[#1251] 'astronomical body part' - change parent #1252
Conversation
… material entity'
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I heartily approve this, but a high level change requires consensus - what do you think @pbuttigieg, are we ready for this? |
dr-shorthair
changed the title
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I ask the question what benefit do we get from keeping My understanding of |
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Makes sense to me, but I am open to hearing counter arguments |
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I think that would be over-interpreting 'fiat object part', it says nothing
about 2D boundaries. But this serves to illustrate that there is a lot of
subjective interpretation in these BFO classes! (that the definitions are
subjective is not a novel observation -- there has been a debate about
boundaries and granularities in BF for as long as I can remember...)
If there *is* some property relating to boundaries that we feel is
important for some use case, then one compromise would be to instead assert
this as a has-characteristic axiom at whatever level of ENVO we feel
appropriate. But I am not sure even this is necessary.
…On Wed, Nov 24, 2021 at 2:45 PM Simon Cox ***@***.***> wrote:
@dr-shorthair <https://github.com/dr-shorthair> requested your review on:
#1252 <#1252>
'astronomical body part' - change parent .
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@cmungall I'm certainly no expert but I was getting that from the elucidation of fiat object part. Again I'm not sure what this buys us to continue including it in ENVO.
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ah yes, my mistake, sorry! but the point remains, if it's important for users to be able to know which terms in ENVO represent things with fiat 2D boundaries we could add this as a property. |
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I'm not sold on this - as we have seen time and again, most geographical entities are delimited by fiat, and different communities will set different boundaries (coasts, riparian zones, ...). Including different definitions to align with different community usages means we should acknowledge the fiat nature of the boundaries. |
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I suppose that depends on whether you see
as a fiat choice. I agree that different communities will set different rules and supporting observations. But the general sense is that a delimitation that emerges from rules that are designed to encode natural phenomena is qualitatively different to a rule that is based on drawing an arbitrary line on a map/landscape. On the other hand, if there is no 'natural' delimitation, then is there any partition of space that is not fiat? In which case 'fiat' is not a particularly useful distinction. |
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Seems to me that there is a subjective continuum between what is 'fiat' and things that have 'hard' boundaries. Perhaps the distinction is based on the degree to which multiple observers would all agree on the same boundary. Consensus being the criteria for 'hard' boundaries, and valid alternate interpretations being the criteria for fiat: some authority makes a decision abut the interpretation that will be used. So the boundary of the 'Empire State building' (as a non-fiat example) and the boundary of the Rhine River flood plain (fiat--requires adoption of one interpretation of 'floodplain' and the available observation evidence). Can ontological distinction be made between an 'object' (non-fiat, there is consensus, or close enough, about its boundaries) and 'fiat objects', with boundaries based on interpretation of entity definition and observation evidence. In this view, there are likely astronomical body parts that are 'objects' and parts that are 'fiat objects'. |
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FWIW, there seems to be unending debate about these matter. E.g., see Barry Smith and Mark Do Mountains Exist. |
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@wdduncan thanks for the reference - I vaguely recall seeing it before, but now I have a more immediate interest in the question. Nevertheless, I agree with your proposition that the classification 'fiat' is not useful unless it assists reasoning. Since http://purl.obolibrary.org/obo/BFO_0000024 currently has no axioms, then it currently does not. I'm generally skeptical of the utility of any sub-class that doesn't formally differentiate itself from the parent. |
I mostly agree with this too. I think there is probably some value in keeping the BFO term as it add a differentia to humans readers, but it does not add anything to machine systems or reasoning capabilities. Perhaps I could suggest two possible options?
Thoughts? |
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Not sure if Seems simpler to classify entities under Do we have any clear examples of fiat objects? military training area may be such a case, since its boundaries are decided upon by fiat. Note, this sense of 'fiat' is different than entities having fuzzy boundaries, which is how Smith et al. using the term 'fiat'. |
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On Thu, Dec 2, 2021 at 7:24 PM Bill Duncan ***@***.***> wrote:
If we want to classify mounts, deserts, caves, etc. as fiat objects, it
would be useful if the fiat nature served some purpose in terms of
reasoning. Currently, fiat object doesn't seem to serve such a purpose.=
Exactly! It should serve some purpose. Reasoning is one of many possible
use cases
Another use case might be that curators may find it useful to separate fiat
objects from true objects. However, this is not true of any curator I know
Maybe there is some other purpose for these upper level divisions we are
not aware of?
I always like to think of ontologies in terms of genetics, and consider
doing a "deletion test". What is the phenotype of deleting an axiom from an
ontology?
If an axiom can be deleted and it doesn't affect any computational use, or
any use by human beings, and doesn't affect any projected future use, and
if the ontology can be simplified by deleting the axiom, then it should be
deleted.
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On Fri, Dec 3, 2021 at 12:10 AM Kai Blumberg ***@***.***> wrote:
Nevertheless, I agree with your proposition that the classification 'fiat'
is not useful unless it assists reasoning. Since
http://purl.obolibrary.org/obo/BFO_0000024 currently has no axioms, then
it currently does not. I'm generally skeptical of the utility of any
sub-class that doesn't formally differentiate itself from the parent.
I mostly agree with this too. I think there is probably some value in
keeping the BFO term as it add a differentia to humans readers, but it does
not add anything to machine systems or reasoning capabilities.
Which human readers are served by this differentia? Perhaps there is a
community of ENVO users I am not aware of, but I am not aware of any way in
which this philosophical subjective distinction serves either end-users or
those of us editing the ontology
Perhaps I could suggest two possible options?
1.
keep BFO:0000024 but add an axiom to it presumably linking to BFO:two-dimensional
continuant fiat boundary <http://purl.obolibrary.org/obo/BFO_0000146>
It is bad practice to inject axioms into someone else's ontology
See: OBOFoundry/OBOFoundry.github.io#1443
The route to go here is to request the upstream ontology to make the
change. If the upstream ontology is not able to respond to community
requests in a reasonable way, then we need to consider whether we want a
dependency on that ontology. Every dependency has a combination of benefits
and costs, in this case the costs may be higher than the benefits.
But I think your proposal can be adapted, see below
1.
@cmungall <https://github.com/cmungall>'s compromise suggestion of
dropping BFO:0000024 but instead "assert this as a has-characteristic
axiom at whatever level of ENVO we feel appropriate ... relating to
boundaries that we feel is important for some use case[s]"
Yes. The exact nature of the axiom is not particularly important, so long
as it doesn't interfere with the hierarchy
If the intended recipients of the axiom are humans, then we should add this
as an annotation axiom. For example, a rdfs:comment may be perfectly
appropriate
If the intended recipients include machines, then we should add as a
logical axiom. This could be something like 'has-characteristic some fiat',
where fiat itself has complex axioms pertaining to boundaries. This would
have no loss of reasoning power (in fact there are hooks for far more
reasoning power, as has been observed the current axiom in ENVO is
entailment-silent).
Or it could follow your suggestion above, only we would place the axiom on
the ABP class rather than injecting into BFO
E.g.
1. ABP SubClassOf material entity
2. ABP SubClassOf has_part some BFO:two-dimensional continuant fiat
boundary <http://purl.obolibrary.org/obo/BFO_0000146>
This is logically much better than the current ENVO axioms because we are
explicitly linking to the most relevant BFO class.
It is also far superior from a UX perspective, it simplifies the hierarchy
and doesn't alienate users (most ontology browsers will show axiom 2 above
in a side panel rather than part of the hierarchy)
I still don't think it passes the deletion test, but this seems like a
reasonable compromise
… |
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On Fri, Dec 3, 2021 at 6:23 AM Bill Duncan ***@***.***> wrote:
Not sure if has characteristic would work as an axiom. Perhaps something
like has part some continuant fiat boundary
<http://www.ontobee.org/ontology/BFO?iri=http://purl.obolibrary.org/obo/BFO_0000140>
might work too. But, such a change should be communicated with the BFO
editors for feedback.
exactly - but seem my suggestion to move this axiom down to ABP
Seems simpler to classify entities under material entity rather than
wading into murky issues about what fiat boundaries are.
Yes, yes, yes!!!! it's a philosophical quagmire/minefield, and takes us
into discussions that serve no use case for the ontology
(do quagmires and minefields have fiat boundaries?)
Do we have any *clear* examples of fiat objects? military training area
<http://www.ontobee.org/ontology/ENVO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FENVO_00000561>
may be such a case, since its boundaries are decided upon by fiat. Note,
this sense of 'fiat' is different than entities having fuzzy boundaries,
which is how Smith et al. using the term 'fiat'.
I have no idea what objective criteria to apply to decide whether an ENVO
class is fiat or not.
Why are planets considered objects? Isn't the earth's atmosphere part of
the earth? Where is the boundaries of the earth? Why isn't everything fiat?
(note: this is rhetorical - I don't think there is a useful answer to the
above question)
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Are we all in agreement that ABP should be moved under |
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@pbuttigieg how would you feel about @cmungall's suggestion of removing
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I can only support the proposal to ignore the distinction between fiat object part and object. The question, what characterizes an object, is an open question (I think, the question is not, what a fiat object part is, but rather what a bona fide object is). BFO 1.0 has characterized object and fiat object part in reference to fiat and bona fide boundaries, with the latter being defined as mind-independent demarcations (i.e., they exist independent of any human partitioning activities) that rest on some physical discontinuity or qualitative heterogeneity. The problem with the second criterion (physical discontinuity & qualitative heterogeneity) is that these are very much granularity dependent - at some granularity level, every physical entity becomes a fiat object part. I have discussed this problem here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048603 As a consequence of this critique, in BFO 2.0, the focus has been changed from boundary types to causal unity. But this is still work in progress, I think, because you still find some reference to boundaries (see elucidation for fiat object part). Also,the list of causal unity types suggested in BFO 2.0 is confined to a synchronic approach to causal unity that is associated with a spatio-structural frame of reference - it does not take the dynamic nature of reality into account. I think, a human heart is a functional unit and thus, in a functional frame of reference, a bona fide functional object that exists independent of any human partitioning activities. In the same way, I can demarcate developmental units and evolutionary units. As a consequence, further causal unity types must be added to the list. The main problem here, however, is, that a given entity can be both a fiat object part and a bona fide object, depending on which frame of reference one is applying: spatio-structurally, the human heart is a fiat object part, but functionally it isn't. If you are interested in this discussion, you can read about it here: Since this is all very complicated to manage and communicate to users for annotation purposes, I agree with the suggestion to take a pragmatic approach and ignore the categories of object and fiat object part and add respective information as axioms where needed, thus making this classification an implicit one. |
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Any update on this? |
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@pbuttigieg your thoughts? |
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Can we finish this one? |
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I'll consider the arguments and make a decision for the next release in the next few days. |
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Implementation: 🚧 In progress 🚧
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Do you have a sense of where it impacts, in practice? I totally agree that it is critical not to break things. |
How we write definitions, classes and branches where boundaries matter and have fiat and/xor non-fiat components, the need to identify what kind of fiat boundaries exist (for axiomatisation but also to link with environmental authorities and capture how humans manage environmental systems).
Where the boundaries of a part of something like Earth are declared by fiat. A marine protected area, chunks of the planet designated for weapons testing (as noted above), etc.
This can be said of many upper-level terms that are in wide use. It's also not the primary objective: representation of knowledge is a greater priority relative to whether or not some reasoner understands it (yet). If we define useful subclasses of the fiat boundaries (e.g. designated by national authorities), then this changes |
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I don't think anyone is arguing that fiat objects don't exist. Rather, the issue that the default operating procedure seems to be that every astronomical body part is categorized as fiat, and this is too strong (for reasons already stated). |
Yes, that has been demonstrated. |
So, are you arguing that every |
Hmm. I think I can see where @pbuttigieg is going here. When considering natural spatial entities, the envelope is inevitably arbitrary, or at least strongly determined by the discipline or application, or scale. But perhaps the distinction is really a BFO question, and not an ENVO issue. |
Sure. I think things like Earth's left hemisphere and geopolitical regions (e.g, cities) are fiat objects. However, I doubt that most scientists think of geographical features like lakes and archipelagos as being fiat objects (at least not in the sense in which Earth's hemispheres are fiat). Something to think about: what is the principle at work for defining an organic group as a material entity, but defining an archipelago as a fiat object? Given the difficulties of rigorously defining of what it means to be a fiat object (aside from clear acts of human intention), I think it is better to default to defining things like lakes and mountains (an other astronomical body parts) as material entities. At least that way you aren't saying some wrong. That is, all fiat objects are material entities, but not all material entities are fiat objects. This (I think) will make the ontology more clear to the community. If someone wants an entity to be a fiat object, we should make the reasons why really clear: that is, in what sense is the object being defined merely by human convention? |
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@wdduncan you answered the inverse question. As @pbuttigieg has argued, and I agree, pretty much every material entity in the natural world is strictly a fiat-object, when considering some applications and scale. What I want to know is if there are any material objects that do not (arguably) have fiat boundaries? If the answer is no, then the classes are identical and we don't need the distinction. |
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In BFO materialEntity has subclasses 'object', 'fiat object part', and 'object aggregate'. Making 'astronomical body part' a subclass of materialEntity dodges the whole (subjective, context-dependent) problem of distinguishing an 'object' from an 'object part' or 'object aggregate' (is a forest an object, object part or an object aggregate?) ABP meets the axiom for materialEntity |
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Hello all - it is Sunday (here), but ontology never rests, I suppose . Can't do a point-by-point, and tapping away on a smartphone, but here's a sense of where I'm headed, informed by the exchange above.
I'm doing some ontosurgery to set the basis for the above. We'll run with that for the next release and see where it gets us. |
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@dr-shorthair Sorry if I didn't understand your question/point. There are (IMHO) never ending arguments about this. I think it comes down to what you mean by 'fiat'. I think a reasonable way to think of a fiat object is that it is an object whose boundary exists b/c of human convention. This is not perfect, but I think it is good enough. Having a fiat boundary is not exactly the same as having fuzzy boundaries (at some level of scale), or being capable of being divided in some arbitrary fashion. |
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@pbuttigieg if you're going down that road, you could bite the non-BFO bullet: materialEntity
Objects have parts that are necessarily other objects an astronomical body part is an object that is part of an astronomical body (which is an object). Most APBs would probably be fuzzy objects. object aggregation: this needs some discussion-- is it a bunch of disconnected objects (a forest), or an object with many parts (an automobile). Call the mereology team. |
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Let me try and summarize where we are at with this. I know there are a lot of side issues going on, but I want to focus solely on this PR which is to change the parentage of ABP to from fiat object part to material entity. I believe we have achieved consensus on this issue. On Aug 28, @pbuttigieg says:
So we are all in agreement, ABP should be under material entity. This is the entire scope of the PR. @pbuttigieg also says:
it looks like the last release is https://github.com/EnvironmentOntology/envo/releases/tag/v2021-05-14, a year and a half ago. If we are all in agreement, I don't see a reason to block this PR on other unscoped work? |
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I'm not done with my edits - apologies for the delay, but I don't want to lose the process so far |
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We are approaching the 2nd anniversary of this PR @pbuttigieg - it looks like you have a separate PR going: It looks like this introduces a new intermediate class "fiat part of an astronomical object" in between ABP and BFO:FoP. This is an improvement as it introduces a within-ENVO grouping, but I don't think it addresses the concerns raised on this PR. New structure: 
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I think we've addressed this in recent merges |
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from 'fiat object part' to 'material entity'
Fixes #1251