Summary

There are two important messages from this brief survey of bio-ontologies: the first is that ontologies are being used within the community to provide knowledge input to databases and applications. The second message is that all these ontologies are very different and specific to their intended use. TaO is an ontology of bioinformatics tasks and so contains such concepts as AccessionNumber and ProteinId, which are not part of the world of molecular biology. The TaO could not be substituted for EcoCyc's ontology. GO is an ontology of gene product function and RiboWeb represents knowledge of Ribosomal subunit structure, data and methodologies. As GO is used for database annotation, it holds a fine level of detail whereas the TaO is quite shallow, but precision is gained during query formulation by joining concepts together. Even if one ontology could be developed, individual applications would only use a subset, leading to a requirement of highly modular ontologies with minimised dependencies and assumptions between them. That ontology use influences the content and nature of the knowledge captured within an ontology is not a contradiction of the knowledge holding ability of ontologies. Not only does the purpose determine the scope and granularity to which the same knowledge is represented in different ontologies, but conceptualisations may differ without one being incorrect. For example, TaO describes that DNA may be translated to protein. This is wrong in molecular biological terms, but is a feature of bioinformatics - so conceptualisations of the same domain may differ. Sometimes a constraint is necessary for an application and sometimes it is not needed for another, this simply changes what knowledge is captured or how it is captured, it does not change the knowledge itself.