- From: William Bug <William.Bug@DrexelMed.edu>
- Date: Mon, 10 Jul 2006 10:20:48 -0400
- To: Phillip Lord <phillip.lord@newcastle.ac.uk>
- Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>
- Message-Id: <A30DE111-1B1E-4479-BECC-3AD77950F974@DrexelMed.edu>
Dear Philip, I agree with every comment you make - 100%. Thanks for taking the time to address some of these issues. See below for very brief addenda. Cheers, Bill On Jul 10, 2006, at 6:36 AM, Phillip Lord wrote: > >>>>>> "WB" == William Bug <William.Bug@DrexelMed.edu> writes: > > WB> 5) OWL isn't perfect for representing formal ontological > WB> frameworks - besides we're just representing terminologies, not > WB> building an ontology > > > OWL is sufficient for representing terminologies as far as I can tell. > To suggest that it isn't perfect for representing formal ontologies is > true, but slightly misleading. We don't have a perfect methodology for > representing formal ontologies. That OWL is not perfect is therefore a > relatively trivial statement. > > > WB> a) Even when assembling a terminology, you will be > WB> hard pressed not to represent some implicit semantic relations > WB> in your graph. > > Not sure how this relates to OWL. It doesn't. That's just another aspect of the debate from which this whole constellation of issues has arisen. > > > > WB> b) Work is ongoing to expand the semantic expressivity > WB> of OWL (see Chris M.'s comment re: including a formalism to > WB> accommodate time). > > It's worth mentioning that there are some difficult constraints with > respect to time. Don't quote me on this, as I am well out of my area > of knowledge. However, within the constraints of a decidable logic, > we do not yet know how to represent time based statements, while still > maintaining expressivity in other ways. > > The point is that the limitations in OWL expressivity are often > deliberate, not an over-sight. Agreed on all points. My hope is there are some "low hanging fruit" on the issue of time as relates to development and disease processes where even achieving partial expressivity for time, we'll be able to make some progress. In the context of several projects I'm working on - especially the BIRN project where the focus is neurodegenerative disease - small steps in the right direction to accommodate formal representation of durations and points in time in an ontological context will be a big help, so long as they don't lead us down a path precluding re-use later of what we do now, once formalisms to support the larger steps become available. > > > WB> 6) We can leave it to others to create XSLT converters to move > WB> the XML-only resources into the RDF++ space > WB> Philip & Chris M. have both given clear answers to > WB> this ill-advised use of XSLT. > > I think you may have misinterpreted this. My point is that XSLT is not > good for operating on RDF because there are many syntactic ways of > representing the same thing. In general, I wouldn't use XSLT at all as > I hate it, but that's a different issue. This was exactly how I took your point. Sorry for any confusion. I think Chimezie's follow-up point to your comment is also important to take into account here. XSLT is a means to this end, so long as you have a very clear application in mind and are willing to invest the manual labor required to map the semantics in the body of your XSLT document, this is a viable route. I believe all those who've weighed in on this topic so far would agree there's little point in going in the opposite direction, unless you are only looking to take the RDF instances you created through the forward process - exactly as they were with no changes of any kind - and turn them back to their XML-only equivalent. The overwhelming majority of modifications you'd likely make to the RDF instances would leave you with semantic ambiguities or enriched expressions no longer supported by the XSD you are trying to translate back to. As Chimezie pointed out, it is not an accident, but a deliberate design goal to create an XML binding for semantic web formalisms. My fear is the fact this XML --> XSD ==> XSLT --> RDF route is available leads some to believe using XML-only is a "safe" option to expressing semantic information now even if you may eventually want to move that information into the RDF++ space. This perception can especially be the case when assembling a strictly hierarchical terminological resource. My concerns are: 1) In representing complex, biomedical terminologies, you can rarely stick to a pure, hierarchical graph, one where you are careful to use only one type of relation - e.g., 'is_a' subsumption only, ONE of the MANY types of mereological relation, etc.. There are definitely ways of representing terminologies that include this additional complexity in XML-only; however, once you proceed to include that additional semantic subtlety, you are really making much more work for yourself by not moving into RDF++. 2) If you are expressing the terminology without any lexical variety and focussed on strict 'is_a' subsumption (i.e., hypernym--hyponym relations ONLY - no synonyms, no homographic homonyms, no meronyms, etc.), then the terms you pick - "preferred" terms, if you will - really just become stand in human-readable labels in an ontological graph, where the graph itself is purely semantic in nature. You would again be better off to represent that now in RDF++ where the syntax is specifically designed to support concise representation of such a graph. If you extend that approach by creating separate graphs for 'is_a' subsumption, specific mereological graphs to represent different manners of "parthood", etc. - you are then really making MUCH MORE work for yourself by avoiding RDF++ technologies for expressing your terminology. To express my opinion on this issue with a bit more nuance: RDF++ specs+tools (I include OWL in this "universe"), are not the most complete - or the only - means to formally express semantic info. If you are aware of the limits of the technology, however, and determine you can still accommodate the KE/KR/KD problem in hand, if you plan your design with these limits in mind, RDF++ can be extremely concise and semantically expressive - and - from my point of view - of much greater value for expressing semantic information than the XML-only approach. > > > Phil Bill Bug Senior Analyst/Ontological Engineer Laboratory for Bioimaging & Anatomical Informatics www.neuroterrain.org Department of Neurobiology & Anatomy Drexel University College of Medicine 2900 Queen Lane Philadelphia, PA 19129 215 991 8430 (ph) 610 457 0443 (mobile) 215 843 9367 (fax) Please Note: I now have a new email - William.Bug@DrexelMed.edu This email and any accompanying attachments are confidential. This information is intended solely for the use of the individual to whom it is addressed. Any review, disclosure, copying, distribution, or use of this email communication by others is strictly prohibited. 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Received on Monday, 10 July 2006 14:46:04 UTC