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]
