Highly literate ontologies

There is still a lot of discussion about exactly what ontologies should represent, but what is generally agreed is that they formalise and relate to some relatively complex areas of knowledge. While ontology environments allow rich descriptions of the relationship between the entities inside the ontology (because this is what an ontology is), they often do not provide the same rich environment to describe the knowledge that they represent. OWL does, for instance, supports annotations which allows an ontology developer to add comments to many parts of the ontology. But these comments, do not contain markup, sectioning or any of the standard facilities authors use when writing documents. Our solution to this builds on Tawny-OWL, our highly-programmatic environment for ontology development. This provides a rich environment, which allows abstraction, automation and extension, while still being entirely textual. As a result, it is possible to integrate this form of ontology with similar textual environments for documentation such as LATEX, or AsciiDoc. We call the result a literate ontology, in reference to literate programming. The result can be ”tangled” to produce either a document or ontology. However, manipulating mixed syntax formats is difficult. Generally, the text editor either supports the literate form or programmatic (ontology) form best. To address this, we have developed what we call ”lenticular views” – essentially, the source code can be presented either in an ontology-centric or a document-centric view. Either form can be changed, giving the author a powerful and unique environment for creating literate ontologies. Or alternatively, semantic documents where the ontology formalises the document. We demonstrate this with our literate amino-acid ontology which is also a part of the developing manual for Tawny-OWL.