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bridge CHEBI:role to BFO:role
In GO there is an axiom: role EquivalentTo role
This equates the role class in CHEBI to the one used in RO, and catches cases when chemical roles (specifically dependent continuants) are accidentally used as chemicals (material entities).
When I merge several OBO ontologies together, like GO, Uberon, MP, and HP, I often run into disjointness violations with use of chemical roles. Generally this is because this bridging axiom is randomly placed in GO and not imported into other ontologies.
Can we add this axiom to RO? It would be nice to have this shared across all these ontologies. Maybe this will be the sort of thing COB is used for down the road, but this is an immediate problem and RO is a nice central place.
I'm putting an example explanation for one of these problems in the next comment.
aminoaciduria EquivalentTo Nothing
-
aminoaciduria SubClassOf aciduria
-
aciduria EquivalentTo has part some
(increased amount and (inheres in some
(acid and (part of some urine))) and (has modifier some abnormal))
-
acid SubClassOf chemical role
-
chemical role SubClassOf role
-
role EquivalentTo role
- role SubClassOf realizable entity
-
role EquivalentTo role
-
chemical role SubClassOf role
-
urine EquivalentTo excreta and (produced by some kidney)
-
excreta EquivalentTo organism substance and (output of some excretion)
-
organism substance SubClassOf part of some multicellular organism
-
multicellular organism SubClassOf multicellular anatomical structure
- multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular)
-
multicellular organism SubClassOf multicellular anatomical structure
-
organism substance SubClassOf part of some multicellular organism
-
excreta EquivalentTo organism substance and (output of some excretion)
-
acid SubClassOf chemical role
-
aciduria EquivalentTo has part some
(increased amount and (inheres in some
(acid and (part of some urine))) and (has modifier some abnormal))
- part of o existence starts during or after SubPropertyOf: existence starts during or after
- independent continuant DisjointWith specifically dependent continuant
Axiom Impact
Axioms used 1 times
- role EquivalentTo role [go-base.owl]
- aciduria EquivalentTo has part some (increased amount and (inheres in some (acid and (part of some urine))) and (has modifier some abnormal)) [mp-base.owl]
- excreta EquivalentTo organism substance and (output of some excretion) [uberon-base.owl]
- urine EquivalentTo excreta and (produced by some kidney) [uberon-base.owl]
- multicellular anatomical structure EquivalentTo anatomical structure and (has quality some multicellular) [uberon-base.owl]
- realizable entity SubClassOf specifically dependent continuant [bfo-classes-minimal.owl]
- role SubClassOf realizable entity [bfo-classes-minimal.owl]
- acid SubClassOf chemical role [chebi.owl]
- chemical role SubClassOf role [chebi.owl]
- aminoaciduria SubClassOf aciduria [mp-base.owl]
- anatomical structure SubClassOf existence starts during or after some zygote stage [uberon-base.owl]
- organism substance SubClassOf part of some multicellular organism [uberon-base.owl]
- multicellular organism SubClassOf multicellular anatomical structure [uberon-base.owl]
- independent continuant DisjointWith specifically dependent continuant [bfo-axioms.owl]
- existence starts during or after SubPropertyOf: relation between physical entity and a process or stage [ro.owl]
- relation between physical entity and a process or stage Domain independent continuant [ro.owl]
- part of o existence starts during or after SubPropertyOf: existence starts during or after [uberon-base.owl,ro.owl]
Ontologies used:
- bfo-axioms.owl (http://purl.obolibrary.org/obo/ro/bfo-axioms.owl)
- uberon-base.owl (http://purl.obolibrary.org/obo/uberon/uberon-base.owl)
- chebi.owl (http://purl.obolibrary.org/obo/chebi.owl)
- bfo-classes-minimal.owl (http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl)
- go-base.owl (http://purl.obolibrary.org/obo/go/go-base.owl)
- mp-base.owl (http://purl.obolibrary.org/obo/mp/mp-base.owl)
- ro.owl (http://purl.obolibrary.org/obo/ro.owl)
One question we should look at before I fully endorse this is why exactly the axiom is not imported from go. Is it in go or go plus?
It's in go-base.owl (and go-plus.owl). It's not in go.owl; I don't think folks should be importing from go.owl if they're doing cross-ontology work, because it filters out all external references.
So maybe that’s the right thing to do, move to go plus across the board? Is there anything speaking against that?
On Fri, 18 Jun 2021 at 21:25, Jim Balhoff @.***> wrote:
It's in go-base.owl (and go-plus.owl). It's not in go.owl; I don't think folks should be importing from go.owl if they're doing cross-ontology work, because it filters out all external references.
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@matentzn not sure I follow - @balhoff said it was in go-plus already?
But in any case, I think this is moot, it doesn't belong in GO. See: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1443 (and see my comment from 3 days ago about the relationship between injected axioms and base files, which seems to me to be undefined).
I like Jim's pragmatic suggestion of moving this to RO. Obviously CHEBI is the correct place, but we know that it is hard for CHEBI to provide axioms like this. RO is a good substitute as it is fairly central. I think we should follow the practice recommended in the injection ticket, and tag it as an intentional injection, and we could get CHEBI's "signature" on it.
But let's look at the deeper problem here: over-enthusiasm in use of BFO. We are constantly seeing these kinds of issues caused by over-used of BFO classes instead of plain common-sense classification. One characteristic of these issues is that the tests to find them are highly brittle (as is in evidence here), and frequently manifest themselves downstream where they become hard and costly to debug.
Let's look at this example with CHEBI modeling "acid" as a role. If we were following common-sense, we would model "acid" as a chemical entity and not a role, as per every definition of acid, ever, e.g
- https://goldbook.iupac.org/terms/view/A00071
- https://en.wikipedia.org/wiki/Acid
In fact even the text definition in CHEBI itself says this is a molecular entity:
- https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_37527
- An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
If ontologies really want to over-ontologize and represent ordinary things using confusing BFO classes, this should be clearly signified in both the label and the definition. E.g. "acid role". But really the most sensible thing to do here is just model it consistent with the text definition: a molecular entity that is capable of X.
It's time we in OBO stopped setting ourselves pointless crossword puzzle reasoning exercises that consume a lot of time and energy and focused on solving real problems. We must simplify our ontologies and avoid pointless costly abstractions that don't solve actual biologists' needs.
@cmungall I totally agree with your points. However it seemed a lower barrier task to slip this axiom into RO rather than ask for a reworking of the CHEBI hierarchy. 😅 But probably we've been avoiding the real issue for too long. Given that experienced ontology editors make this "mistake" over and over again, it's probably not the right model.
Do you think the situation is as clear-cut for "hormone"? That's another one which frequently causes trouble.
I agree with all you say: fwiw, my whole point was that maybe, instead of pulling from go.owl, all our ontologies that refer to go should instead use go-plus; but obviously yeah your points go much deeper than that. so then, so what should we do then? organise meeting with chebi and ask them to reconsider the role branch?
On Mon, 21 Jun 2021 at 00:31, Jim Balhoff @.***> wrote:
@cmungall https://github.com/cmungall I totally agree with your points. However it seemed a lower barrier task to slip this axiom into RO rather than ask for a reworking of the CHEBI hierarchy. 😅 But probably we've been avoiding the real issue for too long. Given that experienced ontology editors make this "mistake" over and over again, it's probably not the right model.
Do you think the situation is as clear-cut for "hormone"? That's another one which frequently causes trouble.
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@balhoff I brought this up again in the COB repo here https://github.com/OBOFoundry/COB/issues/169
Instead of pulling from go.owl, all our ontologies that refer to go should instead use go-plus
I strongly support this. It will massively improve integration and co-ordination. It is particularly important for phenotype ontologies where patterns commonly define compound entities using GO-consistent patterns.
On the broader ticket - it makes sense for bridging axioms such as the one discussed in this ticket to live in an upper ontology. Not sure whether it makes sense for them to live only in COB - forcing any ontology who wants it to adopt broader COB commitments.
It happened again (https://github.com/obophenotype/human-phenotype-ontology/issues/7224) so I opened a PR: #528
This is already in COB
https://github.com/OBOFoundry/COB/blob/a2f7141c1e30e87352cb656a224fd31027d92701/src/ontology/components/cob-to-external.tsv#L107-L108
