-
Notifications
You must be signed in to change notification settings - Fork 47
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
This is a proposed update that changes inheres in to the characteristic of model #284
Conversation
This change intends to apply to quality only or apply to 'specifically dependent continuant' including 'realizable entity' like disposition and role. |
This PR needs to be done against ro-edit rather than ro... I promised to do this but have not yet |
It's a bit hard to tell, but it looks like the changes have more than just this change. Could someone check? |
There is an additional complication beyond just migrating the edits to the edit file. TL;DR - characteristic-of can't be a super-property of a property representing what the current BFO2 reference calls inheres-in For the phenotype work, the assumption was always that the relation linking the quality to the IC/process was functional. We set this out here: We didn't just make this up. It was entirely our understanding at that time (pre BFO formalization in a non-PDF form) that inheres-in was intended to be functional. See equation A7 in Fabian, Pierre, and Barry's paper, which we took to be canonical: (note that paper explicitly deferred on QoPs) So if the URI we are using becomes the super-property of what is now what the BFO2 reference calls inheres-in, we cannot declare this to be functional with inducing the same characteristic on BFO2:inheres_in, which is not intentional according to the reference, due to the following definition that was introduced for relational qualities: If we want to declare RO_0000052 as functional, then this has to become a sibling of BFO2:inheres_in. This goes further than what we all agreed upon. An alternate option is that BFO2 abandons its approach to RQs and adopts the one we use in PATO where inheres-in is used as a functional relation, and the additional relatum for a RQ gets a different object property (currently awkwardly called 'towards'). This is more in the spirit of the Neuhaus paper I think. (FWIW, I think the PATO community may be the only one using RQs, and they cause widespread confusion). |
Discussed this on the call 6/4 which Chris M could unfortunately not join. Consensus that some solution needs to appear fast, and that Chris M needs to weigh in if what Alan is proposing above works for him. |
Discussed on RO call today, all in agreement, see https://docs.google.com/document/d/19dhzj5QoliQZQgDJRczI878rLtexzMDo1g0K9_LRUWk/edit# We will implement this structure (names not yet decided):
We will decide on labels shortly. |
can you tell ,me where process qualities fit in here?
is the idea that they would be SDCs that would depend on processes?
…On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***> wrote:
Discussed on RO call today.
We will implement this structure (names not yet decided):
- [new] characteristic of or inheres in [domain: SDC, range: Thing]
- RO_0000052 functional characteristic of [properties: functional]
- inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
IC]
We will decide on labels shortly.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=AB7KUNY3BOHIGUDA5BK6NPLQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AB7KUN3XV2MV4TGR7WSLJQ3QCBVB3ANCNFSM4F7LSHUQ>
.
|
On Tue, Jun 4, 2019 at 12:14 AM Chris Mungall ***@***.***> wrote:
For the phenotype work, the assumption was always that the relation
linking the quality to the IC/process was functional. We set this out here:
http://webont.org/owled/2007/PapersPDF/paper_40.pdf
We didn't just make this up. It was entirely our understanding at that
time (pre BFO formalization in a non-PDF form) that inheres-in was intended
to be functional. See equation A7 in Fabian, Pierre, and Barry's paper,
which we took to be canonical:
http://ontology.buffalo.edu/bfo/SQU.pdf
I'm not reading that as functional in the sense you mean. From SQU: "If v
is a d-place quality, then v inheres in d entities or there is an entity
which inheres in d entities ..."
i.e. you can inhere in more than one entity. They talk about d-place
qualities.
I'm still trying to grok the formal notation.
Alan
|
On Tue, Jul 30, 2019 at 10:34 PM Alan Ruttenberg <[email protected]>
wrote:
On Tue, Jun 4, 2019 at 12:14 AM Chris Mungall ***@***.***>
wrote:
> For the phenotype work, the assumption was always that the relation
> linking the quality to the IC/process was functional. We set this out here:
>
> http://webont.org/owled/2007/PapersPDF/paper_40.pdf
>
> We didn't just make this up. It was entirely our understanding at that
> time (pre BFO formalization in a non-PDF form) that inheres-in was intended
> to be functional. See equation A7 in Fabian, Pierre, and Barry's paper,
> which we took to be canonical:
> http://ontology.buffalo.edu/bfo/SQU.pdf
>
I'm not reading that as functional in the sense you mean. From SQU: "If v
is a d-place quality, then v inheres in d entities or there is an entity
which inheres in d entities ..."
My understanding of what you mean by inheres in is function: A quality can
inhere in only one entity.
My understanding of A7: A quality can inhere in only one tuple of entities.
…
i.e. you can inhere in more than one entity. They talk about d-place
qualities.
I'm still trying to grok the formal notation.
Alan
|
On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***> wrote:
Discussed on RO call today.
We will implement this structure (names not yet decided):
- [new] characteristic of or inheres in [domain: SDC, range: Thing]
- RO_0000052 functional characteristic of [properties: functional]
- inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
IC]
We will decide on labels shortly.
This makes the assumption that a process characteristic is a SDC. The
problem here is that SDCs only and necessarily depend on independent
continuants that aren't spatial regions, or specifically dependent
continuants , but not processes. One might argue that
functional-characteristic-of is a distinct relation from s-depends-on, but
that would still leave a SDC with a s-depends-on relation to who-knows-what.
I think the change needs to be coupled with a revision of PATO:Quality.
a class process-characteristic is added.
PATO:Quality becomes quality or process-characteristic,
Then the question is where process-characteristic lies in the BFO
hierarchy. We haven't worked all the way through this, but currently I
think some might be continuants and some might be occurrents based on
whether they can be temporally sliced or not (duration:yes, rate:no). A
more careful review of the existing PATO process qualities might shed
light. Maybe some of us can get together to do that. A safe bet, though
I'm not sure how happy Barry would be about it, would be to do the
following:
Add subclass of occurrent : occurrent-process-characteristic
Add a subclass of continuant: continuant-process-characteristic
Add a defined class process-characteristic =
occurrent-process-characteristic OR continuant-process-characteristic
Add a defined class characteristic = process-characteristic or SDC
Make domain of 'characteristic of or inheres in' characteristic
Make domain of 'functional characteristic of' characteristic
As usual, the labels are placeholders that I'm not vested in.
Alan
… —
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ>
.
|
My simpler proposal, in order to just get something logically consistent
out now, is to drop the SDC constraint on the domain of 'characteristic
of'. A refactoring of PATO has been promised for at least five years, so we
should not make that the 'first step'.
On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg <[email protected]>
wrote:
… On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***>
wrote:
> Discussed on RO call today.
>
> We will implement this structure (names not yet decided):
>
> - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> - RO_0000052 functional characteristic of [properties: functional]
> - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> IC]
>
> We will decide on labels shortly.
>
This makes the assumption that a process characteristic is a SDC. The
problem here is that SDCs only and necessarily depend on independent
continuants that aren't spatial regions, or specifically dependent
continuants , but not processes. One might argue that
functional-characteristic-of is a distinct relation from s-depends-on, but
that would still leave a SDC with a s-depends-on relation to
who-knows-what.
I think the change needs to be coupled with a revision of PATO:Quality.
a class process-characteristic is added.
PATO:Quality becomes quality or process-characteristic,
Then the question is where process-characteristic lies in the BFO
hierarchy. We haven't worked all the way through this, but currently I
think some might be continuants and some might be occurrents based on
whether they can be temporally sliced or not (duration:yes, rate:no). A
more careful review of the existing PATO process qualities might shed
light. Maybe some of us can get together to do that. A safe bet, though
I'm not sure how happy Barry would be about it, would be to do the
following:
Add subclass of occurrent : occurrent-process-characteristic
Add a subclass of continuant: continuant-process-characteristic
Add a defined class process-characteristic =
occurrent-process-characteristic OR continuant-process-characteristic
Add a defined class characteristic = process-characteristic or SDC
Make domain of 'characteristic of or inheres in' characteristic
Make domain of 'functional characteristic of' characteristic
As usual, the labels are placeholders that I'm not vested in.
Alan
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <
#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=ADJX2ISPDHZGSLJ6536227TQCGCOZA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ADJX2IVSRRUZICEC6IK2CKDQCGCOZANCNFSM4F7LSHUQ>
.
--
Bjoern Peters
Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
|
On Wed, Jul 31, 2019 at 9:49 AM bpeters42 ***@***.***> wrote:
My simpler proposal, in order to just get something logically consistent
out now, is to drop the SDC constraint on the domain of 'characteristic
of'.
Doing that will get rid of 1/2 the problems. There's still the question of
*what is* the domain, and leaving it unconstrained will mean that there
will be terms without a path to BFO root as well as opportunity for
nonsense assertions, such as asserting a material entity as characteristic
of something.
A refactoring of PATO has been promised for at least five years, so we
should not make that the 'first step'.
Didn't understand what you mean here.
Alan
…
On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg ***@***.***>
wrote:
> On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***
>
> wrote:
>
> > Discussed on RO call today.
> >
> > We will implement this structure (names not yet decided):
> >
> > - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> > - RO_0000052 functional characteristic of [properties: functional]
> > - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> > IC]
> >
> > We will decide on labels shortly.
> >
> This makes the assumption that a process characteristic is a SDC. The
> problem here is that SDCs only and necessarily depend on independent
> continuants that aren't spatial regions, or specifically dependent
> continuants , but not processes. One might argue that
> functional-characteristic-of is a distinct relation from s-depends-on,
but
> that would still leave a SDC with a s-depends-on relation to
> who-knows-what.
>
> I think the change needs to be coupled with a revision of PATO:Quality.
>
> a class process-characteristic is added.
> PATO:Quality becomes quality or process-characteristic,
>
> Then the question is where process-characteristic lies in the BFO
> hierarchy. We haven't worked all the way through this, but currently I
> think some might be continuants and some might be occurrents based on
> whether they can be temporally sliced or not (duration:yes, rate:no). A
> more careful review of the existing PATO process qualities might shed
> light. Maybe some of us can get together to do that. A safe bet, though
> I'm not sure how happy Barry would be about it, would be to do the
> following:
>
> Add subclass of occurrent : occurrent-process-characteristic
>
> Add a subclass of continuant: continuant-process-characteristic
>
> Add a defined class process-characteristic =
> occurrent-process-characteristic OR continuant-process-characteristic
>
> Add a defined class characteristic = process-characteristic or SDC
>
> Make domain of 'characteristic of or inheres in' characteristic
>
> Make domain of 'functional characteristic of' characteristic
>
> As usual, the labels are placeholders that I'm not vested in.
>
> Alan
>
>
>
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
>
#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
> >,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
> >
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <
#284?email_source=notifications&email_token=ADJX2ISPDHZGSLJ6536227TQCGCOZA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845
>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ADJX2IVSRRUZICEC6IK2CKDQCGCOZANCNFSM4F7LSHUQ
>
> .
>
--
Bjoern Peters
Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=AAB3CDXZPSGG7L6UHFKNLN3QCGJ6FA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HJ2LY#issuecomment-516857135>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AAB3CDRMCFPRUWGKVW2CRD3QCGJ6FANCNFSM4F7LSHUQ>
.
|
Well, wouldn't it be nice to get rid of 1/2 the problems?
On Wed, Jul 31, 2019, 9:55 AM Alan Ruttenberg <[email protected]>
wrote:
… On Wed, Jul 31, 2019 at 9:49 AM bpeters42 ***@***.***>
wrote:
> My simpler proposal, in order to just get something logically consistent
> out now, is to drop the SDC constraint on the domain of 'characteristic
> of'.
Doing that will get rid of 1/2 the problems. There's still the question of
*what is* the domain, and leaving it unconstrained will mean that there
will be terms without a path to BFO root as well as opportunity for
nonsense assertions, such as asserting a material entity as characteristic
of something.
> A refactoring of PATO has been promised for at least five years, so we
> should not make that the 'first step'.
>
Didn't understand what you mean here.
Alan
>
>
> On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg <
***@***.***>
> wrote:
>
> > On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall <
***@***.***
> >
> > wrote:
> >
> > > Discussed on RO call today.
> > >
> > > We will implement this structure (names not yet decided):
> > >
> > > - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> > > - RO_0000052 functional characteristic of [properties: functional]
> > > - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> > > IC]
> > >
> > > We will decide on labels shortly.
> > >
> > This makes the assumption that a process characteristic is a SDC. The
> > problem here is that SDCs only and necessarily depend on independent
> > continuants that aren't spatial regions, or specifically dependent
> > continuants , but not processes. One might argue that
> > functional-characteristic-of is a distinct relation from s-depends-on,
> but
> > that would still leave a SDC with a s-depends-on relation to
> > who-knows-what.
> >
> > I think the change needs to be coupled with a revision of PATO:Quality.
> >
> > a class process-characteristic is added.
> > PATO:Quality becomes quality or process-characteristic,
> >
> > Then the question is where process-characteristic lies in the BFO
> > hierarchy. We haven't worked all the way through this, but currently I
> > think some might be continuants and some might be occurrents based on
> > whether they can be temporally sliced or not (duration:yes, rate:no). A
> > more careful review of the existing PATO process qualities might shed
> > light. Maybe some of us can get together to do that. A safe bet, though
> > I'm not sure how happy Barry would be about it, would be to do the
> > following:
> >
> > Add subclass of occurrent : occurrent-process-characteristic
> >
> > Add a subclass of continuant: continuant-process-characteristic
> >
> > Add a defined class process-characteristic =
> > occurrent-process-characteristic OR continuant-process-characteristic
> >
> > Add a defined class characteristic = process-characteristic or SDC
> >
> > Make domain of 'characteristic of or inheres in' characteristic
> >
> > Make domain of 'functional characteristic of' characteristic
> >
> > As usual, the labels are placeholders that I'm not vested in.
> >
> > Alan
> >
> >
> >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <
> >
>
#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
> > >,
> > > or mute the thread
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
> > >
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
>
#284?email_source=notifications&email_token=ADJX2ISPDHZGSLJ6536227TQCGCOZA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845
> >,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/ADJX2IVSRRUZICEC6IK2CKDQCGCOZANCNFSM4F7LSHUQ
> >
> > .
> >
>
>
> --
> Bjoern Peters
> Professor
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <
#284?email_source=notifications&email_token=AAB3CDXZPSGG7L6UHFKNLN3QCGJ6FA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HJ2LY#issuecomment-516857135
>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/AAB3CDRMCFPRUWGKVW2CRD3QCGJ6FANCNFSM4F7LSHUQ
>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=ADJX2IRAKE5KC6RIILK77UTQCGKVFA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HKNIY#issuecomment-516859555>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ADJX2IUJH7LGMOEACQOUTWLQCGKVFANCNFSM4F7LSHUQ>
.
|
On Wed, Jul 31, 2019 at 10:56 AM bpeters42 ***@***.***> wrote:
Well, wouldn't it be nice to get rid of 1/2 the problems?
It would. I'm just not sure if the new problems offset the benefit.
… On Wed, Jul 31, 2019, 9:55 AM Alan Ruttenberg ***@***.***>
wrote:
> On Wed, Jul 31, 2019 at 9:49 AM bpeters42 ***@***.***>
> wrote:
>
> > My simpler proposal, in order to just get something logically
consistent
> > out now, is to drop the SDC constraint on the domain of 'characteristic
> > of'.
>
>
> Doing that will get rid of 1/2 the problems. There's still the question
of
> *what is* the domain, and leaving it unconstrained will mean that there
> will be terms without a path to BFO root as well as opportunity for
> nonsense assertions, such as asserting a material entity as
characteristic
> of something.
>
>
> > A refactoring of PATO has been promised for at least five years, so we
> > should not make that the 'first step'.
> >
>
> Didn't understand what you mean here.
>
> Alan
>
>
> >
> >
> > On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg <
> ***@***.***>
> > wrote:
> >
> > > On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall <
> ***@***.***
> > >
> > > wrote:
> > >
> > > > Discussed on RO call today.
> > > >
> > > > We will implement this structure (names not yet decided):
> > > >
> > > > - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> > > > - RO_0000052 functional characteristic of [properties: functional]
> > > > - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> > > > IC]
> > > >
> > > > We will decide on labels shortly.
> > > >
> > > This makes the assumption that a process characteristic is a SDC. The
> > > problem here is that SDCs only and necessarily depend on independent
> > > continuants that aren't spatial regions, or specifically dependent
> > > continuants , but not processes. One might argue that
> > > functional-characteristic-of is a distinct relation from
s-depends-on,
> > but
> > > that would still leave a SDC with a s-depends-on relation to
> > > who-knows-what.
> > >
> > > I think the change needs to be coupled with a revision of
PATO:Quality.
> > >
> > > a class process-characteristic is added.
> > > PATO:Quality becomes quality or process-characteristic,
> > >
> > > Then the question is where process-characteristic lies in the BFO
> > > hierarchy. We haven't worked all the way through this, but currently
I
> > > think some might be continuants and some might be occurrents based on
> > > whether they can be temporally sliced or not (duration:yes,
rate:no). A
> > > more careful review of the existing PATO process qualities might shed
> > > light. Maybe some of us can get together to do that. A safe bet,
though
> > > I'm not sure how happy Barry would be about it, would be to do the
> > > following:
> > >
> > > Add subclass of occurrent : occurrent-process-characteristic
> > >
> > > Add a subclass of continuant: continuant-process-characteristic
> > >
> > > Add a defined class process-characteristic =
> > > occurrent-process-characteristic OR continuant-process-characteristic
> > >
> > > Add a defined class characteristic = process-characteristic or SDC
> > >
> > > Make domain of 'characteristic of or inheres in' characteristic
> > >
> > > Make domain of 'functional characteristic of' characteristic
> > >
> > > As usual, the labels are placeholders that I'm not vested in.
> > >
> > > Alan
> > >
> > >
> > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> > >
> >
>
#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
> > > >,
> > > > or mute the thread
> > > > <
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
> > > >
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <
> >
>
#284?email_source=notifications&email_token=ADJX2ISPDHZGSLJ6536227TQCGCOZA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845
> > >,
> > > or mute the thread
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/ADJX2IVSRRUZICEC6IK2CKDQCGCOZANCNFSM4F7LSHUQ
> > >
> > > .
> > >
> >
> >
> > --
> > Bjoern Peters
> > Professor
> > La Jolla Institute for Allergy and Immunology
> > 9420 Athena Circle
> > La Jolla, CA 92037, USA
> > Tel: 858/752-6914
> > Fax: 858/752-6987
> > http://www.liai.org/pages/faculty-peters
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
>
#284?email_source=notifications&email_token=AAB3CDXZPSGG7L6UHFKNLN3QCGJ6FA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HJ2LY#issuecomment-516857135
> >,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/AAB3CDRMCFPRUWGKVW2CRD3QCGJ6FANCNFSM4F7LSHUQ
> >
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <
#284?email_source=notifications&email_token=ADJX2IRAKE5KC6RIILK77UTQCGKVFA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HKNIY#issuecomment-516859555
>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ADJX2IUJH7LGMOEACQOUTWLQCGKVFANCNFSM4F7LSHUQ
>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=AAB3CDRNHKXVSQMGUEPCLIDQCGR3PA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HQ33A#issuecomment-516885996>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AAB3CDRVBECRHBXS5DCMI63QCGR3PANCNFSM4F7LSHUQ>
.
|
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Should not be merged - this PR is now serving as more of a ticket for a new PR. See other comments
I vote for this
BS
On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg <[email protected]>
wrote:
… On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***>
wrote:
> Discussed on RO call today.
>
> We will implement this structure (names not yet decided):
>
> - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> - RO_0000052 functional characteristic of [properties: functional]
> - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> IC]
>
> We will decide on labels shortly.
>
This makes the assumption that a process characteristic is a SDC. The
problem here is that SDCs only and necessarily depend on independent
continuants that aren't spatial regions, or specifically dependent
continuants , but not processes. One might argue that
functional-characteristic-of is a distinct relation from s-depends-on, but
that would still leave a SDC with a s-depends-on relation to
who-knows-what.
I think the change needs to be coupled with a revision of PATO:Quality.
a class process-characteristic is added.
PATO:Quality becomes quality or process-characteristic,
Then the question is where process-characteristic lies in the BFO
hierarchy. We haven't worked all the way through this, but currently I
think some might be continuants and some might be occurrents based on
whether they can be temporally sliced or not (duration:yes, rate:no). A
more careful review of the existing PATO process qualities might shed
light. Maybe some of us can get together to do that. A safe bet, though
I'm not sure how happy Barry would be about it, would be to do the
following:
Add subclass of occurrent : occurrent-process-characteristic
Add a subclass of continuant: continuant-process-characteristic
Add a defined class process-characteristic =
occurrent-process-characteristic OR continuant-process-characteristic
Add a defined class characteristic = process-characteristic or SDC
Make domain of 'characteristic of or inheres in' characteristic
Make domain of 'functional characteristic of' characteristic
As usual, the labels are placeholders that I'm not vested in.
Alan
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <
#284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
>
> .
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#284?email_source=notifications&email_token=AB7KUNZBRFBLI66WC6L5C5TQCGCOXA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AB7KUN2RXQ5VVQFQPATJOIDQCGCOXANCNFSM4F7LSHUQ>
.
|
More specifically, I vote for the part of what Alan wrote highlighted in
yellow below
BS
…On Thu, Aug 1, 2019 at 1:02 PM Barry Smith ***@***.***> wrote:
I vote for this
BS
On Wed, Jul 31, 2019 at 8:45 AM Alan Ruttenberg ***@***.***>
wrote:
> On Tue, Jul 30, 2019 at 12:38 PM Chris Mungall ***@***.***>
> wrote:
>
> > Discussed on RO call today.
> >
> > We will implement this structure (names not yet decided):
> >
> > - [new] characteristic of or inheres in [domain: SDC, range: Thing]
> > - RO_0000052 functional characteristic of [properties: functional]
> > - inheres_in [equivalent to inheres in in the bfo2 ref doc] [range:
> > IC]
> >
> > We will decide on labels shortly.
> >
> This makes the assumption that a process characteristic is a SDC. The
> problem here is that SDCs only and necessarily depend on independent
> continuants that aren't spatial regions, or specifically dependent
> continuants , but not processes. One might argue that
> functional-characteristic-of is a distinct relation from s-depends-on, but
> that would still leave a SDC with a s-depends-on relation to
> who-knows-what.
>
> I think the change needs to be coupled with a revision of PATO:Quality.
>
> a class process-characteristic is added.
> PATO:Quality becomes quality or process-characteristic,
>
> Then the question is where process-characteristic lies in the BFO
> hierarchy. We haven't worked all the way through this, but currently I
> think some might be continuants and some might be occurrents based on
> whether they can be temporally sliced or not (duration:yes, rate:no). A
> more careful review of the existing PATO process qualities might shed
> light. Maybe some of us can get together to do that. A safe bet, though
> I'm not sure how happy Barry would be about it, would be to do the
> following:
>
> Add subclass of occurrent : occurrent-process-characteristic
>
> Add a subclass of continuant: continuant-process-characteristic
>
> Add a defined class process-characteristic =
> occurrent-process-characteristic OR continuant-process-characteristic
>
> Add a defined class characteristic = process-characteristic or SDC
>
> Make domain of 'characteristic of or inheres in' characteristic
>
> Make domain of 'functional characteristic of' characteristic
>
> As usual, the labels are placeholders that I'm not vested in.
>
> Alan
>
>
>
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
> #284?email_source=notifications&email_token=AAB3CDULUMSJMLCM4IUNLSTQCBVB3A5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3ESFFY#issuecomment-516498071
> >,
> > or mute the thread
> > <
> https://github.com/notifications/unsubscribe-auth/AAB3CDQI2QMOW2FZJIUJBZTQCBVB3ANCNFSM4F7LSHUQ
> >
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#284?email_source=notifications&email_token=AB7KUNZBRFBLI66WC6L5C5TQCGCOXA5CNFSM4F7LSHU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3HD4TI#issuecomment-516832845>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AB7KUN2RXQ5VVQFQPATJOIDQCGCOXANCNFSM4F7LSHUQ>
> .
>
|
new PR here: #442 |
No description provided.