From: Werner C. in S. <wer...@ec...> - 2005-09-07 07:38:13
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> Regarding the example above, I'm not sure how I would go about > differentiating themes from patient participants. An entity playing a theme role did not undergo any change during the process. This is typical for motions. A patient does undergo change. > > derives_from is a relation between two continuants - what I would like to > know is the nature of the relation between "plasmatocyte differentiation" > and the continuant "plasmatocyte" If the plasmocyte actively changes itself, it is "agent", otherwise "patient" >> > If we consider it to be a participant, then surely the precursor is >> > also a participant. In this case our class level relation should >> > discriminate between these variations of participation (although we >> > can actually obtain this from the derives_from relation between the >> > two continuant classes, this is a little awkward) >> >> No, it is not awkward. The same entity can enjoy different sorts of >> participation in the same process. See my example above. > > So are you saying it is sufficient to state the following in the ontology > > "plasmatocyte differentiation" has_participant "plasmatocyte" > "plasmatocyte differentiation" has_participant "hemocyte precursor" > "plasmatocyte" derives_from "hemocyte precursor" > > (in fact the second fact can be derived from the other two) yes. And possibly changes has_participant in has_agent or has_patient whatever is the case > In this particular example, there is no loss of knowledge, but this may > not always be the case, see "cysteine biosynthesis" below > > Even in the above example, there is no loss of knowledge, but the > situation from the point of view of a user browsing the ontology I share Alan Rector's view that the "model of use" is different from the ontology. First build the ontology right, then worry about how the user may want to browse through it. >> > An analagous example would be "cysteine biosynthesis", which has less >> > debatable temporal boundaries. Is cysteine a participant in its own >> > manufacture? If not, what is the appropriate relation to use? >> >> There is some process through which a cysteine molecule is created. The >> molecule starts to exist at a certain time, build out of other >> components. >> Again, I think that here the transformation and derivation relationships >> can >> be used, but to be sure, I must first check what cysteine is composed of. > > I don't think so - we just can't have class-level binary derives_from > relations between most molecular entities, because different pathways in > different species matbolise things in different ways I was not talking at class-level yet. But the species argument isn't a good one. Then we can always differentiate between species-X-cysteine-biosynthesis, etc >> Well, has_agent is still a very general relationship. There are more >> detailed causally involved participatient kinds such as "instrument", >> "enabler", "catalyst", "hamperer", "preventer", ... (I'm just giving some >> names to make the issues clear). >> >> > An example illustrating the agency/non-agency participation >> > distinction: "neuroblast activation". Here the neuroblast is a >> > participant in the activation, but without agency (it is the thing >> > being activated). >> >> hence "patient" right > > OK, it looks like we have one very definite outcome of this discussion so > far, which is the addition of a new relation to our ontology. > > If patient is the opposite role to agent, would this new relation be > called "has_patient", in opposition to has_agent? I think this name would > trip a few people up - hence my suggestion of "has_inactive_participant" I don't care that much about names, as long as the definitions are clear. The names that I give below are the standard ones in semantic role theories What we need are additional roles for: PATIENT: the role played such the entity playing that role is not actively driving the process but undergoes some change ENABLER: the role played such the entity playing that role is neither AGENT, neither PATIENT but is required to participate or the process would not happen INSTRUMENT: the role played such the entity playing that role is used by the AGENT to carry out the process, but the AGENT's action is not directed towards it. > To summarise: > > Can we have relations between GO and cell for classes such as "T cell > proliferation" without _explicitly_ invoking an ontology of populations? No. But introducing a high level entity which is collection or aggragate or something alike is not difficult. Thomas Bittner wrote a paper on it. > What is the more specific relation to use in processes such as > proliferation, metabolism and the participating continuants? There are a few: see my list above. Werner |