Friday, January 27, 2006
[145] ß [parallel discussion on generative
methodology
Experience in Reasoning with the Foundational Model of Anatomy in OWL DL
This paper by Zhang, Bodenreider and Golbreich
http://helix-web.stanford.edu/psb06/zhang_s.pdf
"Experience in Reasoning with the Foundational Model of Anatomy in OWL DL is outstanding.
The entire paper is clear and expresses a major effort in taking large important frame based representation (in Protege-frames) and translating the entire construction to OWL DL.
Such translations are critical to establishing data and process interoperability in the bioinformatics resources, and as a consequence in the B-2-B and B-2-G resources. The translation technique explains the differences and similarities between Protégé-frames ontology constructions and Protégé OWL ontology constructions.
The "Semantic Web" (SW) can then be seen in its full realization, and with this we more comfortably understand the enormous benefits that will come IF the SW ideal is perfectly realized.
"Knowledge Engineering" operates within the "First School of Semantic Science", and as such recognizes that there are in fact limitations to what can be modeled in OWL (DL, Lite, or Full).
Extended discussions on this are being developed and posted ... for example
http://www.ontologystream.com/beads/nationalDebate/362.htm
lies out the viewpoint of the "Second School of Semantic Science".
..including an full acknowledgement of the value of moving bioinformatics data from relational (SQL) data schema into frames type ontologies or OWL type ontologies.
It must be observed that all ontology formalism is not “theSameAs” the union of Protege-frames plus OWL (DL, Lite, Full); and that what lies outside of this union is significantly different from the formalism in the union. By union, one can mean two things
1) the actual systems that have been developed to this point
2) the potential of all systems that could be build using the SW viewpoint
But these SW ontologies are steps.... to something that is not commonly understood - and perhaps not fully understood by any human today.
This is just a note to thanks the authors of this excellent paper.
The Taos Research Institute
Taos, New Mexico