Pass One: IOB Chunking
Pass Two: Classification
CliNER is designed to run out-of-the-box and be as lightweight as possible. However, there are also options for enabling additional features in order to achieve better prediction results. By changing the config file located at $CLICON_DIR/config.txt, you can enable modules that extract additional Machine Learning features using the GENIA tagger and UMLS databases. See the README for info about how to obtain these modules. Here is the organization for how features are extracted from given input text.
Adding your reader/writer is done by adding a file in the $CLICON_DIR/clicon/notes. The file should be named note_%s.py (where %s is the name of your format). Inside this file, you must define an object named Note_%s (where %s is again your format name). This class must inherit from the AbstractNote object. Now all that remains is defining the abstract methods inherited from the base class and you will be able to read any formats you need.
All format specifications (be it through CLI, python scripts, etc) all check the ''notes'' directory to determine what formats the system can read.