On Jan 11, 2007, at 5:30 PM, Xiaoshu Wang wrote:

That is why I consider the OBO Foundry's wording "the original URI
should still point to the old term or concept, even if it is deprecated"
(From William Bug) is a bit self-contradicted.

Just to be clear, I was quoting Dirk here from his post to this thread, not the OBO Foundry. The wording of the related OBO Foundry principles (http://obofoundry.org/) is:

"3. The ontology possesses a unique identifier space within OBO."

"4. The ontology provider has procedures for identifying distinct successive versions."

This wording was kept purposefully vague, because there was apparently much discussion no real consensus regarding exactly what to recommend as an implementation strategy, and strategies might differ according the formalism being used (OBO vs. OWL vs. RDF, for instance). At least that was my understanding.

This is very much similar to the strategies that have been devised over the last several decades for managing controlled vocabularies (CVs). The A&I industry that uses CVs to index academic literature must deal with term deprecation and have done over the years. One of the problems when you are dealing with CVs is, since there is a lack of consistent, formally sound underlying semantic framework, even if you've developed a means of tracking changes in the CV, and all the annotations you've created with the terms - annotations of the scientific literature or experimental data repositories - have been dated so you can track the chronology of usage relative to the evolution of the CV, there is still no clear way to address the issue Vipul mentioned, namely how has the change made to a term in the CV effected the semantic entailments. Though CV and thesaurus curators have tried to develop best practices over the ages to address this specific question (some of which are in SKOS), just as Vipul mentions, these are for human consumption at best (and don't really do a very effective and consistent job of communicating the changes in entailed meaning to humans very well, for that matter). They most definitely do provide what is needed for automatic reasoners to negotiate the change in semantic entailment.

Explicit semantic frameworks are designed to over come some of this deficit, with their focus on DEFINITIONS. Many terms in CVs completely lacked definitions or when they had them, lacked a consistent means to express the intended meaning and usage of a term. The biomedical ontology community has slowly come to recognize - with input from applied, formal ontologists, medical informaticists, and various C.S. investigators such as logic programming & DL experts and computational linguists contributing to this field - that there must be a primacy given to definitions (think "defined class" in OWL). Of course, we are still working on the preferred means of provided consistent definitions, and it's not at all clear where the field currently stands on this issue. Practitioners from the fields I list in the previous sentence have different ways of specifying what a definition is - though one does hope they can all ultimately be kept commensurate (a pipe dream?).

The point Trish was making regarding how this is dealt with effectively across formalisms (OBO vs. OWL, for instance) is well taken. I don't believe this has been worked on directly.

However, creating metadata tags to track the evolution of the semantic graph is a task OBI has begun to tackle directly (https:// www.cbil.upenn.edu/fugowiki/index.php/ RepresentationalUnitMetadataTable). There are many properties - still under discussion, as Trish says - this is very much a work in progress - specifically designed to track the evolution of the underlying semantic graph. If you search on "Bill Bug follow-up", you'll clearly see what I'm referring to. I group these as the AnnotationProperties concerned with details related to "CLASS_ID/ CLASS AXIOMS//CLASS ASSERTIONS". The more I've thought through what is presented on that OBO Wiki page - much of it coming from the MSI, NCIT, BIRN, & MAGE communities within OBI - the more I think there's a need for a even a few more of these properties to track a bit more detail on the semantic graph as it evolves over time.

I'm pretty much convinced there's a need to provide this highly granular versioning within the TBox. I completely agree with Chimezie's point. In the ABox, things are completely different, though as Kei pointed out, versioning of accession numbers for GENBANK entries is certainly an major issue. To my mind, you can think of a GENBANK entry as having a place both in the ABox and the TBox, depending on how you believe the implied semantics in that artifact are best represented. There is the experimental evidence that led to the original submission of a particular sequence of whatever sort and creation of the GENBANK record. That evidence is in the ABox, as I see it. Then there is the record itself, which subsequently is referred to by many who derive their own sequence evidence through experiments and point to that record as the defining, granular type for their particular piece of evidence. I know this issue has engendered a great deal of discussion amongst those working on the Sequence Ontology and within the GO Consortium and GO user community. I can't say my view is representative of those discussions, and my sense is they did not necessarily reach a consensus opinion on the issue. There has been significant work on this issue, but I don't think there is not complete agreement here of exactly where the boundary is between TBox and the ABox. I'm speaking in the abstract here, of course. If someone creates a set of assertions in a particular DL formalism representing a GENBANK record and all its many referents, it will be quite clear on the entailments of that formalism where the boundary lies. What I'm saying is I don't believe there is a consensus on how one should formalize this issue.

Oops - gotta go, or I'll miss my 10 year old's school concert!

Cheers,
Bill


Bill Bug
Senior Research 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 - [EMAIL PROTECTED]




Reply via email to