I have recently decided to actually do a "Independent Reading/Research" course and the topic which I have been suggested was if Ontology could be used well enough in a Bio-Informatics program. I am wondering if anyone can suggest some programming languages where Ontology is widely used, and some books =). Thanks and rates are a gift for helping.

Ontology: "the study of the nature of being, existence or reality in general, as well as of the basic categories of being and their relations. Traditionally listed as a part of the major branch of philosophy known as metaphysics, ontology deals with questions concerning what entities exist or can be said to exist, and how such entities can be grouped, related within a hierarchy, and subdivided according to similarities and differences."

There's a list of "prominent ontologists" at the bottom of that entry: Aristotle, Spinoza, Leibniz, Kant, Hegel, Husserl, Heidegger, Gadamer, Quine, Wittgenstein. That's pretty much a reading list for a philosophy major.

Heidegger's Being and Time is a major text in the field.

I'm not certain how all that could be related to bio-informatics, unless you mean something different from what is described there. Maybe you could connect some of those things to Husserl, or Deleuze, or maybe Merleau-Ponte via biocybernetics or systems biology or applied mathematics.

I doubt such a programming language exists, but if it does, I'm curious to hear about it.

Something like this?

https://www.clinbioinformatics.org/cbopublic/
http://anil.cchmc.org/Bio-Ontologies.html
http://mmcif.rcsb.org/pubs/bioinfo00.pdf
http://bib.oxfordjournals.org/cgi/reprint/7/2/207

From what I've seen, ontologies of this sort are typically specified in XML.

Interesting. Looks like I'll have to expand my understanding of the meaning of the word ontology. I would have grouped all that under taxonomy, but looking over those sites, I see that there's more going on there than taxonomy.

I only used the word ontology in the context of semantic knowledge representation (a bit more than taxonomy, as every process, word, relation needs a way to be described)

I got a bit interested in OWL (Web Ontology Language) for a while but got a bit disappointed by the project.

This page is a good start : http://en.wikipedia.org/wiki/Ontology_language

CycL is something I would have looked more in depth if I had more free time. Cyc, OpenCyc and Cycorp are probably the closest project we have from an AI as of today.

My admittedly very limited understanding of ontology in the bioinformatics domain is related to semantic web much as Yvanhoe mentioned. There has been some work done in chemistry, biochemistry, bioinformatics, cheminformatics, etc. in an attempt to define ontologies for various domains. I haven't seen much done to unify or bridge between those efforts, however. I think that much like semantic web itself these are still in their infancy.

Looking over those links, the focus on vocabulary and semantic networks suggests to me that the scientific effort has roots in the philosophical efforts I mentioned in my first post.

I did a course in ontologies as part of my undergraduate degree. The book we used was "Ontological Engineering" by Gomez-Perez, Fernandez-Lopez and Corcho. I didn't really use the book all that much, so I'm not in much of a position to recommend it, but flicking through it, it seems to cover all the standard stuff you'd expect in a course on ontologies, like OWL, KIF, description logics etc.

(Most ontologies aren't expressed in XML! There's special logics for describing ontologies.)

I'm certain that the XML specification of ontologies that I've seen (bioinformatics and cheminformatics) are more an implementational detail rather that a theoretical construct.