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Re: Versioning vs Temporal modeling of Patient State

From: William Bug <William.Bug@DrexelMed.edu>
Date: Fri, 12 Jan 2007 07:40:10 -0500
Message-Id: <97718484-B7CE-4D82-A3A9-5C8BDC9873D5@DrexelMed.edu>
Cc: "Bijan Parsia" <bparsia@cs.man.ac.uk>, <dirk.colaert@agfa.com>, <wangxiao@musc.edu>, "w3c semweb hcls" <public-semweb-lifesci@w3.org>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
The IFOMIS work Dirk, Kirsten, and others have cited on referent  
tracking is definitely important work to review in this light.  I'd  
not been familiar with the model theoretic work Bijan mentions, but  
clearly that is important.

Werner Ceusters also has a list - a Google list I believe - on  
referent tracking.

This work - and related work on "speech acts" - is most definitely  
relevant to this discussion and very specifically is designed to  
address ABox.  As the citations given indicate, most of this work has  
been done in the clinical domain with a focus on patient records,  
which was the origin of this thread and would be directly relevant to  
the Use Case Nigam put out there.

Some of that work has begun to seep into the discussions regarding  
the sort of GENBANK issues Kei mentioned, but its still really just  
discussion to my knowledge.  As you could tell from the way I couched  
my description of that problem, clearly referent tracking is a big  
part of what must be accomodated in that domain as well - both in  
terms of the actual content and evolution of a record  in GENBANK,  
TrEMBL, etc., as well as the many ways in which researchers link to  
and reference such records.

Also - the work I was mentioning regarding TBox focussed, highly  
granular revisions, has been informally discussed by NCBO folks  
including Chris Mungal, Fabian Neuhaus, Barry and others - again with  
an eye toward providing reasoning services to support this  
requirement of the nature of what Bijan, Dirk and others mention  
below.  This is associated with the discussions on this topic amongst  
both BIRN, OBI, and NCIT participants but has all been very informal  
so far - AFAIK.

One of the things I would point out regarding the metadata properties  
I was referring to, is this was really meant to be just a simple,  
"low hanging fruit" approach to a much more complicated problem.   
There was not thought given to how one would actually construct  
automatic means to mediate reasoning on - or even just representing -  
the evolving semantic graph.  The idea was simply - many biomedical  
ontology development projects have begun to notice the pressing need  
for version control which appears to be required at a very granular  
level.  Standard source version control systems - e.g., CVS, SVN,  
etc. - just make the problem worse in my opinion.  This is where I'd  
differ with the point Vipul makes.  It's not that there are NO  
aspects of the software version process relevant to this issue.  It's  
just I believe there are complex issues in this domain - some of  
which Bijan mentioned - some of which I mention below regarding  
application the traditional approach to employing CVs for literature  
annotation - that extend greatly beyond what the common practice in  
software version control is intended to support.  In that domain,  
highly granular version management has been required, and I believe  
something like it will be required in the ontology development space  
as well.  Perhaps that's just a qualification and rewording of the  
point Vipul was trying to make.

SKOS, as I mentioned, does try to absorb some of what has been done  
on this issue in the A&I/library science world in relation to CV  
application to the literature annotation process.  This has long been  
recognized in that field as extremely important to the proper  
curation of a CV/taxonomy/classification scheme/thesaurus.  In that  
domain, if you step back a bit from the details and ask - what is the  
intended purpose of a CV in that domain - the answer clearly is to  
improve both precision and recall (F-measure from standard IR) for  
boolean, term-based queries.  Anyone who has used MEDLINE over the  
years has learned the utility of this approach - and its limitations  
(the barrage of false positives and unknown number of false negatives  
that typically still effect query results).  There is no doubt just  
looked at empirically that having the people who are annotating the  
literature use a CV greatly improves the F-measure of the search  
system used to mine the resulting inverted indexes.  However, I know  
from time working with the creators of the Biological Abstracts, that  
it took months of training for the "indexers" to get good at  
consistently applying CV terms - and a lot of QA/QC was still needed  
to constantly monitor the output.  The reason really comes down to  
the lack of complete, detailed definitions and lack of a formal,  
semantic graph really left way too much leeway for indexers, even  
when a moderate amount of effort was dedicated to incentivizing  
indexers.  Having said that, when highly specific definitions were  
used, it was found indexers both greatly slowed in the annotation  
output AND use of CV terms went way down, both of which are really at  
odds to the intended goal of the process (back to F-measure), which  
is to provide maximal annotation given according to a CV.  Even with  
this work, BIOSIS (publishers of the Biological Abstracts) and really  
all the A&I vendors I knew of, still required a huge educational  
staff that would constantly travel the world providing demos and  
updates to librarians, so they could be kept informed on how best to  
use the resulting CV indexes.

It was still clearly an art to maximize F-measure - one that very  
much depended on quality and structure of the CV/classification  
scheme/taxonomy, the talents of the indexers applying the CVs in the  
annotation process and the talents of the info. retrieval experts/ 
librarians in constructing queries. By far the most confounding  
aspect of this process was the need to alter indexer and searcher  
practice, as CV changes were introduced - as was of course inevidible  
- both due to changes in the *world* and changes in *knowledge  
representation*, as Bijan describes it below.  It was partly because  
of this, that various CV curatorial practices were developed that  
again are partially represented in SKOS - fields such as "scope  
notes", "history notes", etc., which all relate to the versioning  
issue in this context, but, of course, are designed for human  
consumption and are not particularly useful to KE/KR algorithms.

My sense - as you can see in that OBI Wiki page I cited - is there is  
a need to provide such curation support in the ontology development  
process both to address the lexical issues as has been historically  
done in info. science/library science, as well as to address semantic  
graph evolution.  Both of these requirements arise due both to  
changes in *world* and QA/QC performed on the KR (changes in  
*knowledge*).  My sense is in providing this first simple step - a  
shared collection of AnnotationProperties used across the community  
when building OWL-based ontologies - we provide the structure  
required to develop software tools to help automate the process.   
Nothing extending to the complexity of automatic reasoning, but just  
something to address the need quickly - a structured model for these  
processes, if you will, that can evolve toward the more complex  
"referent tracking" and "speech act" formalism.  This stop-gap isn't  
nearly enough to fully address this complex issue, but it should be  
relatively easy to implement and to put into practice (with a minimal  
amount of automated support for ontology curators), and if done  
correctly, should be something that can migrate to the more complex  
approach later.  Providing too complex a strategy for addressing this  
versioning issue now might prohibitively slow the ontology  
development process as it is being carried out by various community  
biomed. ontology development projects.

As you can tell, this is just a suggestion which OBI, BIRNLex, and a  
few other ontology developers have just begun to implement, so this  
is most definitely a work-in-progress.

Having a review of the topic, as Vipul suggests, at this stage in the  
game by the several folks who've provided valuable pointers and  
feedback, would be a wonderful idea, I think.


On Jan 12, 2007, at 6:26 AM, Kashyap, Vipul wrote:

> Is there any work in the literature related to:
> - Defining what and when a version is?
> - Do all updates necessarily lead to a new version?
> - Is there a utility to instance versioning?
> The observation about the utility of knowledge base update and  
> revision is an
> astute one. IMHO the utility of instance versioning is not clear  
> either.
> Just my 2 cents,
> ---Vipul
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb- 
>> lifesci-
>> request@w3.org] On Behalf Of Bijan Parsia
>> Sent: Friday, January 12, 2007 5:28 AM
>> To: dirk.colaert@agfa.com
>> Cc: wangxiao@musc.edu; 'w3c semweb hcls'; public-semweb-lifesci-
>> request@w3.org
>> Subject: Re: Versioning vs Temporal modeling of Patient State
>> On Jan 12, 2007, at 9:36 AM, dirk.colaert@agfa.com wrote:
>>> Recently I had an interesting conversation with Werner Cuesters,
>>> professor in Bufallo and colleague of Barry Smith. He has some
>>> theory about ontology maintenance and versioning and it considers
>>> both "classes" and "instances". Both can change either because you
>>> made en error, either you view on the world changed, either because
>>> the world changed . It turns out that you can only handle changes
>>> if you know for each change exactly what de reason of the change
>>> was. That reason should be documented in the system.
>> [snip]
>> The standard lingo for this is that a change to the knowledge base
>> due to a change in the *world* is called an *update* whereas a change
>> in your knowledge base due to a change in *your knowledge* of the
>> (current static) world is called a *revision*. The locus classicus
>> for this, IMHO, is:
>> 	<http://citeseer.ist.psu.edu/417296.html>
>> Following there model theoretic accounts, there is a spate of work
>> defining reasoning services that compute the updated or revisied
>> knowledge base given a proposed update or revision. E.g., recently:
>> 	<http://lat.inf.tu-dresden.de/~clu/papers/archive/kr06c.pdf>
>> The utility of model oriented revision and update for expressive
>> logics is, IMHO, not fully established, though it is conceptually
>> useful in my experience. There is, of course, a large chunk of work
>> on revising (and even updating) belief *bases*, that is, attending
>> primarily to the *asserted* set of formulae.
>> Hope this helps.
>> Cheers,
>> Bijan.

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
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

Received on Friday, 12 January 2007 12:40:35 UTC

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