Molecule Role is a hierarchical ontology which contains the molecular functional group names, the abstract molecule names and the concrete molecule names collected from literature manually. This classification is based on a conceptual classification of molecular roles in protein interaction and signal transduction.
Publication: Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi and Ken Ichiro Fukuda. 2004. "An Ontology for Annotation of Signal Transduction Pathway Molecules in the Scientific Literature: Molecule Role Ontology". Comparative and Functional Genomics, Dec, 2004.
Event Ontology is an ontology that organizes the concepts and terms of pathway objects such as sub-pathways, biological processes and experimental environments appearing in the cellular pathway (e.g. signal transductions, disease pathways, metabolic pathways, etc.) The concepts in the Event Ontology were manually extracted from scientific articles and text books. Each concept has a link to Gene Ontology if possible.
Publication: Tatsuya Kushida, Toshihisa Takagi, Ken Ichiro Fukuda. 2006. "EVENT ONTOLOGY: A PATHWAY-CENTRIC ONTOLOGY FOR BIOLOGICAL PROCESSES". The Pacific Symposium on Biocomputing (PSB) 2006(accepted)