|Cc:||ontolog-forum@xxxxxxxxxxxxxxxx, James Malone <malone@xxxxxxxxx>|
|From:||Michel Dumontier <michel.dumontier@xxxxxxxxx>|
|Date:||Thu, 13 Jan 2011 11:46:12 -0500|
You're making some pretty bold statements without appropriate analysis:
1) there are ontologies listed in the NCBO bioportal with more than subclass axioms, but it may be the case that the NCBO web service only provides subclasses from the original ontologies - so.... if you look at the source files, you'll see that they are much richer than this
also note that the bioportal service consumes many formats (OBO, RRF, OWL, LEXGRID) and generates a common representation
2) it certainly is the case that many terminologies were never designed with formal methods in mind, and that the formalization to OWL leads to an erroneous representation. We have made some effort to accurately translate OBO ontologies that make use of the Relation Ontology with appropriate OWL constructs:
3) is entirely speculative and creates no opportunity for meaningful discourse.
4) not true - particularly of biomedical ontologies where the terminology sources have many uses - they have value as common terminology for annotation purposes, data integration, and statistical analysis. More sophisticated uses include consistency checking and classification, and I would agree that that feature is under-utilized, but that doesn't invalidate the efforts thusfar.
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