Taking a view on bio-ontologies

We present a technique for separating knowledge representation from application specific views that are currently often conflated within bio-ontologies. Many ontologies contain information for two tasks; one to represent the knowledge of some field of interest and another to support an application through providing views over ontologies that present the terms in a useful way for an application. We analyse this phenomenon in some bio-ontologies and suggest this separation of layers as a solution. We leave dedicated ontology languages like OWL and OBO to represent the knowledge of a field of interest, and use a more lightweight vocabulary, namely SKOS, to capture
application specific views. We use this technique to encode a number of views inside the Experimental Factor Ontology. Each of these views serves a special purpose to different user communities; however, it does ensure the underlying ontology can remain for the annotation and integration of biological data. OWL and SKOS together provide a powerful, standards based, mechanism to reconstitute annotated biological data for many different application domains.