[BlueObelisk-discuss] BODR relicensing to CCZero

Discussion:

Egon Willighagen

2012-01-26 20:21:28 UTC

Hi all,

since we just had a patch for BODR data, this may be the best moment
to discuss the future of BODR... there are still several projects
using it, though it may that Kalzium stopped using it (not entirely
sure)...

There are a few patches / bug reports, which I will want to apply, and
I also want to move away from XML towards RDF, and to write a few
tools to create easier to parse files, which previously has been done
by software using the data. Making it RDF means it can be more easily
shared in the semantic web, and this automatically be easily
accessible by websites, etc, etc.

However, I also like to see the data relicensed to CCZero, which is
pretty much in line with the MIT license, but CCZero is better suited
for data. Effectively, we're waiving all rights, allowing anyone to do
with the BODR data they like. This is what the MIT license also
allows, but still is a license. Adoption of the CCZero license is
perfectly in line with the ODOSOS ideas of the Blue Obelisk.

I will forward this message to everyone who contributed data to the
BODR data (this list of AUTHORS can be found in the source code
repository) to ask permission to make this change of 'license' to
CCZero (which technically is a waiver, not a license). I will
summarize here.

Somehow, I feel I have asked for this before, but I could not find any
reference of it in my email archives.

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
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

Jean Brefort

2012-01-30 08:47:54 UTC

Permalink

Hi Egon,

I agree with the proposed BODR license change.

Cheers,
Jean

Post by Egon Willighagen
Hi all,
since we just had a patch for BODR data, this may be the best moment
to discuss the future of BODR... there are still several projects
using it, though it may that Kalzium stopped using it (not entirely
sure)...
There are a few patches / bug reports, which I will want to apply, and
I also want to move away from XML towards RDF, and to write a few
tools to create easier to parse files, which previously has been done
by software using the data. Making it RDF means it can be more easily
shared in the semantic web, and this automatically be easily
accessible by websites, etc, etc.
However, I also like to see the data relicensed to CCZero, which is
pretty much in line with the MIT license, but CCZero is better suited
for data. Effectively, we're waiving all rights, allowing anyone to do
with the BODR data they like. This is what the MIT license also
allows, but still is a license. Adoption of the CCZero license is
perfectly in line with the ODOSOS ideas of the Blue Obelisk.
I will forward this message to everyone who contributed data to the
BODR data (this list of AUTHORS can be found in the source code
repository) to ask permission to make this change of 'license' to
CCZero (which technically is a waiver, not a license). I will
summarize here.
Somehow, I feel I have asked for this before, but I could not find any
reference of it in my email archives.
Egon

Etienne Rebetez

2012-02-06 10:35:25 UTC

Permalink

Post by Egon Willighagen
Hi all,

Post by Egon Willighagen
since we just had a patch for BODR data, this may be the best moment
to discuss the future of BODR... there are still several projects
using it, though it may that Kalzium stopped using it (not entirely
sure)...

Kalzium is still using it. Last year I pushed a few patches to upstream and
they have been applyed. The only thing that is not yet in bodr are the
oxidation states I added last summer.
(Kalzium only uses the elements.xml, isotopes.xml and spectra.xml files)

Post by Egon Willighagen
There are a few patches / bug reports, which I will want to apply, and
I also want to move away from XML towards RDF, and to write a few
tools to create easier to parse files, which previously has been done
by software using the data. Making it RDF means it can be more easily
shared in the semantic web, and this automatically be easily
accessible by websites, etc, etc

Thats cool. But it may take a while until Kalzim has changed the parsing code.

Post by Egon Willighagen
However, I also like to see the data relicensed to CCZero, which is
pretty much in line with the MIT license, but CCZero is better suited
for data. Effectively, we're waiving all rights, allowing anyone to do
with the BODR data they like. This is what the MIT license also
allows, but still is a license. Adoption of the CCZero license is
perfectly in line with the ODOSOS ideas of the Blue Obelisk.
I will forward this message to everyone who contributed data to the
BODR data (this list of AUTHORS can be found in the source code
repository) to ask permission to make this change of 'license' to
CCZero (which technically is a waiver, not a license). I will
summarize here.
Somehow, I feel I have asked for this before, but I could not find any
reference of it in my email archives.
Egon

Regards
Etienne

Egon Willighagen

2012-02-06 12:41:39 UTC

Permalink

Hi Etienne,

On Mon, Feb 6, 2012 at 11:35 AM, Etienne Rebetez

Post by Etienne Rebetez

Kalzium is still using it.

That is great news!

Post by Etienne Rebetez
Last year I pushed a few patches to upstream and
they have been applyed. The only thing that is not yet in bodr are the
oxidation states I added last summer.
(Kalzium only uses the elements.xml, isotopes.xml and spectra.xml files)

OK, I will keep this in mind. Is this filed as a patch on SourceForge
yet? And, would you be OK to donate this under CCZero?

Post by Etienne Rebetez

Thats cool. But it may take a while until Kalzim has changed the parsing code.

Well, that is one of the things I am exploring now: what formats do we
want the data to be available in. And the current XML formats has
already been requested, so, there will be no need to update parsers,
unless you want to parse in data no longer being parsed.

So, the idea is to have one data bundle, and one bundle with scripts
to convert the RDF into other formats.

Egon

Etienne Rebetez

2012-02-06 14:07:23 UTC

Permalink

Post by Egon Willighagen
Hi Etienne,
On Mon, Feb 6, 2012 at 11:35 AM, Etienne Rebetez

Post by Etienne Rebetez

Kalzium is still using it.

That is great news!

Also happy to hear that bodr is alive:)

Post by Egon Willighagen

OK, I will keep this in mind. Is this filed as a patch on SourceForge
yet? And, would you be OK to donate this under CCZero?

No, not yet. The data is not complete.
But I could make a patch of the current kalzium/element.xml file to show the
current difference.
The CCZero licence seems fine to me.

Post by Egon Willighagen

Post by Etienne Rebetez

Thats cool. But it may take a while until Kalzim has changed the parsing code.

Well, that is one of the things I am exploring now: what formats do we
want the data to be available in. And the current XML formats has
already been requested, so, there will be no need to update parsers,
unless you want to parse in data no longer being parsed.
So, the idea is to have one data bundle, and one bundle with scripts
to convert the RDF into other formats.

Ah, ok. Now i get it.

Post by Egon Willighagen
Egon

Geoffrey Hutchison

2012-02-06 15:14:12 UTC

Permalink

Post by Etienne Rebetez
Kalzium is still using it. Last year I pushed a few patches to upstream and
they have been applyed. The only thing that is not yet in bodr are the
oxidation states I added last summer.

Open Babel uses it, but not via XML. And the MolCore project will likely use BODR more directly.

-Geoff

Egon Willighagen

2012-02-06 20:31:51 UTC

Permalink

Geoff,

Post by Geoffrey Hutchison

Open Babel uses it, but not via XML. And the MolCore project will likely use BODR more directly.

you contributed data at some point too... happy with making that CCZero?

Egon