Sorry that I left the meeting before the voting occurred. I think that I participated in most of the related discussion in the meeting. As I view it, the proposal is reasonable. This is a feasible way towards an eventual and timely release of BFO 2 with a consensus. Therefore, I vote in favor of the proposal.
Best wishes,
Oliver He
University of Michigan
--
You received this message because you are subscribed to the Google Groups "bfo-owl-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
bfo-owl-deve...@googlegroups.com.
To post to this group, send email to
bfo-ow...@googlegroups.com.
Visit this group at
http://groups.google.com/group/bfo-owl-devel?hl=en-US.
For more options, visit https://groups.google.com/groups/opt_out.
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
Hi all,
Sorry I couldn't make it to the call. Few things are unclear to me in the below:
- I thought the only issue to using the "whole" BFO2 were the temporalized relations, and that we would therefore release BFO2 as-is, and people that don't want to use those relations just don't use them. Given this, why do we still need variants?
What are the proposed variants?
- I am not very keen on releasing variants, as this will create version issues again. My main objection to BFO1.2 was having people relying on different versions which would be confusing when importing several resources that rely on different versions. How does the multiple release of variants address this concern?
- Who will maintain those variants, and what is the time commitment? I am worried they will be maintained ad-hoc with no real update (or non synchronized with other variants), and/or people will make local updates that don't match other variants.
Those may have been discussed during the call but it is probably worth clarifying here and on the wiki page.
On Wed, Apr 24, 2013 at 1:06 PM, Melanie Courtot <mcou...@gmail.com> wrote:
Hi all,
Sorry I couldn't make it to the call. Few things are unclear to me in the below:
- I thought the only issue to using the "whole" BFO2 were the temporalized relations, and that we would therefore release BFO2 as-is, and people that don't want to use those relations just don't use them. Given this, why do we still need variants?It seems that those who plan not to used them are worried about the confusion arising from their presence.What are the proposed variants?We're working on them. At one end, I'm hoping only a minimal set can be removed, as suggested by my work with James (e.g keep those relations like inheres_in_at_all_times that are not (I hope) controversial). At the other extreme is removing all of them (suggested as a possibility by Chris)
- I am not very keen on releasing variants, as this will create version issues again. My main objection to BFO1.2 was having people relying on different versions which would be confusing when importing several resources that rely on different versions. How does the multiple release of variants address this concern?
Variants are strict subsets of the official version (slims). They conform to what we documented as part of our id policy, having the same ontologyIRI and different versionIRI. I don't believe there is cause for concern as the consequence of importing both would not be any change in meaning, or clash, it would simply be the presence of the additional relations.There is a minor issue that might need to be checked having to do with the order in which imports are added, and whether the first import of some version might cause a subsequent one not to load. I think this is probably manageable. It wouldn't happen in loading triple stores, only when using DL reasoning tools, if at all.
- Who will maintain those variants, and what is the time commitment? I am worried they will be maintained ad-hoc with no real update (or non synchronized with other variants), and/or people will make local updates that don't match other variants.
I plan to incorporate their building into the BFO build script, as I don't believe it to be technically difficult. So they would be a byproduct of the standard build.
Those may have been discussed during the call but it is probably worth clarifying here and on the wiki page.We discussed all these on the call, and hopefully they are recorded in the minutes. I do think we should start documenting this, but would prefer to have more the details be worked out and to have it be on a separate page, linked to from the vote page, so as not to make the vote page too intimidating.Please let me know if you think these answers adequately address the concerns you have.Best,Alan
On Apr 24, 2013, at 10:26 AM, Alan Ruttenberg wrote:On Wed, Apr 24, 2013 at 1:06 PM, Melanie Courtot <mcou...@gmail.com> wrote:
Hi all,
Sorry I couldn't make it to the call. Few things are unclear to me in the below:
- I thought the only issue to using the "whole" BFO2 were the temporalized relations, and that we would therefore release BFO2 as-is, and people that don't want to use those relations just don't use them. Given this, why do we still need variants?It seems that those who plan not to used them are worried about the confusion arising from their presence.What are the proposed variants?We're working on them. At one end, I'm hoping only a minimal set can be removed, as suggested by my work with James (e.g keep those relations like inheres_in_at_all_times that are not (I hope) controversial). At the other extreme is removing all of them (suggested as a possibility by Chris)I'm afraid that all temporalized relations must by default be regarded as controversial and difficult until proved otherwise.I'm attaching v1.2 of my critique. I did not address *all* temporalized relations, but one of the take-home messages is that the problems run deep and we must be careful about relying on intuititions. Many people were surprised that the at-all-times forms of part_of and has_part were not inverses. This was counterintuitive, but was entailed by the FOL.inheres-in-at-all-times is difficult too. inheres-in-at-all-times has no inverse declared in bfo2. It probably should be declared the inverse of bearer-of-at-some-times.Most of us would want to use the BFO2 subset that excludes bearer-of-at-some-times and swap in atemporal bearer-of instead:
In fact, I would take particular care to scrutinize Dependent Continuant-based relations very carefully, because it's not clear to me how to model determinates in BFO2 OWL. There may be further surprises lurking in the gaps.
In addition, any at-all-times relation is problematic, as it entails a commitment regarding rigid classes. See my critique for why this is a major problem.
With TRs, it's in for a penny, in for a pound.
- I am not very keen on releasing variants, as this will create version issues again. My main objection to BFO1.2 was having people relying on different versions which would be confusing when importing several resources that rely on different versions. How does the multiple release of variants address this concern?
Variants are strict subsets of the official version (slims). They conform to what we documented as part of our id policy, having the same ontologyIRI and different versionIRI. I don't believe there is cause for concern as the consequence of importing both would not be any change in meaning, or clash, it would simply be the presence of the additional relations.There is a minor issue that might need to be checked having to do with the order in which imports are added, and whether the first import of some version might cause a subsequent one not to load. I think this is probably manageable. It wouldn't happen in loading triple stores, only when using DL reasoning tools, if at all.There is another issue we did not address.O1 may wish to import BFO2-minimal, and take additional relations from ROHowever, O1 may import another ontology (say IAO) that itself imports the complete BFO2.The subset strategy becomes pointless here.
It's not insurmountable. It would be possible to make an alternate version of the intermediate ontology that imports the minimal ontology.
It's not clear the extent to which this will be a problem for different ontologies.
- Who will maintain those variants, and what is the time commitment? I am worried they will be maintained ad-hoc with no real update (or non synchronized with other variants), and/or people will make local updates that don't match other variants.
I plan to incorporate their building into the BFO build script, as I don't believe it to be technically difficult. So they would be a byproduct of the standard build.
Those may have been discussed during the call but it is probably worth clarifying here and on the wiki page.We discussed all these on the call, and hopefully they are recorded in the minutes. I do think we should start documenting this, but would prefer to have more the details be worked out and to have it be on a separate page, linked to from the vote page, so as not to make the vote page too intimidating.Please let me know if you think these answers adequately address the concerns you have.Best,AlanCritique attached below.
--
-- the bfo-devel group prefers that conversations on matters related to the specification take place on the mailing list so that other team members and users can follow how decisions are made. Please ensure you tell your mail application to respond to all.
---
You received this message because you are subscribed to the Google Groups "bfo-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bfo-devel+...@googlegroups.com.
Oh, I didn't see this. Apologies for the duplicate.
On Apr 24, 2013, at 12:38 PM, Melanie Courtot wrote:
> Hi all,
>
> Thanks for the answers. Chris, we had noted an issue with inverses at http://code.google.com/p/bfo/issues/detail?id=81
This one pertains to participation. With TRs, each relation must be examined individually, unless we can abstract some high level patterns
> . IIRC at the time Alan explained why those relations were not inverse; I'll admit being very confused about this (which came up several times in the past, e.g., http://code.google.com/p/bfo/issues/detail?id=73)
> My main question was, assuming we agree that we want an option to not use temporalized relation, wouldn't it be possible to just release BFO2 including those, and people just don't use them?So there are two issues:
1. reuse of the same URI for a TR and an AR. I think we should be conservative and avoid this.
2. whether there is an official subset of BFO or whether others make one
One one level #2 is not so important. People who don't want to make their own subset can just use the one available from a RO purl.
However, I think that there is some advantage to the BFO2 group in being the official purveyors of the subset. By providing the subset it's in part an implicit acknowledgment that there are issues with the TRs and some users may wish to start with the non-TR subset, and possibly mix this with ARs.
> Seems like this would solve quite a bit of issues, from having to produce different variants to having to deal with resources importing resources importing different variants? For example, I don't know many projects that use "zero-dimensional temporal region" but it doesn't hurt to have it in the file.Yes, I agree. Most groups will just want to pick and choose a minimal subset. But I think it helps to divide the axioms in advance for people.
Having a subset doesn't stop people trying out the relations.
> It would also allow people to try the relations out if they wish - if there is a need to single them out easily in the hierarchy we could label them as "experimental-TR-inheres_in_at_all_times". That would probably help with possible confusion?
Hi all,I think it would be helpful to consider the less technical obo-format foundry participants here. What do they need to be good citizens? If we don't consider how to bring them into the fold, we will end up with an even bigger divide between those that develop in OBO and those that develop in OWL. In that sense, I favor creation of a slim that is the lightest-weight version (e.g. likely no temporalized relations) that we need people to adhere to, or else we will get no adherence at all.
Regardless of the implementation strategies and BFO2 content in the end, we will absolutely need documentation, training, and outreach describing how to use the new BFO and design considerations.
I am not entirely in the loop here, so apologies if you all have already discussed. I just wanted to point out how much of the BFO2 work is quite unbeknownst to much of our community.
>I agree. I am not sure I understand the difference between BFO_0000056 for "participates in" (atemporal) and "participates in at some time" (as per http://code.google.com/p/bfo/issues/detail?id=163). When doing the mapping I thought those were equivalent. That being said if there is any confusion we should avoid reusing URIs.
> 1. reuse of the same URI for a TR and an AR. I think we should be conservative and avoid this.
- CONs
- we don't solve the issue of different resources importing different subsets. For example, if IAO imports BFO2 "whole" resources importing IAO will import BFO2 whole (even if they chose to import a subset for themselves)
On Wed, Apr 24, 2013 at 4:09 PM, Chris Mungall <cjmu...@lbl.gov> wrote:
Oh, I didn't see this. Apologies for the duplicate.
On Apr 24, 2013, at 12:38 PM, Melanie Courtot wrote:
> Hi all,
>
> Thanks for the answers. Chris, we had noted an issue with inverses at http://code.google.com/p/bfo/issues/detail?id=81
This one pertains to participation. With TRs, each relation must be examined individually, unless we can abstract some high level patterns
> . IIRC at the time Alan explained why those relations were not inverse; I'll admit being very confused about this (which came up several times in the past, e.g., http://code.google.com/p/bfo/issues/detail?id=73)
Every relation, TR or not, should be examined individually.> My main question was, assuming we agree that we want an option to not use temporalized relation, wouldn't it be possible to just release BFO2 including those, and people just don't use them?So there are two issues:
1. reuse of the same URI for a TR and an AR. I think we should be conservative and avoid this.I've requested at least a plausibility argument of how it could be a problem. Is that really too much to ask??
2. whether there is an official subset of BFO or whether others make one
One one level #2 is not so important. People who don't want to make their own subset can just use the one available from a RO purl.
However, I think that there is some advantage to the BFO2 group in being the official purveyors of the subset. By providing the subset it's in part an implicit acknowledgment that there are issues with the TRs and some users may wish to start with the non-TR subset, and possibly mix this with ARs.
Look, there is isn't a problem making them, and we've agreed to document the controversy. Whether the problems are with the TRs or the people I am uncertain, but we need not, implicitly or not, fix on either interpretation.Melanie, I really don't think the issue of whether we should have variants is something we should debate. It is routine that we have variants in the form of slims and we've lived with it for a long time without problems.> Seems like this would solve quite a bit of issues, from having to produce different variants to having to deal with resources importing resources importing different variants? For example, I don't know many projects that use "zero-dimensional temporal region" but it doesn't hurt to have it in the file.Yes, I agree. Most groups will just want to pick and choose a minimal subset. But I think it helps to divide the axioms in advance for people.
Having a subset doesn't stop people trying out the relations.
> It would also allow people to try the relations out if they wish - if there is a need to single them out easily in the hierarchy we could label them as "experimental-TR-inheres_in_at_all_times". That would probably help with possible confusion?
I'd rather not have their label be so. It's my contention, remember, that these relations are well defined and sound, if not necessarily covering all use cases or being easy to teach.
On Apr 24, 2013, at 1:34 PM, Alan Ruttenberg wrote:On Wed, Apr 24, 2013 at 4:09 PM, Chris Mungall <cjmu...@lbl.gov> wrote:
Oh, I didn't see this. Apologies for the duplicate.
On Apr 24, 2013, at 12:38 PM, Melanie Courtot wrote:
> Hi all,
>
> Thanks for the answers. Chris, we had noted an issue with inverses at http://code.google.com/p/bfo/issues/detail?id=81
This one pertains to participation. With TRs, each relation must be examined individually, unless we can abstract some high level patterns
> . IIRC at the time Alan explained why those relations were not inverse; I'll admit being very confused about this (which came up several times in the past, e.g., http://code.google.com/p/bfo/issues/detail?id=73)
Every relation, TR or not, should be examined individually.> My main question was, assuming we agree that we want an option to not use temporalized relation, wouldn't it be possible to just release BFO2 including those, and people just don't use them?So there are two issues:
1. reuse of the same URI for a TR and an AR. I think we should be conservative and avoid this.I've requested at least a plausibility argument of how it could be a problem. Is that really too much to ask??Umm, you snipped the part of my email where I provided this:But was is it even necessary for me to do this? Surely it's obvious that if one group is using BFO_0000053 as in "bearer of" (atemporal) and another group is using BFO_0000053 to mean "bearer of at SOME times" we're going to run into difficulties. Don't you think it's kind of sensible to try and avoid that?
And what's with the "is this really too much to ask?". Really? I wrote an entire critique where many of these issues were laid out. Is it too much to ask you to read this?
M
At this stage it doesn't seem safe for us to use identifiers in the BFO ID space for atemporal relations, as we have no guarantee they won't be reused in a different way.
I would therefore recommend that those of us using atemporal relations should mint new URIs for these - probably RO URIs. This is very unfortunate and will cause some churn but I don't see what the alternative is.
2. whether there is an official subset of BFO or whether others make one
One one level #2 is not so important. People who don't want to make their own subset can just use the one available from a RO purl.
However, I think that there is some advantage to the BFO2 group in being the official purveyors of the subset. By providing the subset it's in part an implicit acknowledgment that there are issues with the TRs and some users may wish to start with the non-TR subset, and possibly mix this with ARs.
Look, there is isn't a problem making them, and we've agreed to document the controversy. Whether the problems are with the TRs or the people I am uncertain, but we need not, implicitly or not, fix on either interpretation.Melanie, I really don't think the issue of whether we should have variants is something we should debate. It is routine that we have variants in the form of slims and we've lived with it for a long time without problems.> Seems like this would solve quite a bit of issues, from having to produce different variants to having to deal with resources importing resources importing different variants? For example, I don't know many projects that use "zero-dimensional temporal region" but it doesn't hurt to have it in the file.Yes, I agree. Most groups will just want to pick and choose a minimal subset. But I think it helps to divide the axioms in advance for people.
Having a subset doesn't stop people trying out the relations.
> It would also allow people to try the relations out if they wish - if there is a need to single them out easily in the hierarchy we could label them as "experimental-TR-inheres_in_at_all_times". That would probably help with possible confusion?
I'd rather not have their label be so. It's my contention, remember, that these relations are well defined and sound, if not necessarily covering all use cases or being easy to teach.I would suggest, at a minimum, that some kind of indication of what use cases are covered and not covered are provided as part of the TR documentation.
Then people can be better informed about whether to use them or some alternative.
For examples of use cases that are not covered, I refer people to my critique
--
-- the bfo-devel group prefers that conversations on matters related to the specification take place on the mailing list so that other team members and users can follow how decisions are made. Please ensure you tell your mail application to respond to all.
---
You received this message because you are subscribed to the Google Groups "bfo-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bfo-devel+...@googlegroups.com.
On Wednesday, April 24, 2013, Chris Mungall wrote:On Apr 24, 2013, at 1:34 PM, Alan Ruttenberg wrote:On Wed, Apr 24, 2013 at 4:09 PM, Chris Mungall <cjmu...@lbl.gov> wrote:
Oh, I didn't see this. Apologies for the duplicate.
On Apr 24, 2013, at 12:38 PM, Melanie Courtot wrote:
> Hi all,
>
> Thanks for the answers. Chris, we had noted an issue with inverses at http://code.google.com/p/bfo/issues/detail?id=81
This one pertains to participation. With TRs, each relation must be examined individually, unless we can abstract some high level patterns
> . IIRC at the time Alan explained why those relations were not inverse; I'll admit being very confused about this (which came up several times in the past, e.g., http://code.google.com/p/bfo/issues/detail?id=73)
Every relation, TR or not, should be examined individually.> My main question was, assuming we agree that we want an option to not use temporalized relation, wouldn't it be possible to just release BFO2 including those, and people just don't use them?So there are two issues:
1. reuse of the same URI for a TR and an AR. I think we should be conservative and avoid this.I've requested at least a plausibility argument of how it could be a problem. Is that really too much to ask??Umm, you snipped the part of my email where I provided this:But was is it even necessary for me to do this? Surely it's obvious that if one group is using BFO_0000053 as in "bearer of" (atemporal) and another group is using BFO_0000053 to mean "bearer of at SOME times" we're going to run into difficulties. Don't you think it's kind of sensible to try and avoid that?If I knew what bearer-of (atemporal) meant, I could respond. But I really don't and I don't think you do either.
And what's with the "is this really too much to ask?". Really? I wrote an entire critique where many of these issues were laid out. Is it too much to ask you to read this?I read and commented on it. You don't seem to want to understand the responses. The main criticisms were that the generic relation proposed just doesn't work as an instance relation, and that most of the problems that were identified as TR issues were really issues with specific versus generic relations.
There were also comments about user burden, and the difficulty of using the relations correctly. However I disagree that a valid alternative to trouble using relations is to use relations that have no way of being shown to be true.MAt this stage it doesn't seem safe for us to use identifiers in the BFO ID space for atemporal relations, as we have no guarantee they won't be reused in a different way.I addressed this already. We (foundry) have a policy that we don't change meaning. They wont be used in a different way - new terms would be created.
It seems far more likely that the atemporal terms will be used differently as we don't even know what correct usage of the now is.
I would therefore recommend that those of us using atemporal relations should mint new URIs for these - probably RO URIs. This is very unfortunate and will cause some churn but I don't see what the alternative is.The alternative is the be conservative about pre-worry about some of these concerns and instead act when you know something specific.
2. whether there is an official subset of BFO or whether others make one
One one level #2 is not so important. People who don't want to make their own subset can just use the one available from a RO purl.
However, I think that there is some advantage to the BFO2 group in being the official purveyors of the subset. By providing the subset it's in part an implicit acknowledgment that there are issues with the TRs and some users may wish to start with the non-TR subset, and possibly mix this with ARs.
Look, there is isn't a problem making them, and we've agreed to document the controversy. Whether the problems are with the TRs or the people I am uncertain, but we need not, implicitly or not, fix on either interpretation.Melanie, I really don't think the issue of whether we should have variants is something we should debate. It is routine that we have variants in the form of slims and we've lived with it for a long time without problems.> Seems like this would solve quite a bit of issues, from having to produce different variants to having to deal with resources importing resources importing different variants? For example, I don't know many projects that use "zero-dimensional temporal region" but it doesn't hurt to have it in the file.Yes, I agree. Most groups will just want to pick and choose a minimal subset. But I think it helps to divide the axioms in advance for people.
Having a subset doesn't stop people trying out the relations.
> It would also allow people to try the relations out if they wish - if there is a need to single them out easily in the hierarchy we could label them as "experimental-TR-inheres_in_at_all_times". That would probably help with possible confusion?
I'd rather not have their label be so. It's my contention, remember, that these relations are well defined and sound, if not necessarily covering all use cases or being easy to teach.I would suggest, at a minimum, that some kind of indication of what use cases are covered and not covered are provided as part of the TR documentation.Sure, assuming you will do the same for the relations you plan to uses. No double standards. But I think you will have a harder time at this because you don't have formal definitions.
Then people can be better informed about whether to use them or some alternative.Assuming they have comparative information about the alternative. Thus far this does not exist.
For examples of use cases that are not covered, I refer people to my critiqueDo I really have to assemble a comparable collection about the proposed alternative?
I would like some others to analyze the critique in light of the errors and issues I've noted.