ATLAS is a joint initiative of NIST, MITRE and the LDC to build a general purpose annotation architecture and a data interchange format. The starting point is the annotation graph model, with some significant generalizations. An LREC paper describes the model.
The ATLAS project is no longer actively supported - a Java-implementation of the ATLAS APIs exists under the name of jATLAS. A software implementations that support ATLAS annotation exist: Calisto