[Fwd: Re: [seek-kr-sms] ontology/folder UI design in Kepler]

[Shawn Bowers]

I think the problem was that cmaps let you put the terms into what you 
thought was a hierarchy, but actually wasn't ... i.e., the gui of cmaps 
  is very misleading and doesn't actually help one model the domain (it 
just lets you draw "boxes" and "lines")

In terms of my "completely changing the way it was organized", I have to 
disagree slightly.  I made some additional observations after you 
clarified your responses to some questions I asked of your original 
cmap.   I think though, that the original cmap you sent was much more 
enlightening than my "rearanging" ... it highlighted some interesting 
relationships / views on the terms, and also spurred some conversations 
on how we can provide useful modeling tools/guidelines.

In fact, as Mark pointed out, even some simple "ontology creation 
guides" (i.e., modeling pitfalls, good practices, etc.) may be extremely 
useful. As are examples, I think.

In terms of your question as to what ontologies are needed -- I think 
it's been pretty clear: The best way to figure out what ontologies are 
needed is to move case by case, then generalize. We should also keep in 
mind the applications we're shooting for (i.e., data discovery and 
integration) -- here are two datasets x and y, here is the ontology 
needed to describe x and y, do we have enough information to usefully 
move towards integrating them? no ... ok, what else is needed ... etc. 
Alternatively, how might one "reuse/discover" x and y, and would the 
query they ask find them?

We shouldn't forget too that much of what Rich did is generally 
applicable, but maybe needs some "refactoring/simplification" to make it 
more "digestable".



Shawn



> hoping that we will work through some examples in Davis, because no, BEAM (that
> would be me) is not constructing ontologies on their (my) own.  I looked at
> Rich's ontologies this summer, and played with some concept maps for the
> biodiversity case, but I think we need to be much more explicit about what is
> needed.  I could (and have) spent a good deal of time coming up with things that
> aren't particularly useful.  The only meetings that BEAM is now having are in
> conjunction with other teams (like the KR/SMS/BEAM meeting in Davis), so if you
> want ecologists to develop these, you need to work it in the agenda.  If we get
> to the point where I have a good sense of exactly what ontologies are needed,
> then I would be happy to recruit some ecologists for a working meeting focused
> on ontology generation, as long as there is someone there who can ensure that
> what we come up with fits the formal requirements.
> 
> Deana
> 
> 
> 
> Quoting Bertram Ludaescher <ludaesch at ucdavis.edu>:
> 
> 
>>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)
>> > _______________________________________________
>> > 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)