, available fields in the API are listed here, and an R package is available.
http://www.ncbi.nlm.nih.gov/books/NBK25500/
Retrieve identifiers of articles that match search criteria.
Fetch full records