The other day I was trying to find a paper that talks about the need for ontologies in biology that dated sometime around the early 90s - way before OWL and the Semantic Web. I couldn't find the paper I was thinking about, but here are some others that are pretty good that seem to follow at least the same themes:
"Ontologies for molecular biology": "Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning."
"Ontological Foundations for Biology Knowledge Models": This one was good because it talked about processes and transformations which is where the rules and inferencing stuff comes in.
"Toward Principles for the Design of Ontologies Used for Knowledge Sharing": While not specifically about biology, this is probably the most cited paper and it's what I often think about when you're explaining ontologies and the process of improvement that occurs when you make one.
"Bio-ontologies: current trends and future directions": This covers the process and the parts that make a good ontology on the web. I guess the key for the use of the Web for ontologies is a means to share knowledge. It also has a good history of ontologies going back to the 1600s.
And this one is one of the original GO papers, "Gene Ontology: tool for the unification of biology".
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