Formal Concept Analysis for Ontologies and their Annotation Files

A generic formal concept analysis tool Multi-FCA takes as input a set of objects and a set of attributes describing those objects with the restriction that the attributes exist as concepts in an ontological terminology. It produces a variety of concept lattices, incorporates the characteristics of the structure of the ontological terminology in the creation of the concept lattices, provides options for tailoring the creation of the concept lattices based on user needs, and permits 3D visualization of the results. The initial domain for evaluating Multi-FCA is genomic research; specifically a formal context consists of objects that are genes or gene products and attributes that are annotating terms from an ontological terminology such as the Gene Ontology.