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Can you detail how it simplifies things? Do we still need occurrent versus
continuants relations? What
Kinds of inference and queries does it support? How is continuity between a@t1
and a@t2 established at the instance level - I.e how do we know they are both
'a' and determine rigid values, such as name or species.
Original comment by alanruttenberg@gmail.com
on 4 Feb 2013 at 4:03
It simplifies things because if we assume generical relatedness as the default
in existing OBO ontologies (according to the interpretation of relations in OBO
syntax), then the migration would be straightforward. Whoever wants to restrict
the relation to "at some time" can do it by postcoordination as demonstrated in
the example.
In my opinion this approach is compatible with one, e.g. part-of relation. It
is always binary, as between continuants it can only be used if the continuants
are temporally qualified. To prevent the linkage between continuants and
occurrent, one axiom suffices: Occurrent subClassOf part-of only Occurrent
It supports transitivity in its standard use case, but the combination of a
transitive relation with the "at some time" relation is no longer transitive,
as expected.
Continuity between a@t1 and a@t2 at the instance level assured because the
instances are not referred to as a@t1 or a@t2 but just as a
In a triplet representation it would look like
< a has-timestamp t1>
< a has-timestamp t2>
But it is not straightforward. I don't have a clear solution - but it is also
unclear how it should look like if we use temporalized relations, e.g.
< a has-part-at-some-time b>
< a has-part-at-some-time c>
How would you introduce timestamps here?
I think in both cases we need to introduce blank nodes which would correspond
to sth like a@t1
I haven't tested it, but one could make the following assertions (using the
standard example human as a rigid class and student as an anti-rigid class):
Student subClassOf Human
Student subClassOf 'at some time' some (not Student)
Not sure what are the consequences of it, I haven't tested it.
But I guess nobody expects that we solve the rigidity problem with a simple OWL
formalism. Perhaps if we move further to some kind of fourdimensionalism, but I
guess that this is not agreeable
Original comment by steschu@gmail.com
on 4 Feb 2013 at 11:18
It doesn't support sound inference of transitivity. Any entailment of
transitivity is unsound unless the times align in all models. Since
transitivity is inferred whether or not that is known, and as in any case in
which it is unknown it is possible to create a set of assertions in which the
times do not align, an entailment of transitivity in such a case would be
unsound.
It would be as if in the current BFO2 draft part-of-at-some-times was asserted
to be transitive.
Original comment by alanruttenberg@gmail.com
on 5 Feb 2013 at 4:04
I think this approach is promising. Maybe Stefan could flesh out some more
examples (tqc2.owl is a little abstract!).
It would be great to this proposal embedded in CLIF somehow. This would be for
purposes of clarification and validation, users would not see the CLIF.
Failing that examples and counterexamples are good. Alan, can you give an
example of unsound inference of transitivity entailed by this model.
My intuition is that this proposal aligns well with the RO 2005 paper (I think
this is what Stefan means when he says "interpretation of relations in OBO
syntax").
Original comment by cmung...@gmail.com
on 5 Feb 2013 at 5:09
Failing that examples and counterexamples are good. Alan, can you give an
example of unsound inference of transitivity entailed by this model.
Add
TimeInstant subClassOf TemporalInterval
t1 instanceOf TimeInstant
t2 instanceOf TimeInstant
t1 differentFrom t2
a1 hasTimeStamp t1
b1 hasTimeStamp t2
A = {a1}
B = {b1}
Now despite the fact that we have said that
- There is only one instance of A:a1
- There is only one instance of B:b1
- a1 doesn't exist at the same time as b1 (they are atSomeTime distinct time instants)
The same inference as before is found: A is determined to be a subclass of
HAS_CONTINUANT_PART_SOME_C
This inference disappears (and the ontology makes sense again) if you remove
the transitivity axioms on has_part, part_of
So: The transitivity is incorrectly inferred in this case.
Original comment by alanruttenberg@gmail.com
on 5 Feb 2013 at 6:05
These axioms extend tqc2.owl, correct?
Is it not the case that the inference is valid but the ontology is
inconsistent? Unfortunately we can't detect the inconsistency, noted by Stefan:
"However, OWL cannot avoid invalid statements such as
rel (continuant1@T1, continuant2@T2) with T1 =/= T2"
[there may be some practical techniques we can use detect some of these
inconsistencies]
Are there examples of incorrect inferences that start from a coherent set of
axioms?
You say "This inference disappears (and the ontology makes sense again) if you
remove the transitivity axioms on has_part, part_of" - but how does the
ontology make sense, if two TQCs from different times are connected via part_of?
Original comment by cmung...@gmail.com
on 5 Feb 2013 at 6:30
BFO OWL cannot solve all temporal reasoning problems when dealing with instance
data.
Also temporally qualified relations relating instance data are problematic, e.g.
NOW: StefansHeart part-of-all-times StefansBody
This statement has no timestamp attached. It will be invalid if I die tomorrow
and my heart is transplanted.
With TQCs, we would get from the upper level ontology 'x rdf:Type bfo:TQC' for
each instane x that is used with some continuant-to-continuant relation. The
test for temporal consistency would have to occur outside DL, anyway.
Original comment by steschu@gmail.com
on 5 Feb 2013 at 7:42
See a draft version of the pre-Graz BFO2 (without temporalized relations)
enhanced by 'temporally qualified continuant', 'at some time', and a value
restriction for entity
http://code.google.com/p/bfo/source/browse/trunk/src/ontology/owl-schulz/bfo_tqc
.owl
Original comment by steschu@gmail.com
on 5 Feb 2013 at 8:10
However, OWL cannot avoid invalid statements such as rel (continuant1@T1, continuant2@T2) with T1 =/= T2"
Are there examples of incorrect inferences that start from a coherent set of axioms?
You say "This inference disappears (and the ontology makes sense again) if you remove the transitivity axioms on has_part, part_of" - but how does the ontology make sense, if two TQCs from different times are connected via part_of?
This is a somewhat fair criticism. I will construct an example that doesn't
have this problem - it only needs to arrange temporal regions in which misalign
a
-----
b
-----------
c -----------
This is not an implausible biological scenario during development.
There is a difference between not being able to detect inconsistencies
(incompleteness) and deriving incorrect entailments (unsoundness)
As an example, inconsistent OWL will not be detected by RDF reasoning. But
entailment in OWL will not derive any unsound by RDF inferences.
We may accept incompleteness. We can't accept unsoundness.
Regarding transplantation, this is a problem with the assertions made by
canonical anatomy ontologies. If you are suggesting that the TQC approach
allows a straightforward way to design anatomy ontologies that both preserve
transitive part hood, and also allow for transplantation, please show how.
Original comment by alanruttenberg@gmail.com
on 5 Feb 2013 at 12:13
Surely the issue is one of specifying the circumstances for which a modelling
approach is applicable. Transitive 'part of' + inverse 'has part' make perfect
sense, but only if modelling the aspects of some class of continuant that do
not change over time.
As an example: VFB currently only models static aspects of (canonical) adult
Drosophila brain anatomy. Our queries rely on transitivity of parthood, both
directly and in the derivation of axioms on relations. We would lose lots of
perfectly correct and useful inference if we eliminated transitivity of
parthood.
Original comment by dosu...@gmail.com
on 5 Feb 2013 at 1:28
Important: in terms of OWL (I wouln’t make an ontological claim here),
if x is an non-TQC continuant and x@t1 a temporally qualified one then x =/=
x@t1
In RDF:
<x; rdf:Type; X>
<x; 'at some time'; x@t1>
<x; 'at some time'; x@t2>
< x@t1; 'has timestamp'; t1>
< x@t2; 'has timestamp'; t2>
Part-of transitivity, in its most general form can be expressed by the
following rule using temporalized triples:
<x@t1; 'part of';y@t1>
<y@t1; 'part of';z@t1>
------------------------------
<x@t1; 'part of';z@t1>
Outside OWL we need to check the validity rule:
IF <x@t1; rel ; y@t2> and t1=/=t2, THEN triplet is invalid
The reason ist that the triplet corresponds to the quadruple
< rel, x, y, t1>
This quadruple has only one time argument
Re: consistency check of temporalized triplets:
tentative OWL axiom:
TemporalInstant subClassOf isTimeStampOf only ((not TQC) or TQC and (rel some
(TQC and hasTimestamp Self)))
(not tested yet)
Original comment by steschu@gmail.com
on 5 Feb 2013 at 2:06
I'm wondering about whether this axiom
entity subClassOf
topObjectProperty only
('temporally qualified continuant' or occurrent)
is valid OWL2.
If it is note that this precludes having inverses of relations that go from
(continuant and not tqc) -> tqc, as the inverse would violate the global
restriction on topobjectproperty.
I suspect there will be other issues around that.
I've asked Uli Sattler about this, and to discuss the two approaches - she
should be available next week,
Original comment by alanruttenberg@gmail.com
on 5 Feb 2013 at 4:07
AR: The condition is too strong.
SC: Part-of transitivity, in its most general form can be expressed by the
following rule using temporalized triples:
<x@t1; 'part of';y@t1>
<y@t1; 'part of';z@t1>
------------------------------
<x@t1; 'part of';z@t1>
AR: You aren't specifying what it means to say x@t1. If t1 is an interval, do
you mean x@t1 'part of' z@t2 is true
a) *Only* when t1 and t2 are the same?
b) as long as t1 part of t2? (this is the sense of RO 2005)
c) at any ti that is part of t1 and part of t2?
The general case is:
<x@t1; 'part of';y@t2>
<y@t3; 'part of';z@t4>
------------------------------
According to a)
t1=t2 and t3=t4 else invalid.
only if t1=t3 is it the case that <x@t1; 'part of';z@t1>
according to b)
Notation: '<' = 'part of'
t1 < t2 or invalid
t3 < t4 or invalid
If t2 < t3 then <x@t1; 'part of';z@t1>
otherwise there is nothing inferred.
According to c)
if not exists(ti) ti < t1 and t1< t2 then invalid (t1 and t2 don't intersect)
if not exists(ti) ti < t3 and t1< t4 then invalid (t3 and t4 don't intersect)
Otherwise
if exists(ti) z < z < t1 and z< t2 and z< t3 and z < t4 then
x@ti 'part of' y@ti
otherwise no inference should be made.
SC: Outside OWL we need to check the validity rule:
IF <x@t1; rel ; y@t2> and t1=/=t2, THEN triplet is invalid
AR: It looks to me that the check is more complicated than that. Also, if you
always have to have t1=t2 then that severely limits the biology you can
describe, no?
Original comment by alanruttenberg@gmail.com
on 5 Feb 2013 at 4:08
SC: Outside OWL we need to check the validity rule:
IF <x@t1; rel ; y@t2> and t1=/=t2, THEN triplet is invalid
AR: It looks to me that the check is more complicated than that. Also, if you
always have to have t1=t2 then that severely limits the biology you can
describe, no?
CM: probably. E.g. we probably only want to perform this test for some rel in a
set of temporally qualified relations. E.g. it would be valid to have some
relations (e.g. transormation_of) connect across times.
Original comment by cmung...@gmail.com
on 5 Feb 2013 at 4:26
STEFAN: I was looking for literature about the problem how instance data can be
temporalized. The only approach which is referred to repeatedly is to reify
object properties.
In our case it would mean:
<p1; rdf:Type; Parthood>
<p1; Whole; y>
<p1; Part; x>
<p1; Time; t1>
<p2; rdf:Type; Parthood>
<p2; Whole; z>
<p2; Part; y>
<p2; Time; t1>
I don't see any way do get the desired inference be DL reasoning here.
Original comment by steschu@gmail.com
on 6 Feb 2013 at 2:01
It seems that this thread is no longer active, but I suppose the issue is not
settled. Would TQC be a reasonable feature to include into the OWL version of
BFO 2? Or can the OBO community cope with the temporally qualified relations
suggested thus far?
Original comment by steschu@gmail.com
on 26 Feb 2013 at 7:44
The OBO community is fairly diverse. I think the reification approach would not
be acceptable but this may not be required for TQCs. I'm not sure the tracker
is the best place to hash this out - I'd like to see more concrete examples in
OWL and some FOL showing the translation.
Original comment by cmung...@gmail.com
on 28 Feb 2013 at 2:25
The reification approach would not be required for TQCs. I just mentioned it
because it is often regarded as the standard approach for expressing n-ary
relations in OWL. It has the problem that it is complex (especially in case it
is expected to support transitivity) and will probably not be well accepted by
the user community.
Original comment by steschu@gmail.com
on 4 Mar 2013 at 10:17
Original issue reported on code.google.com by
steschu@gmail.com
on 4 Feb 2013 at 3:54