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cTAKES

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Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing system for information extraction from electronic medical record clinical free-text. It processes clinical notes, identifying types of clinical named entities from various dictionaries including the Unified Medical Language System (UMLS) - medications, diseases/disorders, signs/symptoms, anatomical sites and procedures.

HIEOS

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HIEOS is an open source implementation of Integrating the Healthcare Enterprise (IHE) Cross Enterprise Document Sharing (XDS.b) and Cross Community Access (XCA) integration profiles.

AETHER

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Aether is a platform. It’s not tool that can just be deployed and used out of the box (but if that’s what you’re looking for, you might want to look at Gather). Instead it’s a set of modules and best practices for the real-time manipulation and publication of data to a destination of your choice.
Aether is for you if:
you already have a large amount of data, but it’s in a format that makes it unwieldy or hard to use
you have a data source and a data location, but you just can’t get them to speak the same language