Issue 15 in bfo: domain and range of 'is preceded by'/'precedes' too narrow?
b...@googlecode.com
Owner: ----
Labels: Type-Defect Priority-Medium
New issue 15 by dosu...@gmail.com: domain and range of 'is preceded
by'/'precedes' too narrow?
http://code.google.com/p/bfo/issues/detail?id=15
domain and range of 'is preceded by', precedes and their child properties
is currently process. But shouldn't this be occurrent?
Here're the current definition:
occurrent: An entity that has temporal parts and that happens, unfolds or
develops through time. Sometimes also called perdurants.
process: A processual entity that is a maximally connected spatiotemporal
whole and has bona fide beginnings and endings corresponding to real
discontinuities.
SubClassOf: occurrent
----
A process must have 'bona fide beginnings and endings corresponding to real
discontinuities', but if i subdivide a process or any other occurrent into
fiat temporal parts, surely they will stand in 'is preceded by' relations
to each other.
Pierre Grenon
defined relation
in an axiomatisation of BFO, temporal order is primitive for time and
there are straightforward, almost trivial, and standard definitional
extensions for any temporal entity (e.g. if two occur at particular
times, the temporal order between the occurring entities follows that
between the corresponding temporal regions)
its credible that in an OWL encoding you would want to have vocabulary
that is notionally defined but for which the encoding contains no
definition
> --
> You received this message because you are subscribed to the Google Groups
> "BFO Discuss" group.
> To post to this group, send email to bfo-d...@googlegroups.com.
> To unsubscribe from this group, send email to
> bfo-discuss...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/bfo-discuss?hl=en.
>
>
b...@googlecode.com
Comment #1 on issue 15 by dosu...@gmail.com: domain and range of 'is
http://code.google.com/p/bfo/issues/detail?id=15
Pierre Grenon replied on BFO discuss:
Selected post Jun 23, 2011; 12:22pm
Re: Issue 15 in bfo: domain and range of 'is preceded by'/'precedes' too
narrow?
Pierre Grenononline
b...@googlecode.com
Comment #2 on issue 15 by dosu...@gmail.com: domain and range of 'is
http://code.google.com/p/bfo/issues/detail?id=15
Clairification:
- this comment refers to the version of BFO found using
http://purl.obolibrary.obo/bfo.owl , which resolves to:
http://bfo.googlecode.com/svn/trunk/src/ontology/bfo2.owl
Older versions may be better in some respects, but do not have the Foundry
compliant BFO URIs I need.
Also - I'm posting this on the BFO google code tracker
http://code.google.com/p/bfo/issues/detail?id=15. I would prefer answers
on this tracker ticket rather than on BFO discuss - or whatever other
mailing lists this might be forwarded to.
Cheers,
David O-S
b...@googlecode.com
Comment #3 on issue 15 by dosu...@gmail.com: domain and range of 'is
http://code.google.com/p/bfo/issues/detail?id=15
Hi Pierre,
Thanks for your reply. I'm afraid I'm rather struggling to follow it. The
problem I have is a simple practical one with the domain and range defined
for this object property: http://purl.obolibrary.org/obo/BFO_0000063 (may
not resolve - probably better to browse to it in Protege after loading
http://purl.obolibrary.obo/bfo.owl). I don't understand why domain and
range are specified as process, rather than occurrent. This choice has
practical implications for my ontology of Drosophila development, for which
I would like to use this object property. I believe that the
relation/object property I am currently using is equivalent to the BFO one,
but I use it between stages. Following the BFO definition for process and
ocurrent, I classify stages as occurrents rather than processes as stages
may have fiat temporal boundaries.
Hope this is now clearer,
David
b...@googlecode.com
Comment #4 on issue 15 by pierregr...@gmail.com: domain and range of 'is
http://code.google.com/p/bfo/issues/detail?id=15
hiya, sorry for the admittedly cryptic first reply, let me try again
I think what you experience is a need for a defined term, but it is not
something that motivates modifying primitive vocabulary. In my
understanding, the file you are accessing and using is a snapshot of a
proposed reference encoding of the basic (!) BFO (BFO2 at that). So it
should contain primitive vocabulary but not all sorts of possible
definitional extensions.
Procedurally, I would argue this file should be kept minimal and if need be
an extended, distinct version with useful extensions be maintained
concurrently. It is likely such an extended version would prove more useful
to many but it is a different sort of work to find the right balance. This
being said there are obvious candidates for straightforward extension, like
the one you mention.
Meanwhile, the quick fix would be to just make this extension in your
ontology: add a super property to BFO2's 'precedes', call it something
like 'my generic precedes', and set domain and range on occurrent. You
could even set them on entity, but it'll be a bit tricky to make sense of
that and could be trickier to axiomatise in OWL.
b...@googlecode.com
Status: Done
Owner: janna.ha...@gmail.com
Comment #5 on issue 15 by janna.ha...@gmail.com: domain and range of 'is
Domain and range for precedes and its inverse, is preceded by, are now
`occurrent' in the current working version of BFO 2.
b...@googlecode.com
Comment #7 on issue 15 by alanrut...@gmail.com: domain and range of 'is
In BFO2 the distinction between processes, processual entities, and fiat
process parts, so David's objection is moot. The current proposed
definition (which I object to because of the use of s-depends)
is "Definition: p is a process = Def. a is an occurrent that has temporal
proper parts and s-depends on one or more material entities. [083-001]".
However resolution of my objection would not change this matter.
The problem with widening the domain and range to occurrent is that it
sanctions precedes relations between, for example, a spatiotemporal region
(which is an occurrent) and a process. That doesn't make any sense at the
moment, and to make it have sense would take work. If the only objection to
process as domain and range is based on David's argument, there is no
reason to change anything. Otherwise a new issue should be raised with the
further objection. I propose this issue be closed with the resolution that
the domain and range be process.
Note: There is no single current working version of BFO2. Janna's remark
refers to the version
https://bfo.googlecode.com/svn/trunk/src/ontology/owl-schulz/bfo.owl r207
b...@googlecode.com
Status: Accepted
Comment #8 on issue 15 by alanrut...@gmail.com: domain and range of 'is
(No comment was entered for this change.)
b...@googlecode.com
Comment #9 on issue 15 by alanrut...@gmail.com: domain and range of 'is
Raised issue regarding BFO2 reference as it doesn't currently define this
relation.
https://groups.google.com/forum/?fromgroups#!topic/bfo-devel/xlkp7_mHq8c
b...@googlecode.com
Comment #10 on issue 15 by dosu...@gmail.com: domain and range of 'is
Far enough. I brought this up because I've been treating stage as a
sibling of process defined as 'any temporal subdivision of a process that
is not itself process.' The idea being that a processes have clearly
defined beginings and ends.
I guess this is arguable though. For context: this comes from wanting to
treat developmental stages as distinct from the processes they subdivide.
Developmental stages are temporal slices of developmental processes
(embryogenesis, oogenesis, wing disc development) defined for the
convenience of easy scoring.
b...@googlecode.com
Comment #11 on issue 15 by dosu...@gmail.com: domain and range of 'is
Fair enough. I brought this up because I've been treating stage as a
sibling of process.
Here's the definition of process that I took from Alan's OWL file and is
still present in Stefan's:
process: A processual entity that is a maximally connected spatiotemporal
whole and has bona fide beginnings and endings corresponding to real
discontinuities.
fide beginnings and endings corresponding to real discontinuities.'
The reason I brought this up is that I use preceded_by extensively (and
v.usefully!) between developmental stage terms. Developmental stages are
based on the timing of appearance or disappearance of easily score-able
structures. So, developmental stages are not, by the above definition,
processes.
I would prefer a solution that keeps stage as a disjoint sibling of
process, as I think this mirrors that way biologists think about it and so
will be useful for error checking. Given that, we need to broaden the
range of preceded_by, even if not to 'occurrent'.
b...@googlecode.com
Comment #12 on issue 15 by alanrut...@gmail.com: domain and range
Hi David,
It's not surprising that owl-ruttenberg has a stale definition - see above
and many other advertisements. But that definition is apparently no longer
on the table. There are a couple of points to make
a) We obviously need to understand and then work with a new version of the
definition of process. Coming to that definition is not a matter for the
OWL effort - it is an issue with BFO2 Reference. Note that the proposed
BFO2 reference does not have a term 'processual entity'.
b) If you have no contest to the current definition, then I'd offer that
this isn't a BFO issue. Rather you could, if desired, define two subclasses
of process corresponding to (I guess) the whole of an organism's life, and
a stage of their life (proper temporal part of the whole). It is unclear
whether, for your purposes, would need any different definition of
preceded_by than is defined for BFO, but that's a matter for you
(developmental anatomists) to sort through.
b...@googlecode.com
Comment #13 on issue 15 by dosu...@gmail.com: domain and range of 'is
Hi Alan,
Taking it outside of BFO might work. But first I want to check -
Given:
Definition: p is a process = Def. p is an occurrent that has temporal
embryogenesis, oogenesis and 'wing disc metamorphosis' and also every
possible temporal slice of these processes?
If this is the case, then I would still want at least 'developmental
process' and 'developmental stage' as disjoint sibling SubClasses of
process, defined along the lines I've already discussed. But it surprises
me that others would not be interested in this as a general distinction.
b...@googlecode.com
Comment #14 on issue 15 by haen...@ohsu.edu: domain and range of 'is
I am not up to date on this discussion, but I wholeheartedly agree with
David that we need a precedes relation between occurrents that have fiat
boundaries to represent stages. This cannot be in an extended file or a
quick fix - if we don't have this in a core BFO release, the anatomical
ontologies will not use BFO (and in fact most do not now for this and other
reasons).
Is there a requirements document outlining the anatomy needs? It would seem
this would be helpful to ensure they are met.
b...@googlecode.com
Comment #15 on issue 15 by alanrut...@gmail.com: domain and range
Hi David,
As I said, I don't like the current BFO2 Reference definition. One of the
reasons is that I have no way of formally evaluating your question, because
I don't think an s-depends relation between occurrents and continuants
makes any sense. Second, I don't like having (or not) temporal parts as a
differentia because being a temporal part seems more of a formal ontology
sort of thing rather than a physically grounded kind of thing.
That said, I think it is the intention that the term subsume your cases.
Those classes, then, should, IMO, go in some more specific ontology
(perhaps CARO? GO?) .
Regarding fiat and bona fide boundaries of processes, I don't know how to
determine this distinction on process boundaries, so I personally wouldn't
want there to be such a distinction. I think the right abstraction has to
do with whole organismal lives versus proper parts of them.
Melissa, the proposal isn't to put preceded_by in a separate file, but
rather that if David wants the subclasses 'developmental process'
and 'developmental stage' then those should live not in BFO, as they are
too specific for BFO. The proposal I made (leave domain/range of process as
process) is compatible with that scenario.
b...@googlecode.com
Labels: -Type-Defect Type-BFO2-Reference
Comment #16 on issue 15 by alanrut...@gmail.com: domain and range
b...@googlecode.com
Comment #17 on issue 15 by dosu...@gmail.com: domain and range of 'is
determine this distinction on process boundaries, so I personally wouldn't
want there to be such a distinction. I think the right abstraction has to
do with whole organismal lives versus proper parts of them."
processes as well as to the process that is development of the whole animal.
(ii) Do you believe that processes that end have no bona-fide temporal
boundary that is there end. e.g.- about 42 years ago, I gastrulated. I am
not gastrulating right now. Would you maintain that the point in time at
which I stopped gastrulating can only be defined by fiat. Is the temporal
boundary that is the end of me gastrulating a different sort of temporal
boundary during to the one I declare by fiat to have occurred 5 minutes
after this instance of gastrulation started?
b...@googlecode.com
Yu Lin
Can you give me the linguistic meaning of 'fiat' and 'bona fide' here?
I just recently reading Sowa's 'Processes and Causality':
http://www.jfsowa.com/ontology/causal.htm
I do like his notion of continuous process and discrete process.
The discrete process can be used for describing events and stages in his theory.
I wonder if we can borrow something from there.
However, is there any biological process that is not continuous?
In the case of developmental biology, is there any distinct boundary
for different developmental stages?
Best,
Asiyah
b...@googlecode.com
Comment #19 on issue 15 by alanrut...@gmail.com: domain and range
David asks: "Do you believe that processes that end have no bona-fide
gastrulated. I am not gastrulating right now. Would you maintain that the
point in time at which I stopped gastrulating can only be defined by fiat.
Is the temporal boundary that is the end of me gastrulating a different
sort of temporal boundary during to the one I declare by fiat to have
occurred 5 minutes after this instance of gastrulation started?"
it seems complete. If the temporal projection of the process is defined to
end when that occurs then we have some information about the process.
First, remember that a process boundary is a spatiotemporal boundary. So it
isn't enough to say the time to make a process boundary. But first look at
the temporal boundary. When is the end of gastrulation? When the last cell
necessary to complete the structure first starts to exist? When it falls
into some position (which)? Just before the next cell division?
As for spatial extent, what is it? Is it the sum of the spatial regions of
the cells? Are there not metabolites with various functions surrounding the
anatomical structure? How far out do these go? How much of that contributes
to the spatial extent of the process.
I think there are enough questions to merit my assessment that,
ontologically, making these distinctions is no simple matter.
GO:0007369
Definition
A complex and coordinated series of cellular movements that occurs at the
end of cleavage during embryonic development of most animals. The details
of gastrulation vary from species to species, but usually result in the
formation of the three primary germ layers, ectoderm, mesoderm and endoderm.