Knowledge acquisition, semantic text mining, and security risks in health and biomedical informatics

Table 1 Summary of contents, structure, and representation of several bio-ontologies (from Stevens et al[3])

Ontology	Application scenario	Modularised?	Domain-oriented component	Task-oriented component	Generic component	Instances	Detail level	KR
GO	Controlled vocabulary for database annotation	Partially	Drosophila, mouse and yeast gene function gene product function, process and cellular location and structure	×	×	√	High	×
EcoCyc	Database schema	√	Escherichia coli genes, metabolism, regulation, signal transduction and metabolic pathways	Visualization of biochemical reactions and layout of genes with chromosome	√	√	High	Frames
MBO	Community reference	√	Shallow	Shallow	√	×	Low	×
RiboWeb	Database schema	√	Ribosome Components, covalently bonded molecules, biological macromolecules, regions of molecules	Experimental detail, techniques for analysing data, publication	√	√	High	Frames
TaO	Common access ontology-based search	Partially	Proteins, enzymes, motifs, secondary and tertiary structure, functions and processes, subcellular structure and chemicals, including cofactors. The larger model includes nucleic acid and genes	Bioinformatics search and analysis tasks	√	×	High	DLs