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A good overview of the entire field of Artificial Intelligence can be found on the website of the AAAI (American Assoc. of Artificial Intelligence) in their AI Overview section.
A very popular senior/graduate-level textbook is Artificial Intelligence: A Modern Approach by Stuart Russell and Peter Norvig. The book describes the nature of knowledge, its representation, inference based on knowledge, and many other topics. There are many other good books and online sources described in the AAAI Overview pages just mentioned.
The objects, processes, structures and functions in living system can be organized conceptually to allow orderly representation, searching and manipulation. A major example of this kind of work is UMLS, the Unified Medical Language System developed at NLM, the National Library of Medicine.
"Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics."
The above quote is taken from the abstract of a major multi-author paper, "An Evaluation of Ontology Exchange Languages for Bioinformatics" which was presented at ISMB 2000 (Intelligent Systems in Molecular Biology). (cached)
Another approach is to build ontology management tools for acquiring terms online and bringing them into concordance: "Ontology Acquisition from On-line Knowledge Sources" by Q. Li, P. Shilane, N. F. Noy, & M. A. Musen. In the Proceedings of the AMIA Annual Symposium, Los Angeles, CA. Available as SMI technical report SMI-2000-0850 (2000) (cached)
Ontology problems are closely related to the discovery, extraction and classification of terms. These topics are highlighted in the bibliography by Sophia Ananiadou, elsewhere on this site. (cached)