HL7

HAPI (HL7 application programming interface; pronounced “happy”) is an open-source, object-oriented HL7 2.x parser for Java. HL7 ( http://hl7.org ) is a messaging specification for healthcare information systems. This project is not affiliated with the HL7 organization; we are just writing some software that conforms to their specification. The project was initiated by University Health Network (a large multi-site teaching hospital in Toronto, Canada).http://hl7api.sourceforge.net/

Mirth Connect is the Swiss Army knife of healthcare integration engines, specifically designed for HL7 message integration. It provides the necessary tools for developing, testing, deploying, and monitoring interfaces. 
http://www.mirthcorp.com/products/mirth-connect

http://bioportal.bioontology.org/