Re: BODO - CHEMINF alignment

[Egon Willighagen]

On Sun, Oct 16, 2011 at 9:40 AM, Janna Hastings
<janna.h...@gmail.com> wrote:
> this is fantastic!  Thanks a lot :-)

I have asked past BODO contributors if they are happy with relicensing
their material into CC-BY-SA so that I can use the <definition>s in
CHEMINF, but I have not asked if the CHEMINF project is OK with such
contributions from BODO contributors...

Michel, Nico, Janna, Christoph, Leonid:

are you happy with other people as 'author' on the CHEMINF .owl file?

(I assumed you would...)

Regarding the rich snippets, the BODO <description> parts that contain
the MathML and I have been considering just keeping the BODO name for
that...

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Janna Hastings]

Hi Egon,

I am very happy with having explicit external authorship for terms
with definitions imported from BODO. The idea of CHEMINF is that it
is a community-based project which should accept input from the
community and should in turn give credit where credit is due. :-)

Janna

[Michel Dumontier]

I prefer a open method of attribution, where any contribution, is acknowledged in the list of contributing authors for the ontology and will also be co-authors for any future publication related to this community effort.

Term-level contributions are harder to manage, and unless there is some fancy versioning system behind it that can easily summarize contributions, i'm not sure what the value is, particular when labels and definitions get reworked over time.

m.

--
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com

[Leonid Chepelev]

I prefer a open method of attribution, where any contribution, is acknowledged in the list of contributing authors for the ontology and will also be co-authors for any future publication related to this community effort.

Absolutely agree.

 

Term-level contributions are harder to manage, and unless there is some fancy versioning system behind it that can easily summarize contributions, i'm not sure what the value is, particular when labels and definitions get reworked over time.

The value is a more 'fair' attribution system, which in my case makes me neither happy nor sad, but I can easily see how some contributors may like that. It also seems to be the more aligned current practice in some projects, like CDK, where the author of a particular class is acknowledged, even if that class may be reworked or modified later on. Usually, the difficulty to manage is not cited there.

Just my 2 yen.

Cheers!

[Egon Willighagen]

On Sun, Oct 16, 2011 at 2:22 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
> Term-level contributions are harder to manage, and unless there is some
> fancy versioning system

Like our subversion repository?

> behind it that can easily summarize contributions,
> i'm not sure what the value is,

Well, the issue now is that when we copy/paste stuff from elsewhere,
like BODO (or CDK JavaDoc), that content has ownership already... so,
we will have term-level contributions...

> particular when labels and definitions get reworked over time.

That's the alternative: write labels from scratch, but was hoping not
having to do that too...

[Egon Willighagen]

On Sun, Oct 16, 2011 at 2:30 PM, Leonid Chepelev
<leonid....@gmail.com> wrote:
>> Term-level contributions are harder to manage, and unless there is some
>> fancy versioning system behind it that can easily summarize contributions,
>> i'm not sure what the value is, particular when labels and definitions get
>> reworked over time.
>
> The value is a more 'fair' attribution system, which in my case makes me
> neither happy nor sad, but I can easily see how some contributors may like
> that.

I am happy with having in the ontology just the name of the
contributor at a macroscopic level, and the subversion repository to
more fine-tuned authorship. Would that work for you too?

[Leonid Chepelev]

I am happy with having in the ontology just the name of the

contributor at a macroscopic level, and the subversion repository to
more fine-tuned authorship. Would that work for you too?

If you are asking personally, I am happy either way. For the rest, I was merely speculating as to the feelings of the other members of the project. I certainly feel that all current authors should be asked prior to formalizing the contribution policy, and subsequent authors just agree to existing policy. So, for me, you have the go ahead. As for the others, I am merely speculating about attributions. What I would really like is what Michel mentioned: 

I prefer a open method of attribution, where any contribution, is acknowledged in the list of contributing authors for the ontology and will also be co-authors for any future publication related to this community effort.

I feel this is an important bit. I am happy with everything else, whatever way it goes.

[Michel Dumontier]

On Sun, Oct 16, 2011 at 9:35 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Sun, Oct 16, 2011 at 2:30 PM, Leonid Chepelev
<leonid....@gmail.com> wrote:
>> Term-level contributions are harder to manage, and unless there is some
>> fancy versioning system behind it that can easily summarize contributions,
>> i'm not sure what the value is, particular when labels and definitions get
>> reworked over time.
>
> The value is a more 'fair' attribution system, which in my case makes me
> neither happy nor sad, but I can easily see how some contributors may like
> that.

I am happy with having in the ontology just the name of the
contributor at a macroscopic level, and the subversion repository to
more fine-tuned authorship. Would that work for you too?

Well - I think it's more complicated. Considered the contribution of the person who thought it would be a good idea to add a certain term. Then you have the variety of people that are involved in crafting a definition (say on a mailing list), then you have the actual editor of the term who puts it in the ontology. Then you might have more discussions about this on the mailing list, then you have somebody that goes and makes the modification... etc.

so, for me, SVN level is insufficient to capture the contributions at the term level, and would be an improper metric of "contribution".  Unless you're prepared to develop a system to easily capture each contribution (none exists AFAIK) as ontology meta-data (because it doesn't belong in a domain ontology), then I suggest we forget about this distinction. If the goal is to produce a community ontology, then we should acknowledge all the members in our community for their contributions - whether intellectual in terms of discussions or actual editing of labels/definitions/axioms/etc

m.

 

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Egon Willighagen]

Michel,

On Sun, Oct 16, 2011 at 2:42 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
> Well - I think it's more complicated. Considered the contribution of the
> person who thought it would be a good idea to add a certain term. Then you
> have the variety of people that are involved in crafting a definition (say
> on a mailing list), then you have the actual editor of the term who puts it
> in the ontology. Then you might have more discussions about this on the
> mailing list, then you have somebody that goes and makes the modification...
> etc.
> so, for me, SVN level is insufficient to capture the contributions at the
> term level, and would be an improper metric of "contribution".  Unless
> you're prepared to develop a system to easily capture each contribution
> (none exists AFAIK) as ontology meta-data (because it doesn't belong in a
> domain ontology), then I suggest we forget about this distinction. If the
> goal is to produce a community ontology, then we should acknowledge all the
> members in our community for their contributions - whether intellectual in
> terms of discussions or actual editing of labels/definitions/axioms/etc

So, given the labels and descriptions in BODO, who have been
contributed by a number of people, which I now like to add to CHEMINF
(not the descriptor entry itself, which is a mere identifier that
changes; just the label and description, if they are copied as is)
under CC-BY-SA (two people gave permission to relicense as such at the
time of writing)...

I cannot just copy/paste them. What would you suggest here practically?

[Michel Dumontier]

So, given the labels and descriptions in BODO, who have been
contributed by a number of people, which I now like to add to CHEMINF
(not the descriptor entry itself, which is a mere identifier that
changes; just the label and description, if they are copied as is)
under CC-BY-SA (two people gave permission to relicense as such at the
time of writing)...

I cannot just copy/paste them. What would you suggest here practically?

Do the BODO contributors want to be part of the CHEMINF effort?  If so, and they are making intellectual contribution to CHEMINF.  If they do not want to be part of CHEMINF, then we won't acknowledge them (except indirectly via BODO).

m.

 

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Egon Willighagen]

On Sun, Oct 16, 2011 at 3:22 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
>> So, given the labels and descriptions in BODO, who have been
>> contributed by a number of people, which I now like to add to CHEMINF
>> (not the descriptor entry itself, which is a mere identifier that
>> changes; just the label and description, if they are copied as is)
>> under CC-BY-SA (two people gave permission to relicense as such at the
>> time of writing)...
>>
>> I cannot just copy/paste them. What would you suggest here practically?
>
> Do the BODO contributors want to be part of the CHEMINF effort?

I do not know.

> If so, and they are making intellectual contribution to CHEMINF.  If they do not want
> to be part of CHEMINF, then we won't acknowledge them (except indirectly via
> BODO).

Except for the fact that they have copyright over the descriptions and
labels... do I understand correctly this is why you said we need finer
acknowledgement which we currently cannot / do not do?

[Michel Dumontier]

On Sun, Oct 16, 2011 at 10:39 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Sun, Oct 16, 2011 at 3:22 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
>> So, given the labels and descriptions in BODO, who have been
>> contributed by a number of people, which I now like to add to CHEMINF
>> (not the descriptor entry itself, which is a mere identifier that
>> changes; just the label and description, if they are copied as is)
>> under CC-BY-SA (two people gave permission to relicense as such at the
>> time of writing)...
>>
>> I cannot just copy/paste them. What would you suggest here practically?
>
> Do the BODO contributors want to be part of the CHEMINF effort?

I do not know.

> If so, and they are making intellectual contribution to CHEMINF.  If they do not want
> to be part of CHEMINF, then we won't acknowledge them (except indirectly via
> BODO).

Except for the fact that they have copyright over the descriptions and
labels...

Did we agree to using copyrighted content in CHEMINF? 

I don't think this fits the bill for an open ontology effort.

m.

 

do I understand correctly this is why you said we need finer
acknowledgement which we currently cannot / do not do?

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Egon Willighagen]

On Sun, Oct 16, 2011 at 3:42 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
>> Except for the fact that they have copyright over the descriptions and
>> labels...
>
> Did we agree to using copyrighted content in CHEMINF?

Is CC-BY-SA licensed material not copyrighted then? I would say it
is... it is copyrighted by the current contributors, and we license it
under CC-BY-SA to others...

If we wanted to waive copyright, the ontology should have been CC0 or so...

> I don't think this fits the bill for an open ontology effort.

Please elaborate...

[Michel Dumontier]

On Sun, Oct 16, 2011 at 10:47 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Sun, Oct 16, 2011 at 3:42 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
>> Except for the fact that they have copyright over the descriptions and
>> labels...
>
> Did we agree to using copyrighted content in CHEMINF?

Is CC-BY-SA licensed material not copyrighted then? I would say it
is... it is copyrighted by the current contributors, and we license it
under CC-BY-SA to others...

If we wanted to waive copyright, the ontology should have been CC0 or so...

According to CC-BY-SA, we are free to share and remix BODO provided that we make the attribution. For the sake of simplicity, we can cite BODO as one of our informing sources (to be added in the CHEMINF ontology header). Unless there are other specific instructions for BODO use, I expect this is sufficient.

 

> I don't think this fits the bill for an open ontology effort.

Please elaborate...

I do not want terms and definitions in the ontology to be held in control by others through copyright restrictions - should they ever withdraw their support for inclusion, our effort would be compromised. 

m. 

 

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Egon Willighagen]

On Sun, Oct 16, 2011 at 3:59 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
> I do not want terms and definitions in the ontology to be held in control by
> others through copyright restrictions - should they ever withdraw their
> support for inclusion, our effort would be compromised.

I was not aware CC licenses could be withdrawn... is that really true?

[Michel Dumontier]

On Sun, Oct 16, 2011 at 11:10 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Sun, Oct 16, 2011 at 3:59 PM, Michel Dumontier
<michel.d...@gmail.com> wrote:
> I do not want terms and definitions in the ontology to be held in control by
> others through copyright restrictions - should they ever withdraw their
> support for inclusion, our effort would be compromised.

I was not aware CC licenses could be withdrawn... is that really true?

http://creativecommons.org/licenses/by-sa/3.0/legalcode

7. Termination

1. This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
2. Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above.

m.

 

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

[Egon Willighagen]

On Sun, Oct 16, 2011 at 4:19 PM, Michel Dumontier <michel.d...@gmail.com> wrote:
> http://creativecommons.org/licenses/by-sa/3.0/legalcode
>
> 7. Termination

These two clauses do not say you can withdraw already distributed CC material; in fact, it says you cannot explicitly:

"provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above."

The last part refers, AFAIK, two the first part of seven, reflecting the situation where the users is not in compliance and terminates the license as user.

So, even when the original author decides to relicense the data, or stop distributing it at all, the material still around will remain under the CC license it was originally be made available under.

[Michel Dumontier]

On Sun, Oct 16, 2011 at 11:25 AM, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Sun, Oct 16, 2011 at 4:19 PM, Michel Dumontier <michel.d...@gmail.com> wrote:
> http://creativecommons.org/licenses/by-sa/3.0/legalcode
>
> 7. Termination

These two clauses do not say you can withdraw already distributed CC material; in fact, it says you cannot explicitly:

"provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above."

The last part refers, AFAIK, two the first part of seven, reflecting the situation where the users is not in compliance and terminates the license as user.

So, even when the original author decides to relicense the data, or stop distributing it at all, the material still around will remain under the CC license it was originally be made available under.

yes, you're right. 

m.

 

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers