Re: "factoring out" in the construction of FuGO = the search for "universals"

P.S.: Of course, this whole issue is also very much what Matthias  
Samwald seeks to address in the biO zen ontology framework as well  
(http://neuroscientific.net/index.php?id=43)

On Jul 8, 2006, at 12:55 AM, William Bug wrote:

> Hi All,
>
> I think after following these discussions over the last few weeks  
> about use of ontologies and bridging of ontologies on SW projects,  
> I have to say, I believe the "impedance mismatch" on what different  
> folks mean by ontology and the practical use for ontological  
> resources is way to great to address via email.  As I've said in  
> several neuroinformatics ontology meetings, we really need to start  
> off by agreeing on an ontological framework for the concept ontology.
>
> I'm loathe to say this, but maybe this whole issue should be tabled  
> for an F2F meeting.
>
> I really wouldn't want this issue to hold up the real work the  
> HCLSIG has already begun to make useful progress on.  My only fear  
> is these fundamental differences may in fact be incommensurable.
>
> As to the issues Xiaoshu refers here, I think "factoring out" and  
> "modularizing" are two very distinct issues here.
>
> The "factoring out" Trish refers to has a very specific meaning in  
> the current practice of ontology development embodied in the OBO  
> Foundry principles.  It relates to the search for ontological  
> "universals" that can be used to create a subsumption 'is_a'  
> hierarchy.  This approach to formal KR has been very effective both  
> in formal ontological philosophical domains, as well as in AI (see  
> Rodney Brooks' Subsumption Architecture) and computational  
> linguistics.  In the particular case of the foundational ontology  
> being used here (BFO), a continuant (or endurant as labeled in  
> other formalisms) means "entities in the world that endure through  
> time: entities which persist self-identically even while undergoing  
> changes of various sorts" (please see section "1.3 Continuants and  
> Occurrents" in "Biodynamic Ontology" [http://ontology.buffalo.edu/ 
> medo/biodynamic.pdf]).  Similar core entities are defined for other  
> foundational ontologies, though the ontological commitments  
> incurred by using a specific foundational ontology can be quite  
> different (e.g., BFO vs. DOLCE).
>
> To use the example you have chosen, for an anatomist to want to use  
> FuGO and be ontological compatible, they need only use an ontology  
> founded on the same definition of continuants & occurents.  How  
> does this differ from what I think you are claiming.  An anatomist  
> need not necessarily care about the details of FuGO entities  
> bearing no relation to data they intend to semantically integrate  
> with (such as 'LC_instrument') to remain fundamentally compatible  
> with FuGO.  They only need agree on the definition and use of the  
> foundational levels of the ontology they share in common - in this  
> case 'Continuant', 'Independent_ continuant', and 'Object'.  In  
> fact, this would be encouraged by the OBO Foundry participants -  
> use FuGO for formal semantic descriptions of assay/instrument/ 
> reagent provenance and use the Foundational Model of Anatomy to  
> deal with anatomy (right now, just human anatomy, but that is being  
> worked on) - both of which are founded on BFO.
>
> The "modularization" you refer to via namespaces relates to a  
> conceptually different issue, as I see it.  Even though the use of  
> namespace - especially in XML & RDF - has advanced to something  
> considerably beyond its original application of simply avoiding tag/ 
> term/name "collisions", the "modularization" namespaces can support  
> in XML space is distinctly different from the "factoring out" of  
> universals to which Trish referred.
>
> Using the namespace facility inherent in XML formalisms might be a  
> useful way of enabling people to exchange different world views for  
> sub-regions of the graph, that's true.  But it is by no means a  
> requirement.  One should still expect whether or not you are using  
> namespaces to chop up or modularize different portions of the  
> ontological graph, you are still following the same principle of  
> extrapolating to universals, even if the universals for  
> "namespace_a"'s coverage of the cardinal parts of a liquid  
> chromatographic apparatus differed from the universals defined for  
> "namespace_b"s coverage of the cardinal parts of a liquid  
> chromatographic apparatus .
>
> If namespaces were used as the primary means of "factoring out"  
> universals, you could end up with quite a proliferation of  
> namespaces for FuGO - in the extreme - one for every node in the  
> graph.
>
> It may be of some use to separate the different ontological sources  
> using namespaces.   For instance, there may be some utility to  
> specifying the BFO elements in their own namespace, so as to  
> clearly separate those entities created by the FuGO group, and  
> those derived directly from BFO.  In the end, however, the ontology  
> construction performed by the FuGO group is very much wedded via  
> subsumption to the many ontological commitments made in BFO, so  
> it's not clear to me there would be anything to gain from doing  
> this, apart from making the layers separable for curatorial  
> purposes.  For instance, if FuGO v1.0 is build off BFO v1.0, having  
> them in separate namespaces may be useful should a new new v1.1 of  
> BFO be released.  Migrating FuGO v1.0 to use BFO v1.1 could be  
> easier to do, if they were namespace distinct, but, of course, in  
> doing so, the altered nature of the ontological contract would  
> require you to bump the version of FuGO once you've done this AND  
> probably perform quite a bit of manual review to determine whether  
> the FuGO graph is still valid when linked to v1.1 of BFO.
>
> This is an issue we've begun to examine on the BIRN Ontology Task  
> Force.  The BIRNLex knowledge resource we are constructing has an  
> even more complex relation to a variety of external community  
> ontologies, including BFO, FuGO, FMA, PaTO, etc.
>
> My sense of what you are trying to do with O3 is to separate the  
> intensional conceptualzation from the lexicon used to extend this  
> view of the world into a specific application space - for instance,  
> providing a URI for the concepts in the ConcreteOntology.  I am a  
> strong proponent of separating the lexicon from the ontological  
> graph.  Having said that, most of the OBO Foundry ontologies are  
> using terms to label the nodes in the graph just to make them more  
> human readable.  At least where the basic "factoring out" process  
> is concerned, the goal is not to swayed by the lexicon when  
> constructing the ontological graph, and in that sense, they are  
> already separating the extensional view of the semantic network  
> from the intentional conceptualization.
>
> As to the issue of ComplexOntology vs. LocalOntology as you  
> describe it, I think this is very much at odds with the OBO Foundry  
> approach.  All OBO Foundry ontologies are ComplexOntologies in that  
> they are all being adjusted to build off the BFO.  Even more  
> troublesome is the fact these foundational biomedical ontologies  
> are MEANT to be used to create more complex ontologies and DL  
> frameworks through coordination via the OBO Relation Ontology.   
> That would make all ontological development being encouraged by the  
> OBO group break the model you are recommending for maximal ontology  
> re-use and ease of knowledge map integration.
>
> It's also possible O3 is more commensurate with DOLCE than BFO, in  
> which case, I suppose mapping what you describe here to the OBO  
> Foundry principles would require much more thought (and may, in  
> fact, not be possible).
>
> I wish I could understand what you describe at http:// 
> www.charlestoncore.org/ont/2005/08/o3.htm a little better.  I found  
> your Nature Biotech. paper very clear and extremely helpful in  
> several discussions I've been having on the issue of XML vs. RDF,  
> but I really am having a hard time with your description of O3 on  
> that web page.  Is there a publication where you go into this in  
> more detail?
>
> Cheers,
> Bill
>
> On Jul 7, 2006, at 4:02 PM, Xiaoshu Wang wrote:
>
>>
>> Trish,
>>
>>> Comments inline.
>>>
>>>>> Based on that work, I'd like to follow Eric N's penchant for
>>>>> "strawmen" and propose the following amendments to the Proposed
>>>>> Classes to give focus to the discussion:
>>>>>
>>>>> Project
>>>>> Study
>>>>> Hypothesis
>>>>> ...
>>>>
>>>> I honestly think before making the list, we should think about how
>>>> ontology should be modulized and how to develop ontologies
>>> on various
>>>> granualities. I would suggest to start with an ontology
>>> that has a very coarse granuality.
>>>> And developing more detailed ontologies one step at a time.
>>> This is the idea behind FuGE and to some degree FuGO. The
>>> development of FuGE is an effort to factor out the re-usable
>>> bits of modelling an experiment that can be used to describe,
>>> in particular any functional genomics experiment, but perhaps
>>> some sections could be extended to other types of
>>> experiments?. The concepts that AJ has included seem to be
>>> fine with respect to having something to test the proof of
>>> concept of the idea and technology for linking/searching the
>>> data. One thing that may need to be added is something to
>>> indicate the type of experiment so that searches can be
>>> limited in some way. The ways to go about typing the kind of
>>> experiment are many so if needed, that can be left for future
>>> discussions. Depending on how fine grained this effort goes,
>>> perhaps there is some benefit in joining this work to what
>>> has been done, at least with functional genomics experiments,
>>> to develop data standards and exchange formats as these
>>> efforts represent the granularity needed by the community.
>>
>> When I mean "factoring out", I mean by grouping terms under different
>> namespaces.  I just take a brief overlook on FuGO, just taking the  
>> first
>> look that "LC_instrument" is under the same namespace of "continuant"
>> already tells me there is no modulization whatsoever.  (Please  
>> correct me if
>> I am wrong).  If I were an anatomist, who will conduct experiment,  
>> but never
>> care about LC_instrument.  But if I want to use FuGO's continuant,  
>> I would
>> have to buy in the concepts of LC_instrument as well.  Now, what  
>> about some
>> physicist, electrical engineer, do each scientific community  
>> should they
>> ever want or forced to accept LC_experiment?
>>
>> To factor it out, for example, you need to break it at least into two
>> ontologies. One top generic concepts and one lower domain specific  
>> ones.
>> So, at least, people can share the top one without forced to take  
>> the bottom
>> one.  But the right way in my suggested methodology would be at  
>> least be
>> three.  For the simple case, there needs to be at least three: two
>> LocalOntologies + one Profile (see my classification of ontologies  
>> and what
>> I mean by ontology normalization at
>> http://www.charlestoncore.org/ont/2005/08/o3.html). By this way,  
>> if a lower
>> level ontologies want to realign its relations to another high-level
>> ontology, a new profile can be created to associate them.  The  
>> rational for
>> the basis of
>> ontology normalization is to separate ontologies' dependency so  
>> they can
>> gracefully evolve over time... I will stop here.  Otherwise, I  
>> would have to
>> put out my entire manuscript to make it clear.
>>
>> FuGO, in its current form, would be unable to handle the  
>> evolutionary, let
>> alone the revolutionary change of its ontological terms.
>>
>>>> Using ontology implies that if you want to use one assertion of an
>>>> ontology, you must agree to all assertions made in the ontology. A
>>>> detailed monolithic ontology is what we should avoid. I
>>> have thought
>>>> of this problem for quite a while.  The BOSS ontology
>>>> (http://www.charlestoncore.org/ontology/boss) that I
>>> created only has
>>>> a three classes (Study, Protocol and Data) and three pairs
>>> of inverse
>>>> properties.  (Please trust me, I am not trying to promote the BOSS
>>>> ontology here.) What I have really hoped is that we should
>>> think how the ontologies will be shared before start building
>>> the ontology.
>>>>
>>>> The same issue also goes to the overlap between FUGO with
>>> the proposed
>>>> self-descriptive experiement ontology. In fact, I think all
>>> biological
>>>> related ontology will perhaps touche on the topic of
>>> experiment in one
>>>> way or the other.  Hence, if each ontology's designers don't factor
>>>> out their ontology design, the eventual result will be a bunch of
>>>> overlapping monolithic ontologies.
>>
>>> The overlap with the self-descriptive experiment ontology is
>>> actually with both FuGE and FuGO. FuGE provides a model to
>>> capture common components of investigations and to provide a
>>> framework to capture laboratory workflows. FuGO is being
>>> designed to provide a source of descriptors for the
>>> annotation of investigations. The scope of FuGO includes the
>>> design of an investigation, the protocols and instrumentation
>>> used, the data generated and the types of analysis performed
>>> on the data. FuGO is not to model any of these particular
>>> items, but to provide annotation terms as needed by the
>>> collaborating communities. Of course terms/classes will be
>>> needed in the ontology to properly fill out the is_a hierachy
>>> and create needed relationships between classes. Therefore,
>>> in the FuGE model there will be a reference to use an
>>> ontology term from some source and in some cases this will be
>>> FuGO that contains the term. In other cases where an existing
>>> ontology has already been designed, e.g. Foundational Model
>>> of Anatomy, a term from this ontology will be used. FuGE
>>> provides a mechanism to state which ontology the term was
>>> obtained from so this will be present.
>>
>> Hiearchy is not modulization.  A tree is a tree, unless its  
>> braches can
>> exist independently.  Whether an ontology is structured or not,  
>> btw, which
>> ontology does not have a structure? has nothing to do with if the  
>> ontology
>> is monolithic or not.
>>
>> Xiaoshu
>>
>>
>
> Bill Bug
> Senior 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 - William.Bug@DrexelMed.edu
>
>
>
>
>
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Bill Bug
Senior 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 - William.Bug@DrexelMed.edu







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