[Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler]
Bertram Ludaescher
ludaesch at ucdavis.edu
Tue Mar 1 12:49:57 PST 2005
Hi Deana et al:
I guess it's a good time to chime in now, including to throw in some
thoughts from a KE and SEEK SMS (and KR) point of view =B-)
First, the intuitive ontology tool that Deana asked about is already
there (although Shawn and I haven't done a particular good job of
making it available yet). It's the goose feather, oops, I meant the
Sparrow language ;-)
Here is what we had in mind: in our context, creating domain-specific
ontologies is primarily about defining controlled vocabularies. We
might use fancy GUIs for it, or just the keyboard to type in the
controlled vocabulary terms:
measurement.
species_abundance.
biodiversity_index.
biomass_measurement.
ok, you can see how a keyboard is useful for entering controlled
vocabulary terms (unlike, e.g., a mouse). From this to a "formal"
ontology (at least in the sense used earlier in this thread) it is a
small step. E.g., you might want to say that
"biomass measurements are measurements"
Then we should be able to say just that. In fact that's almost valid
Sparrow syntax; exactly we would write (note the small differences):
biomass_measurement ISA measurement.
This is human readable, easy to enter, edit, exchange and parse as
well. Oh, and it can be translated easily into OWL so that other tools
can work with it.
A slightly more complex example is:
"biomass measurements are measurements that only measure biomass"
In Sparrow (goose feather ;-) syntax we would have to slightly tweak
this into the following form:
biomass_measurement ISA measurement AND item_measured ONLY biomass.
So what Shawn meant earlier about "formal ontologies" is this level of
refinement/sophistication that we are after. The good thing about the
notation above (as opposed to just nodes and arrow diagrams) is that
these statements can be translated into OWL (or directly first-order
logic) and provide some constraints about how a biomass measurement
relates to measurements in general, what is being measured etc.
We also need to keep in mind, as was mentioned earlier, that ontology
creation is not what the typical end user of Kepler should be doing.
Ontologies are meant to be created by the *scientific community* (in
this case ecologists) using specialized tools and this process is
often done in concert with the (in)famous KE / KR/CS types
who can provide additional tools to check the consistency of so defined
ontologies, visualize the inferred class hierarchy etc.
But the (passed around) buck does stop there: at the willingness of
the community to actually come up with controlled vocabularies and
simple, but somewhat formal (in the above sense) ontologies.
So I think we do need to create more of those ontologies. Isn't BEAM
doing that? Or who else? Someone should.. we can certainly help.
Let's also see how Kepler and ontologies and all that good stuff
relates (some of this was suggested before, eg. by Laura):
- Kepler is NOT the primary tool to develop, change, update
ontologies. For that there is GrOWL, Protege, and yes Sparrow (it's
built into any OS.. we just need to send you again the simple grammar)
- Kepler should have mechanisms to *annotate* actors (as a whole),
their ports, and datasets. This should normally NOT require changes to
the ontology. Rather one would simply *select* concept names from one
of possibly several pre-defined community ontologies (importing
different ontologies into Kepler should be easy)
- For expert users only: If you feel that you need to define a new
concept on top of an existing ontology, you should be able to do that
as well from Kepler. Clearly, you are not updating the community
ontology (there is a "protocol" for the latter, one needs endorsement
from a consortium such as "Eco-GO" ;-) but rather you are adding to
your "private ontology extensions" much like you would add new words
to your private dictionary in Word ("Add foobar to your private
ontology (y/n)?"). My earlier suggestion would be to be able to define
a new concept in this way, e.g.
my_measurement ISA biomass_measurement AND hasLocation davis.
Then my_measurement and davis might be new concepts which are added to
my personal ontology (along with the Sparrow statement/axiom above),
whereas the other terms come from the existing ontology.
OK, so much for now.
cheers and laters
Bertram
Deana D. Pennington writes:
>
> Shawn,
>
> I think we can use our own experiences to clarify what an ecologist might or
> might not be able to do, at least in the near term. In the few times that I've
> tried to organize a set of terms into an "ontology" for you, and in the times
> I've watched the postdocs/faculty try to do it, none of us have ever given you
> anything remotely close to what you needed. That's definitely a concern, if
> we're going to have the ecologists do it themselves. I honestly don't think
> you're going to get what you want from most ecologists without substantial
> training. I think the likelihood of them going after such training is small.
> Its telling that many of the people at this last workshop took offense when I
> suggested that it would be a good idea for them to learn how to program...and
> the usefulness of that should have been much more obvious to them than the
> usefulness of creating ontologies. I think we are a long way from having a
> community of ecologists who have the skills or desire to invest considerable
> effort learning how to do this. Perhaps eventually we will develop a community
> of ecoinformatics people who are more on the domain side than the IT side, who
> can learn how to do this and work at the interface. For the short term, I don't
> see any way around having a "knowledge engineer" work with the ecologists. But,
> I reserve the right to change my mind when you demonstrate an ontology tool that
> is, in fact, easy to use for a domain person :-)
>
> Deana
>
>
> Quoting Shawn Bowers <sbowers at ucdavis.edu>:
>
> >
> > Some comments:
> >
> > Laura L. Downey wrote:
> > >>Shawn writes:
> > >>I think that this is (or at least was) exactly one of the "missions"
> > in
> > >>SEEK: to get scientists involved in creating and using *formal*
> > ontologies.
> > >
> > >
> > > Using formal ontologies, yes. I have definitely seen some excitement
> > when
> > > semantic mediation has been talked about in a way that will make their
> > jobs
> > > easier -- of finding other data sets they would not otherwise have
> > found,
> > > when identifying actors that would be useful to them that they
> > otherwise
> > > might not have identified etc. And yes, creating the ontologies
> > themselves
> > > too, because they know their domains better than we do, but formally
> > > specifying them so that machines can make use of them? I'm not so sure
> > about
> > > that from what I've seen. But again, remember I'm new to the project
> > so
> > > bringing an outsider perspective and maybe one that needs to be more
> > > informed.
> >
> > I think "formally specifying ontologies" is a loaded phrase ... it is
> > being used to refer to the languages (such as OWL) and tools (such as
> > Protege) that have known deficiencies not only for "domain scientists"
> >
> > but also in general for capturing knowledge. OWL is a W3C specification
> >
> > that is based on XML and is overly verbose (being expressed in XML) and
> >
> > often misused. It is really just an interchange format, and not really a
> >
> > language unto itself (it's meant to encompass many languages so as to be
> >
> > a good middle-ground for tools that use disparate languages). Protege
> >
> > is a tool that is still young and is just starting to be more widely
> > used. It is, however, in many ways still designed for a very small,
> > highly technical user group.
> >
> > Ontology tools should be such that they present a sound and intuitive
> > user model (i.e., the conceptual constructs used to create ontologies),
> >
> > shielding the user from the underlying interchange format. Most tools
> > that are out there essentially present a low-level graphical version of
> >
> > the language, not of these higher-level conceptual constructs. A counter
> >
> > example is CMAP, however, it's model in my opinion is too unconstrained,
> >
> > and offers little support in terms of helping users to create
> > well-designed and "consistent" ontologies.
> >
> > I also think this notion that a domain scientist will "informally"
> > construct an ontology and then pass it off to a "knowledge engineer" to
> >
> > "make it formal" is (a) not a scalable solution, (b) "passes the buck"
> >
> > to an unknown entity (i.e., the non-existent "knowledge engineers"), and
> >
> > (c) in general, is not always a sound approach. (I'm not picking on you
> >
> > here Laura -- these are just some observations; and I'm trying to
> > stimulate some discussion as to what the approach should be for SEEK.)
> >
> > I think in SEEK, this notion of a knowledge engineer has been used in
> > place of providing useful tools to our users. I think if anything, the
> >
> > "knowledge engineer" should be built into the tool -- which is starting
> >
> > to emerge in some other tools, including protege.
> >
> > I think that the challenge in defining a "formal ontology" for a
> > particular domain is that as a user: (1) you need to have a clear
> > understanding of the domain, the concepts, their definitions (very
> > challenging in general), and (2) you need to understand how to represent
> >
> > this information in the knowledge representation language/tool. If a
> > domain scientist gives the knowledge engineer the first item (1), then
> >
> > the scientist could have just as well input the information in a
> > well-designed ontology tool. If the knowledge engineer gives a vague and
> >
> > imprecise description of (1), then the knowledge engineer has no chance
> >
> > of doing (2). My argument is that to "create ways for regular users to
> >
> > provide the appropriate input to the knowledge engineers so that items
> >
> > are formally specified" essentially means that the "regular users" have
> >
> > already specified the ontology -- and they don't need the KE (of course
> >
> > this could be an iterative process, where the KE "holds the hand" of the
> >
> > scientist through the process -- which is again not going to scale and
> >
> > is probably not that practical).
> >
> > Of course, not only do we want to make (2) easy, we also want tools to
> >
> > help scientists/users get to (1). I think there are lots of ways to help
> >
> > users get to (1), e.g., by:
> >
> > - describing a process/methodology, like in object-oriented analysis and
> >
> > design that can help one go from a fuzzy conceptualization to a clearer
> >
> > model (we want to target scientists, however, instead of software
> > designers/developers)
> >
> > - providing tools to help people "sketch" out their ideas before
> > committing to an ontology language (but make it explicit that they are
> >
> > doing the "sketch" as part of a process) ... e.g., by allowing some
> > free-text definitions mixed with class and property defs, etc.
> > Essentially, provide a tool that can facilitate someone to go from
> > informal/unclear to formal/clear.
> >
> > - adopting some known approaches for "cleaning up" an ontology (similar
> >
> > to OntoClean, e.g.)
> >
> > - providing tools that can identify inconsistencies and possible
> > "pitfalls" in the ontology (useful for getting to a clearer, more formal
> >
> > model)
> >
> > - providing lots of examples of "well-defined" ontologies
> >
> > - letting people edit and reuse existing well-formed ontologies (in
> > fact, I think that once we have a basic framework, this will be the
> > typical model of interaction for many scientists ... )
> >
> >
> > In terms of "machine understandable ontologies", this really just means
> >
> > that the ontology is captured in one of these ontology languages, like
> >
> > OWL. It doesn't mean that a scientist should have to literally put
> > their ontology into this language -- that is the job of the tool. Our
> > goal should be to help users specify ontologies using "structured"
> > approaches. That is, essentially in restricted languages that are not
> >
> > as ambiguous and not as unconstrained as natural language -- which is
> > typically done using graphical tools (box and line diagrams). Also, the
> >
> > user should be completely unaware that their definitions are being
> > stored in these low-level languages; which is why the existing tools
> > fail for domain scientists / non computer-science folks.
> >
> >
> >
> >
> > > Is the goal here to figure out a way to allow scientists with no
> > formal
> > > ontology experience to easily specify formal ontologies in a way
> > that
> > > machines can make use of them? That seems like a daunting task to me
> > -- and
> > > one that would require considerable time and resources. Didn't I just
> > read
> > > from Mark (in the IRC convo) that the knowledge engineers themselves
> > have
> > > trouble with their own tools like Protégé? Creating and specifying
> > formal
> > > ontologies is a complex and challenging job even for those trained in
> > it.
> > >
> > > I agree that scientists understand their domains better than others,
> > but
> > > that doesn't mean they understand how to formally represent that
> > domain in a
> > > way that can be utilized by a machine. They user their own
> > experience,
> > > intuition, and knowledge to create ontologies. They make decisions
> > and
> > > understand possible exceptions. But that is a different task than
> > formally
> > > specifying that ontology to a rigid set of rules that can be utilized
> > via
> > > machine processing. I'm thinking that is still a task to be done by
> > a
> > > trained knowledge engineer.
> > >
> > > And if we create ways for regular users to provide the appropriate
> > input to
> > > the knowledge engineers so that items are formally specified in such a
> > way
> > > that the system can make use of them to the benefit of the regular
> > users, I
> > > would see that as a definite win and demonstration of the power of
> > semantic
> > > mediation to make scientists jobs easier.
> > >
> > > Laura L. Downey
> > > Senior Usability Engineer
> > > LTER Network Office
> > > Department of Biology, MSC03 2020
> > > 1 University of New Mexico
> > > Albuquerque, NM 87131-0001
> > > 505.277.3157 phone
> > > 505.277-2541 fax
> > > ldowney at lternet.edu
> > >
> > >
> > >
> > > _______________________________________________
> > > seek-kr-sms mailing list
> > > seek-kr-sms at ecoinformatics.org
> > > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms
> >
> > _______________________________________________
> > seek-kr-sms mailing list
> > seek-kr-sms at ecoinformatics.org
> > http://www.ecoinformatics.org/mailman/listinfo/seek-kr-sms
> >
>
>
>
> **************************
> Dr. Deana D. Pennington
> Long-term Ecological Research Network Office
>
> UNM Biology Department
> MSC03 2020
> 1 University of New Mexico
> Albuquerque, NM 87131-0001
>
> 505-277-2595 (office)
> 505 272-7080 (fax)
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> seek-kr-sms at ecoinformatics.org
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