Spinneret is a structured storage engine that can be thought of as an extended tuple storage system. It takes the best aspects of relational, object, and hierarchical databases and throws away the dead weight associated with those technologies. The benefit of Spinneret is that its data model is incredibly flexible, allowing it to expose its underlying data in any number of ways. It operates similar to an object database, but without hard ties to an originating language, and can also behave like a relational database without the burden of complex joins.
UIMA SDK is a software architecture and framework for supporting the development, integration, and deployment of search and analysis technologies. It can be used to analyze large volumes of unstructured information (text, audio, video, images, etc.) to discover, organize, and deliver relevant knowledge to the client or application end user.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.