Re: [Cdk-user] Clearing 3D coordinates before depiction

[Egon Willighagen]

Can you point us (well, John particularly) to the SMSD code you are using?
I think if he can find the time, he can make some suggestions on how to
replace it with more modern code.

Egon

On Sat, 23 Sept 2023 at 12:55, Tim Dudgeon  wrote:

> Sorry for the late reply. I've been distracted.
> Sorry, I meant DepictionGenerator. CDKMolDepict is my class that's
> running this! Egon found it correctly.
>
> Regarding the version, yes, this is old code, and I can't remember all the
> details.
> I'm not able to update to the latest as I have a dependency on the
> deprecated org.openscience.cdk:cdk-smsd module.
> I did have a discussion some time ago with Egon about removing the
> dependency on the deprecated code, but we never got that resolved.
> So this means that I can only update to version 2.5. which I've now done.
>
> I still find problems with that version. For some reason that I can't
> recall I'm using:
>
> StructureDiagramGenerator g = new StructureDiagramGenerator();
> g.generateCoordinates(mol);
>
> to do the layout prior to calling DepictionGenerator().depict(mol)
>
> This is causing me problems when handling 2D or 3D molfiles.
> I find I can work around it by doing IAtomContainer -> SMILES ->
> IAtomContainer, which works for now.
> I'll need to look more deeply at the code to work out better options.
> There's a lot going on like MCS alignment and highlighting.
>
> Thanks for your help.
>
>
> On Sat, Sep 23, 2023 at 10:45 AM Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>> If you have that discussion here, I can update
>> https://egonw.github.io/cdkbook/migration.html accordingly.
>>
>> Egon
>>
>> On Sat, 23 Sept 2023 at 11:43, John Mayfield 
>> wrote:
>>
>>> Hi Tim,
>>>
>>> It looks like you're using 5 year old CDK 2.2, is that correct?
>>>
>>> build.gradle:
>>> > project.ext.set('cdkVersion', '2.2')
>>>
>>> It's likely just updating will fix the issue. It should be relatively
>>> seamless but let me know if there are any issues and I'll tell you how to
>>> fix it.
>>>
>>> On Sat, 23 Sept 2023 at 06:38, Egon Willighagen <
>>> egon.willigha...@gmail.com> wrote:
>>>
>>>>
>>>> Tim,
>>>>
>>>> I guess you are referring to
>>>> https://github.com/InformaticsMatters/squonk/blob/master/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMolDepict.java
>>>>
>>>> I also looked at the molfile reading in CDKMoleculeIOUtils and it looks
>>>> correct to me, but the hydrogen adding may be a conflicting issue here.
>>>> What is the actual exception (stacktrace) you get?
>>>>
>>>> Like John set, removing the 3D coordinates should not be needed (the
>>>> CDK is designed to allow having both of them in parallel), but if you have
>>>> to, run .setPoint3d(null) on each atom. That should do the trick.
>>>>
>>>> Egon
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, 20 Sept 2023 at 12:05, John Mayfield <
>>>> john.wilkinson...@gmail.com> wrote:
>>>>
>>>>> I have no idea what CDKMolDepict is, a Knime thing?
>>>>>
>>>>> It's probably just not being updated. Testing the following on
>>>>> master/main works as expected (DepictionGenerator computes the 2D as
>>>>> needed, no need to clear the 3D):
>>>>>
>>>>> public static void main(String[] args) {
>>>>> String molfile = "\n" +
>>>>> "  MJ231200  \n" +
>>>>> "\n" +
>>>>> "  5  4  0  0  1  0  0  0  0  0999 V2000\n" +
>>>>> "0.9718   -0.11390.6193 O   0  0  0  0  0  0  0  0
>>>>>  0  0  0  0\n" +
>>>>> "0.94480.0189   -0.2285 S   0  0  0  0  0  0  0  0
>>>>>  0  0  0  0\n" +
>>>>> "   -0.00420.1584   -0.4371 C   0  0  0  0  0  0  0  0
>>>>>  0  0  0  0\n" +
>>>>> "   -0.28820.8589   -0.1053 C   0  0  0  0  0  0  0  0
>>>>>  0  0  0  0\n" +
>>>>> "1.1863   -0.8418   -0.6272 C   0  0  0  0  0  0  0  0
>>>>>  0  0  0  0\n" +
>>>>> "  1  2  2  0  0  0  0\n" +
>>>>> "  2  3  1  0  0  0  0\n" +
&

Re: [Cdk-user] Clearing 3D coordinates before depiction

[Egon Willighagen]

If you have that discussion here, I can update
https://egonw.github.io/cdkbook/migration.html accordingly.

Egon

On Sat, 23 Sept 2023 at 11:43, John Mayfield 
wrote:

> Hi Tim,
>
> It looks like you're using 5 year old CDK 2.2, is that correct?
>
> build.gradle:
> > project.ext.set('cdkVersion', '2.2')
>
> It's likely just updating will fix the issue. It should be relatively
> seamless but let me know if there are any issues and I'll tell you how to
> fix it.
>
> On Sat, 23 Sept 2023 at 06:38, Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>>
>> Tim,
>>
>> I guess you are referring to
>> https://github.com/InformaticsMatters/squonk/blob/master/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMolDepict.java
>>
>> I also looked at the molfile reading in CDKMoleculeIOUtils and it looks
>> correct to me, but the hydrogen adding may be a conflicting issue here.
>> What is the actual exception (stacktrace) you get?
>>
>> Like John set, removing the 3D coordinates should not be needed (the CDK
>> is designed to allow having both of them in parallel), but if you have to,
>> run .setPoint3d(null) on each atom. That should do the trick.
>>
>> Egon
>>
>>
>>
>>
>>
>> On Wed, 20 Sept 2023 at 12:05, John Mayfield 
>> wrote:
>>
>>> I have no idea what CDKMolDepict is, a Knime thing?
>>>
>>> It's probably just not being updated. Testing the following on
>>> master/main works as expected (DepictionGenerator computes the 2D as
>>> needed, no need to clear the 3D):
>>>
>>> public static void main(String[] args) {
>>> String molfile = "\n" +
>>> "  MJ231200  \n" +
>>> "\n" +
>>> "  5  4  0  0  1  0  0  0  0  0999 V2000\n" +
>>> "0.9718   -0.11390.6193 O   0  0  0  0  0  0  0  0
>>>  0  0  0  0\n" +
>>> "0.94480.0189   -0.2285 S   0  0  0  0  0  0  0  0
>>>  0  0  0  0\n" +
>>> "   -0.00420.1584   -0.4371 C   0  0  0  0  0  0  0  0
>>>  0  0  0  0\n" +
>>> "   -0.28820.8589   -0.1053 C   0  0  0  0  0  0  0  0
>>>  0  0  0  0\n" +
>>> "1.1863   -0.8418   -0.6272 C   0  0  0  0  0  0  0  0
>>>  0  0  0  0\n" +
>>> "  1  2  2  0  0  0  0\n" +
>>> "  2  3  1  0  0  0  0\n" +
>>> "  3  4  1  0  0  0  0\n" +
>>> "  2  5  1  0  0  0  0\n" +
>>> "M  END\n";
>>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>>> try (MDLV2000Reader mdlr = new MDLV2000Reader(new
>>> StringReader(molfile))) {
>>> IAtomContainer mol = mdlr.read(bldr.newAtomContainer());
>>> new DepictionGenerator().depict(mol).writeTo("/tmp/tmp.svg");
>>> } catch (IOException e) {
>>> throw new RuntimeException(e);
>>> } catch (CDKException e) {
>>> throw new RuntimeException(e);
>>> }
>>> }
>>>
>>> On Tue, 19 Sept 2023 at 18:15, Tim Dudgeon 
>>> wrote:
>>>
>>>> I'm using StructureDiagramGenerator.generateCoordinates() to create a
>>>> layout before using CDKMolDepict to generate images for molecules, and I've
>>>> hit a problem when using molecules that already have 3D coordinates as
>>>> StructureDiagramGenerator.generateCoordinates() does not generate a new 2D
>>>> layout if 3D coordinates are present, and passing in a molecule with 3D
>>>> coordinates seems to make CDKMolDepict crash badly.
>>>>
>>>> So, what is the best way to clear the 3D coordinates for a molecule, so
>>>> that StructureDiagramGenerator.generateCoordinates() can do its job?
>>>> ___
>>>> Cdk-user mailing list
>>>> Cdk-user@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>>
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>
>>
>> --
>> Inherited disorders can be hard to interpret when multiple biomarkers are
>> involved. A network approach can help bring insight:
>> https://doi.org/10.1186/s13023-023-02683-9
>>
>> --
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Blog: https://chem-bla-ics.blogspot.com/
>> Mastodon: https://scholar.social/@egonw
>> PubList: https://orcid.org/-0001-7542-0286
>>
>

-- 
Inherited disorders can be hard to interpret when multiple biomarkers are
involved. A network approach can help bring insight:
https://doi.org/10.1186/s13023-023-02683-9

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
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Re: [Cdk-user] Clearing 3D coordinates before depiction

[Egon Willighagen]

Tim,

I guess you are referring to
https://github.com/InformaticsMatters/squonk/blob/master/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMolDepict.java

I also looked at the molfile reading in CDKMoleculeIOUtils and it looks
correct to me, but the hydrogen adding may be a conflicting issue here.
What is the actual exception (stacktrace) you get?

Like John set, removing the 3D coordinates should not be needed (the CDK is
designed to allow having both of them in parallel), but if you have to, run
.setPoint3d(null) on each atom. That should do the trick.

Egon





On Wed, 20 Sept 2023 at 12:05, John Mayfield 
wrote:

> I have no idea what CDKMolDepict is, a Knime thing?
>
> It's probably just not being updated. Testing the following on master/main
> works as expected (DepictionGenerator computes the 2D as needed, no need to
> clear the 3D):
>
> public static void main(String[] args) {
> String molfile = "\n" +
> "  MJ231200  \n" +
> "\n" +
> "  5  4  0  0  1  0  0  0  0  0999 V2000\n" +
> "0.9718   -0.11390.6193 O   0  0  0  0  0  0  0  0  0
>  0  0  0\n" +
> "0.94480.0189   -0.2285 S   0  0  0  0  0  0  0  0  0
>  0  0  0\n" +
> "   -0.00420.1584   -0.4371 C   0  0  0  0  0  0  0  0  0
>  0  0  0\n" +
> "   -0.28820.8589   -0.1053 C   0  0  0  0  0  0  0  0  0
>  0  0  0\n" +
> "1.1863   -0.8418   -0.6272 C   0  0  0  0  0  0  0  0  0
>  0  0  0\n" +
> "  1  2  2  0  0  0  0\n" +
> "  2  3  1  0  0  0  0\n" +
> "  3  4  1  0  0  0  0\n" +
> "  2  5  1  0  0  0  0\n" +
> "M  END\n";
> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
> try (MDLV2000Reader mdlr = new MDLV2000Reader(new
> StringReader(molfile))) {
> IAtomContainer mol = mdlr.read(bldr.newAtomContainer());
> new DepictionGenerator().depict(mol).writeTo("/tmp/tmp.svg");
> } catch (IOException e) {
> throw new RuntimeException(e);
> } catch (CDKException e) {
> throw new RuntimeException(e);
> }
> }
>
> On Tue, 19 Sept 2023 at 18:15, Tim Dudgeon  wrote:
>
>> I'm using StructureDiagramGenerator.generateCoordinates() to create a
>> layout before using CDKMolDepict to generate images for molecules, and I've
>> hit a problem when using molecules that already have 3D coordinates as
>> StructureDiagramGenerator.generateCoordinates() does not generate a new 2D
>> layout if 3D coordinates are present, and passing in a molecule with 3D
>> coordinates seems to make CDKMolDepict crash badly.
>>
>> So, what is the best way to clear the 3D coordinates for a molecule, so
>> that StructureDiagramGenerator.generateCoordinates() can do its job?
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 
Inherited disorders can be hard to interpret when multiple biomarkers are
involved. A network approach can help bring insight:
https://doi.org/10.1186/s13023-023-02683-9

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://scholar.social/@egonw
PubList: https://orcid.org/-0001-7542-0286
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Re: [Cdk-user] Extended Fingerprint: what do the features represent?

[Egon Willighagen]

Sorry, this was probably a duplicate. See the other thread.

Egon

On Sat, 2 Sept 2023 at 10:27, Chong Kim San Allen via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:

> Dear Helpdesk,
>
>
>
> I have used CDK to generate the Extended Fingerprints for a couple of
> compounds and I found that certain features are common among my compounds.
> For example, “14” keeps showing up. I would like to know what is “14”? Is
> it a chemical substructure? The default size for Extended Fingerprint is
> 1024 so I was wondering if there is a way to figure out what each of the
> 1024 features represents.
>
>
>
> Similarly, if I generated ECFP6 which has 2^32 features (count version),
> is there a way for me to figure out what each of those features are? If a
> feature appears to have a high count and I wanted to figure out what this
> feature was, is there a command I can use to find out what that feature
> represents?
>
>
>
> Thanks in advance for your help.
>
>
>
> Best,
> Allen
>
>
> --
>
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-- 
Inherited disorders can be hard to interpret when multiple biomarkers are
involved. A network approach can help bring insight:
https://doi.org/10.1186/s13023-023-02683-9

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://scholar.social/@egonw
PubList: https://orcid.org/-0001-7542-0286
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Re: [Cdk-user] Extended Fingerprint: what do the features represent?

[Egon Willighagen]

Dear Allen,

On Wed, 30 Aug 2023 at 01:24, Chong Kim San Allen via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:

> I am wondering if you can tell me which fingerprints generate unfolded
> features and if there is a table of the subgraphs that represents these
> features for these fingerprints?
>

I would recommend doing this:

- make a set of compounds which all hit the particular bin
- for these, find the maximal common substructure

You can do this visually and algorithmically (depending on your use case).

With kind regards,

Egon

-- 
Inherited disorders can be hard to interpret when multiple biomarkers are
involved. A network approach can help bring insight:
https://doi.org/10.1186/s13023-023-02683-9

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
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Re: [Cdk-user] IUPAC name generation

[Egon Willighagen]

The code in legacy was an academic project, but has limited functionality.
There are nowadays a few open source tools that can predict the IUPAC name.
By using OPSIN you can check if that prediction makes sense: OPSIN
generated a chemical structure from the IUPAC name and if that is the same
as the IUPAC that was generated, you have a good shot.

See https://scholia.toolforge.org/topic/Q110408287

Egon


On Thu, 27 Jul 2023 at 17:33, Yong Gao  wrote:

> Hi,
>
>
>
> Has anyone successfully generated IUPAC names from a smiles string? I see
> some code in the legacy module,  but did not see a way to do it. Also, any
> suggestions for doing this with some other open source software?
>
>
>
> Thanks,
>
> Yong
>
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-- 
Inherited disorders can be hard to interpret when multiple biomarkers are
involved. A network approach can help bring insight:
https://doi.org/10.1186/s13023-023-02683-9

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
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[BlueObelisk-discuss] Fwd: CCL: Call for Papers: Free and Open Source Software symposium at ACS Fall 2023 Meeting

[Egon Willighagen]

Hi all,

this seems interesting:

-- Forwarded message -
From: Susi Lehtola susi.lehtola*_*alumni.helsinki.fi <
owner-chemis...@ccl.net>
Date: Wed, 22 Mar 2023 at 17:09
Subject: CCL: Call for Papers: Free and Open Source Software symposium at
ACS Fall 2023 Meeting

Sent to CCL by: Susi Lehtola [susi.lehtola]

Hi,

I would like to inform the list that we are organizing a symposium "Free and
Open Source Software: Harnessing the Power of Data" in the COMP division at
the
2023 Fall ACS meeting held in San Francisco, California, USA on August
13-17,
2023. The symposium is jointly organized by the Molecular Sciences Software
Institute (molssi.org) and the ACS Open Source Software Convergent Research
Community.

Abstract submission is currently open, with the deadline of April 4, 2023.
To
find our symposium, please look under the Computers in Chemistry (COMP)
division
symposium list. We look forward to receiving abstracts related to both
applications and development of free and open source software.

Thank you,
Ashley Ringer McDonald, Cal Poly San Luis Obispo
Susi Lehtola, University of Helsinki
T. Daniel Crawford, Virginia Tech

PS. Personally, I am especially looking forward to hear talks on what sets
free
and open source software aside from alternatives, such as in enabling new
innovations in industry and academia, but all kinds of abstracts related to
the
topic of the symposium will be considered.

--  -

-- 
Predicting binding affinities can be predicted for each protein variant
with a new QSAR model that takes into account the amino acid change:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00701-3

--
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[Wikidata] Re: Challenge of the day (2): ports without located in or next to body of water

[Egon Willighagen]

Thanks, I found it more difficult for regions I do not know, as I am not
familiar with naming conventions, and add them on a map makes it easier to
shorten a todo list:
https://query.wikidata.org/#%23defaultView%3AMap%0ASELECT%20DISTINCT%20%3Fitem%20%3FitemLabel%20%3Fcoordinates%20WHERE%20%7B%0A%20%20%3Fitem%20wdt%3AP31%2Fwdt%3AP279%2a%20wd%3AQ44782%20%3B%20wdt%3AP625%20%3Fcoordinates%20.%0A%20%20MINUS%20%7B%0A%20%20%20%20%3Fitem%20wdt%3AP206%20%3Fsomething%20.%0A%20%20%7D%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%22.%20%7D%0A%7D%0A

Egon

On Sun, 25 Dec 2022 at 11:44, Romaine Wiki  wrote:

> Hi all,
>
> Too many items on Wikidata still miss the basic statements. Perhaps we can
> focus together for a short period of time on a single subject to get this
> fixed.
>
> For example: all items with instance of (P31) (maritime) port should also
> contain the waterbody at which it is located (P206).
>
> When I just ran a query I saw about 6000 ports that are still missing the
> waterbody at which it is located (P206).
>
> Query:
> https://query.wikidata.org/#SELECT%20%3Fitem%20%3FitemLabel%20WHERE%20%7B%0A%20%20%3Fitem%20wdt%3AP31%2Fwdt%3AP279%2a%20wd%3AQ44782%20.%0A%20%20MINUS%20%7B%0A%20%20%20%20%3Fitem%20wdt%3AP206%20%3Fsomething%20.%0A%20%20%7D%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%22.%20%7D%0A%7D%0A
>
> I already did a few myself but for the largest part help is needed. Who
> has ideas and can help getting this statement added to all the items about
> ports?
>
> Thanks!
>
> Romaine
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-- 
Happy holiday season and new year!

--
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Re: [Cdk-user] package-info.java

[Egon Willighagen]

I have never really used this and generally not up to date with JavaDoc
sounds worth figuring out.

Egon

On Fri, 11 Nov 2022 at 05:41, Uli Fechner  wrote:

> Hi,
>
> I would like to do some serious javadoc documentation for the
> soon-to-come RInChI functionality in CDK.
>
> I could either put this at the class level of one of the main entry
> points or - and this would be my preference - in a package-info.java
> at the package level.
>
> As the javadoc generation is a bit fiddly - any known issues when it
> comes to such a package-info.java being picked up..?
>
> Best
> Uli
>
>
> ___
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> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


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Re: [Cdk-user] Getting warning from AminoAcidCountDescriptor

[Egon Willighagen]

On Thu, 10 Nov 2022 at 14:02, John Mayfield 
wrote:

> Can you to open a GitHub issue, thanks. It's likely harmless but should be
> silent so something we can tweak.
>

Set aside the issue, it *should* be silent... this is the code:

https://github.com/cdk/cdk/blob/40b552eb70d2eafce9540b424f22bd0f710693d9/storage/io/src/main/java/org/openscience/cdk/io/cml/CMLHandler.java#L162

It is using the same logger as the rest of the CDK.

Staffan, is this really the only WARN message you get?

Egon

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Re: [Bioc-devel] Question on GPL2 license copyright

[Egon Willighagen]

If that code is not GPL2 and therefore the full package too, then that's a
license infringement.

Wrapping GPL code in other code is generally only allowed when: 1. clean
room reimplementation of the ideas (from what you say not the case), 2. the
reused code has a clean API and can be easily be replaced by something else
(does not seem to be the case either).

Egon

On Wed, 27 Jul 2022 at 17:18, Jiping Wang  wrote:

> Not to my understanding. The core codes (Fortran) from my package were
> identically copied with only function name change in their package. If they
> call functions or import functions from my package, that’s not an issue.
> But instead they just copied my codes and made their package.
>
> From: Jianhong Ou, Ph.D. 
> Date: Wednesday, July 27, 2022 at 10:15 AM
> To: Jiping Wang , bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] Question on GPL2 license copyright
> Does that package import or depend on your package?
>
> From: Bioc-devel  on behalf of Jiping
> Wang 
> Date: Wednesday, July 27, 2022 at 11:03 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Question on GPL2 license copyright
> Hi,
>
> I have a general question about Bioconductor package copyright. I have a
> Bioconductor package. I recently found most of the core codes of my package
> have been mostly copied and packaged into another package and published in
> Bioconductor. Although the new package says it�s a �derivative� of my
> package. But does it violate the copyright under GPL-2?  Thanks.
>
> Best,
> Ji-Ping Wang
>
>
> [[alternative HTML version deleted]]
>
> [[alternative HTML version deleted]]
>
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>


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Super happy with this new eLife paper describing an Open Science project
where we discuss 260 thousand natural products and where they came from,
all 700 thousand pairs linked to their primary literature: "The LOTUS
initiative for open knowledge management in natural products research",
https://doi.org/10.7554/elife.70780

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
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Re: [Cdk-user] Generation of FCFP Fingerprint

[Egon Willighagen]

Dear Woon Yee,

you can use the getFingerprint() method instead.

Egon

On Mon, 25 Jul 2022 at 10:59, #NG WOON YEE# via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:

> Dear Helpdesk,
>
>
>
> I was using CDK (version 2.7) to generate FCFP4 and 6 for the compound
> butyramide (
> https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL1231396.sdf) and
> ethanol (https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL545.sdf)
> from their MolFiles which I got from CHEMBL. I was using the following
> commands in CDK:
>
>
> ---
>
> package ecfp;
>
> import java.io.*;
>
> import com.opencsv.CSVReader;
>
> import com.opencsv.CSVReaderBuilder;
>
> import com.opencsv.CSVWriter;
>
> import com.opencsv.exceptions.CsvException;
>
> import java.util.Arrays;
>
> import java.util.List;
>
> import java.io.FileInputStream;
>
> import java.io.IOException;
>
>
>
> import org.openscience.cdk.exception.CDKException;
>
> import org.openscience.cdk.fingerprint.CircularFingerprinter;
>
> import org.openscience.cdk.fingerprint.ExtendedFingerprinter;
>
> import org.openscience.cdk.fingerprint.ICountFingerprint;
>
> import org.openscience.cdk.interfaces.IAtomContainer;
>
> import org.openscience.cdk.interfaces.IChemObjectBuilder;
>
> import org.openscience.cdk.io.MDLV2000Reader;
>
> import org.openscience.cdk.silent.SilentChemObjectBuilder;
>
>
>
> public class main{
>
>   public static void main(String[] args) throws CDKException,
> IOException {
>
>   String filename =
> "C:\\Users\\NGWO0001\\Downloads\\CHEMBL545.sdf.txt";
>
>   FileInputStream in = new FileInputStream(filename);
>
>   MDLV2000Reader reader = new MDLV2000Reader(in);
>
>   IChemObjectBuilder bldr =
> SilentChemObjectBuilder.getInstance();
>
>   IAtomContainer mol = reader.read(bldr.newAtomContainer());
>
>
>
>   CircularFingerprinter fingerprinter0 = new
> CircularFingerprinter(
>
> CircularFingerprinter.CLASS_FCFP4
>
>   );
>
>
>
>
>
>   System.out.println("FCFP4 Ethanol:");
>
>   ICountFingerprint result0 =
> fingerprinter0.getCountFingerprint(mol);
>
>   for (int k=0, n = result0.numOfPopulatedbins(); k < n; ++k) {
>
>String ans4 = "";
>
>ans4 += result0.getHash(k);
>
>ans4 += " " + result0.getCount(k);
>
>System.out.printf("%s\n",ans4);
>
>   }
>
>
>
>   reader.close();
>
> }
>
> }
>
>
> ---
>
>
>
> The results I got were:
>
>
>
> FCFP4 Butyramide:
>
> -1393198889 1
>
> -1212393386 1
>
> -1131767167 2
>
> 0 4
>
> 2 1
>
> 3 1
>
> 425233353 1
>
> 785469695 1
>
> 824716024 1
>
> 994111779 1
>
> 1429107614 1
>
>
>
> FCFP6 Butyramide:
>
> -1393198889 1
>
> -1212393386 1
>
> -1131767167 2
>
> 0 4
>
> 2 1
>
> 3 1
>
> 425233353 1
>
> 785469695 1
>
> 824716024 1
>
> 994111779 1
>
> 1429107614 1
>
>
>
> FCFP4 Ethanol:
>
> -1212393386 1
>
> 0 2
>
> 3 1
>
> 629394235 1
>
> 824716024 1
>
>
>
> FCFP6 Ethanol:
>
> -1212393386 1
>
> 0 2
>
> 3 1
>
> 629394235 1
>
> 824716024 1
>
>
> I think these results may not be right since I thought that fingerprints
> are supposed to be a series of hash and so they ought to be a series of
> fixed-length integers. However, as you see in the results I got, for
> example, for the FCFP6 for ethanol, one is 10-digits long while others are
> single digits and 9-digits long.
>
>
>
> Can you please tell me what I am doing wrong?
>
>
>
> Thanking you in advance for your assistance and time.
>
>
>
> Best regards,
>
> Woon Yee
> ___
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> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 

Super happy with this new eLife paper describing an Open Science project
where we discuss 260 thousand natural products and where they came from,
all 700 thousand pairs linked to their primary literature: "The LOTUS
initiative for open knowledge management in natural products research",
https://doi.org/10.7554/elife.70780

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Bug#1014635: ant: 'ant -version' reports unexpect compile data

[Egon Willighagen]

Package: ant
Version: 1.10.12-1
Severity: normal
X-Debbugs-Cc: egon.willigha...@gmail.com

Dear Maintainer,

when requesting the version of Apache Ant installed it reports the date on 
which it was compiled,
but the date probably wrong :)

For stable:

$ ant -version
Apache Ant(TM) version 1.10.9 compiled on December 25 1969

For testing:

$ ant -version
Apache Ant(TM) version 1.10.12 compiled on January 17 1970

-- System Information:
Debian Release: 11.3
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 
'stable'), (100, 'bullseye-fasttrack'), (100, 'bullseye-backports-staging')
Architecture: amd64 (x86_64)

Kernel: Linux 5.18.0-0.bpo.1-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ant depends on:
ii  default-jre-headless [java8-runtime-headless] 2:1.11-72
ii  openjdk-11-jre-headless [java8-runtime-headless]  11.0.15+10-1~deb11u1
ii  openjdk-17-jre-headless [java8-runtime-headless]  17.0.3+7-1~deb11u1

Versions of packages ant recommends:
ii  ant-optional  1.10.12-1

Versions of packages ant suggests:
pn  ant-doc  
ii  openjdk-11-jdk [java-sdk]11.0.15+10-1~deb11u1
ii  openjdk-11-jdk-headless [java-compiler]  11.0.15+10-1~deb11u1
ii  openjdk-17-jdk [java-sdk]17.0.3+7-1~deb11u1
ii  openjdk-17-jdk-headless [java-compiler]  17.0.3+7-1~deb11u1

-- no debconf information

Bug#1014635: ant: 'ant -version' reports unexpect compile data

[Egon Willighagen]

Package: ant
Version: 1.10.12-1
Severity: normal
X-Debbugs-Cc: egon.willigha...@gmail.com

Dear Maintainer,

when requesting the version of Apache Ant installed it reports the date on 
which it was compiled,
but the date probably wrong :)

For stable:

$ ant -version
Apache Ant(TM) version 1.10.9 compiled on December 25 1969

For testing:

$ ant -version
Apache Ant(TM) version 1.10.12 compiled on January 17 1970

-- System Information:
Debian Release: 11.3
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 
'stable'), (100, 'bullseye-fasttrack'), (100, 'bullseye-backports-staging')
Architecture: amd64 (x86_64)

Kernel: Linux 5.18.0-0.bpo.1-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ant depends on:
ii  default-jre-headless [java8-runtime-headless] 2:1.11-72
ii  openjdk-11-jre-headless [java8-runtime-headless]  11.0.15+10-1~deb11u1
ii  openjdk-17-jre-headless [java8-runtime-headless]  17.0.3+7-1~deb11u1

Versions of packages ant recommends:
ii  ant-optional  1.10.12-1

Versions of packages ant suggests:
pn  ant-doc  
ii  openjdk-11-jdk [java-sdk]11.0.15+10-1~deb11u1
ii  openjdk-11-jdk-headless [java-compiler]  11.0.15+10-1~deb11u1
ii  openjdk-17-jdk [java-sdk]17.0.3+7-1~deb11u1
ii  openjdk-17-jdk-headless [java-compiler]  17.0.3+7-1~deb11u1

-- no debconf information

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.
 Please use
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[kde-cli-tools] [Bug 429408] kde-open5 changes case of argument

[Egon Willighagen]

https://bugs.kde.org/show_bug.cgi?id=429408

--- Comment #5 from Egon Willighagen  ---
(In reply to Egon Willighagen from comment #3)
> I got here via this StackOverflow workaround for a problem where Slack does

SO link:
https://stackoverflow.com/questions/70867064/signing-into-slack-desktop-not-working-on-4-23-0-64-bit-ubuntu/71062113#71062113

The approach to get the URLs is basically:

```shell
while sleep .1; do ps aux | grep slack | grep -v grep | grep magic; done
```

Can I just say this status of this bug should not be mere NORMAL but actually
is a data corruption bug? Maybe not one of the severest, but annoyingly
annoying.

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[kde-cli-tools] [Bug 429408] kde-open5 changes case of argument

[Egon Willighagen]

https://bugs.kde.org/show_bug.cgi?id=429408

Egon Willighagen  changed:

   What|Removed |Added

 CC||egon.willigha...@gmail.com

--- Comment #3 from Egon Willighagen  ---
I got here via this StackOverflow workaround for a problem where Slack does not
open all workspaces. The SO flow suggests the same upper/lower rewrite by KDE
as a suspect. Here is some data from my machine just now (for privacy I use
fake codes, like WORKSPACEID, xxx, , and zzz, of course with upper/lower
casing exact):

/bin/sh /usr/bin/xdg-open
slack://WORKSPACEID/magic-login///magic-login/zzz-z-z
kde-open5
slack://WORKSPACEID/magic-login///magic-login/zzz-z-z
/usr/lib/slack/slack --enable-crashpad
slack://workspaceid/magic-login///magic-login/zzz-z-z

I hope you trust my translation of my observation, but I can confirm that
WORKSPACEID goed into kde-open5 as upper case, but is converted to lower case
when passed to the `/usr/lib/slack/slack` application. And Slack seems to be
case sensitive as suggested in the SO post: if I upper case back the
WORKSPACEID in the `/usr/lib/slack/slack` call, then it opens properly.

* Slack 4.23.0
* kde-open5/kioclient 5.20.5

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Re: [Cdk-user] [Cdk-devel] Registration ending soon for CDK 20th anniversary symposium on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.

[Egon Willighagen]

Thanks for the reminder!

Egon

On Wed, 19 Jan 2022 at 11:30, Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:

> Dear all,
>
> as announced last November on this list, the CDK 20th anniversary workshop
> will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.
>
> We are reaching the end of the registration period with the hotel, which
> is tomorrow. They might be able to hold the rooms for a tiny little longer,
> but there is no guarantee. At the moment, there are 20 rooms left.
> The closer we get to the event, the more we compete with the regular
> guests for rooms.
> Please consider booking ASAP if you are interested to join. It is really
> nice there :)
>
> For more information including how to register please visit
>
>
> https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647
>
> Kind regards,
>
> Chris
>
> —
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> Phone Secretariat: +49-3641-948171
> http://cheminf.uni-jena.de
> http://orcid.org/-0001-6966-0814
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
>
>
> ___
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>


-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [BlueObelisk-discuss] [Cdk-devel] Registration ending soon for CDK 20th anniversary symposium on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.

[Egon Willighagen]

Thanks for the reminder!

Egon

On Wed, 19 Jan 2022 at 11:30, Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:

> Dear all,
>
> as announced last November on this list, the CDK 20th anniversary workshop
> will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.
>
> We are reaching the end of the registration period with the hotel, which
> is tomorrow. They might be able to hold the rooms for a tiny little longer,
> but there is no guarantee. At the moment, there are 20 rooms left.
> The closer we get to the event, the more we compete with the regular
> guests for rooms.
> Please consider booking ASAP if you are interested to join. It is really
> nice there :)
>
> For more information including how to register please visit
>
>
> https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647
>
> Kind regards,
>
> Chris
>
> —
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> Phone Secretariat: +49-3641-948171
> http://cheminf.uni-jena.de
> http://orcid.org/-0001-6966-0814
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
>
>
> ___
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> cdk-de...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>


-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

[Egon Willighagen]

On Tue, 18 Jan 2022 at 06:53, Robert Hanson via Blueobelisk-discuss <
blueobelisk-discuss@lists.sourceforge.net> wrote:

> Great idea!
>

Okay, no idea where this message is coming from :)

It was indeed a great idea (imho). The first Blue Obelisk paper (
https://pubs.acs.org/doi/10.1021/ci050400b) has had a CC-BY license for
almost 7 years now:
https://sourceforge.net/p/blueobelisk/mailman/message/33816652/ (thx to
funding by Chris).

Egon

-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

[Egon Willighagen]

On Sat, Jan 1, 2022 at 1:10 PM Egon Willighagen 
wrote:

> I intend to push this Euclid 2 and CMLXOM 4, so increasing the major
> version.
>

After Peter's reply, I pushed these to Maven Central.

Egon

-- 

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interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> /
@egonw <https://scholar.social/@egonw>
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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[BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

[Egon Willighagen]

Hi Peter, all,

Most of the dependencies of Euclid/CMLXOM have been updated, with Log4j
giving quite some opportunity to pull in updates for other libraries.

One update still needs to happen, the update from XOM 1.2 to XOM 1.3. This
requires a few API changes: https://github.com/BlueObelisk/euclid/pull/19

The changes are pretty straightforward and are just about return values not
being the more generic Node but the more precise Atttribute/Element.

I intend to push this Euclid 2 and CMLXOM 4, so increasing the major
version.

What do you think?

Egon

-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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[BlueObelisk-discuss] log4j 2.17.0

[Egon Willighagen]

Hi all,

I have just pushed a new Euclid and CMLXOM to Maven Central (via Sonatype)
based on log4j 2.17.0.

Grtz,

Egon

-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
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Re: [BlueObelisk-discuss] Intro + Possible Member

[Egon Willighagen]

On Thu, Dec 2, 2021 at 6:06 AM Suliman Sharif 
wrote:

> Curious to meet other folk in this group. Is there some sort of cryptic
> cheminformatic puzzle I have to solve to join?
>

The puzzle we're all trying to solve is how we can get chemistry to become
a science where knowledge is openly shared.

While we are seeing many promising approaches, the real solution is yet
unknown.

Egon

-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
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Re: [Cdk-user] Support for chemical standardization

[Egon Willighagen]

All the ingredients are there. The thing is, however, that there are
multiple ways to do the standardization. Check what Ola did in Bioclipse-DS
/ Bioclipse-QSAR.

Egon

On Mon, Sep 27, 2021 at 9:24 PM Staffan Arvidsson McShane <
staffan.arvids...@gmail.com> wrote:

> I'm looking for a good way to perform chemical standardization for later
> descriptor and QSAR modeling, to hopefully get more robust results. I've
> searched the CDK javadoc and the cdkbook but haven't found any good matches
> and thus wonder if there's some support within CDK for this task? My
> expertise within the chemical field is limited so I would in the best of
> worlds use something with good defaults and not requiring much tuning or
> know-how and that still yields good results. If none exists within CDK, is
> there a good alternative, possibly within Java or JVM-based languages that
> anyone can recommend?
>
> Best,
> Staffan Arvidsson McShane
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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[Cdk-user] CDK via Bioclipse/Bacting in Python and on Google Collab with pybacting

[Egon Willighagen]

Hi all,

just a quick note that a recent Twitter discussion led to a Python wrapper
for Bacting [0,1] which is a Maven-ized version of (subset of, but growing)
Bioclipse, called pybacting [2] which is available from PyPI and with that
easy to use. Bacting/pybacting is using CDK 2.5.

So, you can actually on Google Collab (or other Jupyter notebook platforms)
do stuff like:

import pybactingprint(pybacting.from_smiles("COC"))

HT to Charles Tapley Hoyt

Egon

0.https://joss.theoj.org/papers/10.21105/joss.02558
1.https://github.com/egonw/bacting
2.https://github.com/cthoyt/pybacting/

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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[BlueObelisk-discuss] CMLXOM 3.2 pushed to Maven Central :)

[Egon Willighagen]

Hi all,

I just pushed CMLXOM 3.2 to Maven Central. After Euclid, this is the second
WWMM package now available from Maven Central (via Sonatype).

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
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Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

[Egon Willighagen]

On Sun, Jul 11, 2021 at 8:51 PM Peter Murray-Rust  wrote:

> As you've probably found the message comes from CMLAtom, and is one of the
> hardcoded validation rules for CML (these would be better done with an
> XPath-type tool like Schematron, but that's irrelevant).
>

That's okay.


> The error makes no sense!
>

Agreed :) It took me a while to figure out that the error was actually not
because of the test, but triggered but something that (did not) happened in
some other test.


>  My guess would be that it's picked up the wrong version of some library.
> I haven't used Java recently - my suggestion would be to see if it is true
> with other Java versions. If I understand it right, the error occurs in the
> repository tests when building the system.
>

Actually, my current understanding is that it is not a dependency, nor a
Java version, but likely a concurrency problem. The factory orchestrating
the generation of the internal data model uses static/global variables and
somewhere it forgot to clean the stack of parents, so that when the
cml:atom is creating, it falsely believes it has an atomArray parent with
an cml:formula grandparent...

In the end, I could work around the problem to have the test (about
removing non-CML attributes) not use cml:atom but cml:cml. I also filed a
bug report to rework the code to not use global variables (which may be
tricky...).

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

[Egon Willighagen]

On Sun, Jul 11, 2021 at 7:29 PM Peter Murray-Rust  wrote:

> I imagine I wrote this code but don't have it on my machine at present.
> Can you give a pointer to the Github repo and I'll have a look - but I'm
> not very optimistic I can help.
>

https://github.com/BlueObelisk/cmlxom


> Would love to see some projects that use CMLXom - it has a lot of
> potential still.
>

Well, this is why I am working on it. The CDK is using it, and as a
consequence Bacting (*) is too. The current CMLXOM has some dependency
versions with security issues.

I found a workaround for the failing test, to use cml:cml instead of
cml:atom. The problem is that it remembers a Stack that does not go with
the CML String being parsed. Hence my suspicion of some concurrency. The
problem basically is the global variables in CMLNodeFactory.

So, with the code base also compiling in GitHub, I will move on next
weekend with updating the pom.xml to prepare for releases via Sonatype for
Maven Central.

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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[BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

[Egon Willighagen]

Hi all,

On Mon, Jun 28, 2021 at 10:22 PM Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> Next up is cmlxom :) (And then a PR for the CDK)
>

I have started working on cmlxom to get it ready for uploading to Maven
Central.

Today I have done the following things:

- update JUnit4
- set up GitHub Actions for compiling and running the tests

But on GitHub there are currently two tests that fail (with Java 11 and 8),
which do not fail locally (with Java 11 and 8). Second, the fail does not
make sense:

java.lang.RuntimeException: nu.xom.ParsingException: Atom grandparent must
be not be formula
at org.xmlcml.cml.base.CMLUtil.parseCML(CMLUtil.java:429)
at
org.xmlcml.cml.base.CMLUtilTest.removeNonCMLAttributes(CMLUtilTest.java:531)

But the CML fragment (a String) in the two failing tests do not have
CMLFormular, and I am puzzled why this exception is thrown... maybe more
later. ideas welcome.

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> /
@egonw <https://scholar.social/@egonw>
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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[BlueObelisk-discuss] Maven Central (was: WWMM & CML -- sunsetting of Mercurial in Bitbucket)

[Egon Willighagen]

Hi all,

every time I want to upload something new to Sonatype and via that to Maven
Central, they changed something. So, Euclid 1.3 instead of Euclid 1.1 is
tomorrow on Maven Central (after rerun of the index), but it can already be
found at:

https://repo1.maven.org/maven2/org/blueobelisk/euclid/1.3/

We have the groupId org.blueobelisk :)

This release is not just what was copied from BitBucket, but actually got
some updated dependencies, fixing several severe security issues. Worth
upgrading.

Next up is cmlxom :) (And then a PR for the CDK)

Egon

On Fri, Jun 25, 2021 at 9:15 PM Egon Willighagen 
wrote:

>
>
> On Fri, Jun 25, 2021 at 4:23 PM Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>> But if you need CMLXOM or other parts to be published in Maven Central,
>>> I'd say go ahead.
>>>
>>
>> Okay, going ahead and will use org.blueoblelisk as Maven groupId
>>
>
> GroupId requested: https://issues.sonatype.org/browse/OSSRH-70540
>
> Egon
>
> --
> This year I am stepping down as co-Editor-in-Chief of the Journal of
> Cheminformatics, because of a conflict of interest with Springer Nature.
> See https://twitter.com/egonwillighagen/status/1403299501947899907
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen>
>  / @egonw <https://scholar.social/@egonw>
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
>


-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> /
@egonw <https://scholar.social/@egonw>
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

On Fri, Jun 25, 2021 at 4:23 PM Egon Willighagen 
wrote:

> But if you need CMLXOM or other parts to be published in Maven Central,
>> I'd say go ahead.
>>
>
> Okay, going ahead and will use org.blueoblelisk as Maven groupId
>

GroupId requested: https://issues.sonatype.org/browse/OSSRH-70540

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> /
@egonw <https://scholar.social/@egonw>
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

On Fri, Jun 25, 2021 at 3:25 PM Oliver Stueker 
wrote:

> Back between Christmas 2019 and the early days of 2020, Mark and I made
> good progress in enabling CI (Travis) on many of the projects.
> At some point I had to stop because I needed to get access to publish
> modules on Maven Central, which took a few days. Then 2020 happened.
>

Indeed.

I haven't touched those repos in 18 months now
>

Yes, I saw that... time has passed by quickly... it's all such a blur


> and I don't know when I'll take the time to continue working on them.
>

This is what we have the Dr. Who model for :)


> I still have the plan to get the jumbo-converters and all their
> dependencies set-up for CI and published to Maven Central, but I don't have
> a timeline, as for me this is just a hobby-project.
>

Understood! (same here)


> At some point I'd even like to work on porting the www.xml-cml.org
> website to use Jekyll and be hosted from a GitHub-repo, so that we can
> expand the dictionaries with Pull-requests.
>

Yes, that sounds good.


> But if you need CMLXOM or other parts to be published in Maven Central,
> I'd say go ahead.
>

Okay, going ahead and will use org.blueoblelisk as Maven groupId

Egon



>
> Cheers,
> Oliver
>
> Oliver Stueker
> Research Consultant, ACENET
> 709.864.3021 | www.ace-net.ca | @computeatlantic
>
> A Compute Canada Regional Partner
>
>
> On Fri, Jun 25, 2021 at 3:46 AM Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>>
>> Hi Oliver, Mark, all
>>
>> On Fri, Dec 13, 2019 at 9:01 PM Oliver Stueker 
>> wrote:
>>
>>> We would like to get your feedback on a number of points:
>>>
>>
>>>- Do you also think that https://github.com/BlueObelisk would be a
>>>good home for the WWMM and CML repositories?  The names wwmm and cml are
>>>already taken on GitHub.com.
>>>
>>> I think it worked out quite well.
>>
>>>
>>>- What are your thoughts?
>>>
>>> What are people's current plans to make modules available on Maven
>> Central? For example, I just discovered the CMLXOM needs updates and needs
>> to be uploaded to Maven Central.
>>
>>- Has anyone already started this?
>>- Should we use io.github.blueobelisk as (new) group ID?
>>
>> I have a Sonatype account and can set something up, but want to make sure
>> no one else is already planning this.
>>
>> Egon
>>
>> --
>> This year I am stepping down as co-Editor-in-Chief of the Journal of
>> Cheminformatics, because of a conflict of interest with Springer Nature.
>> See https://twitter.com/egonwillighagen/status/1403299501947899907
>>
>> -
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen>
>>  / @egonw <https://scholar.social/@egonw>
>> Homepage: http://egonw.github.com/
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: https://www.zotero.org/egonw
>> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> /
@egonw <https://scholar.social/@egonw>
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
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[BlueObelisk-discuss] Bacting paper published (Bacting is a follow up of Bioclipse)

[Egon Willighagen]

Hi all,

because I am not good enough to build the Bioclipse UI in Eclipse in a
reproducible way, two years ago I decided to move Bioclipse to the command
line, Mavenizing things along the way, and this resulted in "Bacting".

The paper was just published this week:
https://joss.theoj.org/papers/10.21105/joss.02558

Bacting 0.0.19 "comes" with the latest OPSIN, CDK, etc. It also explains my
interest in moving some CML components to Maven Central ;)

Egon

-- 
This year I am stepping down as co-Editor-in-Chief of the Journal of
Cheminformatics, because of a conflict of interest with Springer Nature.
See https://twitter.com/egonwillighagen/status/1403299501947899907

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

Hi Oliver, Mark, all

On Fri, Dec 13, 2019 at 9:01 PM Oliver Stueker 
wrote:

> We would like to get your feedback on a number of points:
>

>- Do you also think that https://github.com/BlueObelisk would be a
>good home for the WWMM and CML repositories?  The names wwmm and cml are
>already taken on GitHub.com.
>
> I think it worked out quite well.

>
>- What are your thoughts?
>
> What are people's current plans to make modules available on Maven
Central? For example, I just discovered the CMLXOM needs updates and needs
to be uploaded to Maven Central.

   - Has anyone already started this?
   - Should we use io.github.blueobelisk as (new) group ID?

I have a Sonatype account and can set something up, but want to make sure
no one else is already planning this.

Egon

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[BlueObelisk-discuss] Fwd: [InChI-discuss] NIH Virtual Workshop on InChI, March 22-24, 2021

[Egon Willighagen]

-- Forwarded message -
From: Steve Heller 
Date: Fri, Feb 26, 2021 at 1:35 AM
Subject: [InChI-discuss] NIH Virtual Workshop on InChI, March 22-24,2021
To: inchi-disc...@lists.sourceforge.net 


Click to Register for the NIH Virtual Workshop on InChI, March 22-24, 2021


Note that a few presentation slots remain!  If you would like to speak at
the workshop, please submit your proposed title in the registration
comments field.  The organizing committee will review and respond.

A major theme emerging from the December 2020 NIH Workshop on Ultra Large
Chemistry Databases is the essential role of the IUPAC International
Chemical Identifier (InChI) in our ability to link and query across large
and diverse chemistry data resources.  Therefore, we now seek to bring the
chemistry community together for an update on the development of the InChI
and a discussion of its use in  chemistry, biochemistry, and related
research domains, at the NIH Virtual Workshop on InChI, March 22-24, 2021.
Speakers will report on developments in the InChI field, usage of InChI in
their organization, as well as challenges and areas not yet covered by
InChI.  The virtual workshop is scheduled for three half-days on March
22-24, from 11 AM- 3PM EST and will include short talks and panel
discussions.  Registration is free.
Preliminary list of speakers:
Steve HellerNLM/NCBI/PubChem Project A Brief
History of InChI
Ray Boucher InChI Trust/Wiley  The
IUPAC Chemical Structure Standard - Vision and Future
Gerd Blanke Structure Pendium Technologies GmbH Reaction InChI
(RInChI) - What's Next?
Alex Clark  Collaborative Drug Discovery  Mixtures from
a Software Creator's Perspective: Building Upstream from MInChI
Marc Nicklaus   NCI,  NIH
 Tautomers in InChI
Bob Belford UA Little Rock
 InChI Open Education Resource (OER)
Jonathan GoodmanUniversity of Cambridge InChI with Markush
Variations
Iseult LynchUniversity of Birmingham  Towards an
InChI for Nanomaterials
Jeremy Frey University of Southampton Linking the
Physical and Digital: QR Codes and the InChI
Markus Sitzmann FIZ Karlsruhe   The InChI
Resolver and its Protocol
Richard KiddRSC/InChI Trust Towards
Open-source Development for InChI
Yulia Borodina  FDA
  Usage of InChI in SPL Substance Indexing files
Lutz Weber  OntoChem GmbH   Using InChI and
RInChI for Registering Compound and Reactions Extracted from Literature
István Őri  ChemAxon
Integrating InChI and RInChI Native Libraries into Java Applications
Patricia Bento  EMBL-EBI
 InChI Applications in ChEMBL
Peter Linstrom  NIST
Practical Applications of InChI
John Mayfield   NextMove Software   Data
Compression of InChIKeys and 2D Coordinates
Roger Sayle NextMove Software   InChI
on Wikipedia: Why Many Compounds Have More Than One InChI
Tony Williams   EPA
 The CompTox Chemicals Dashboard and Using InChI as a Mapping Identifier
Connor ColeyMIT
 The Open Reaction Database (ORD) Initiative for Standardizing and
Sharing Organic Reaction Data
John Irwin  UC San Francisco   How ZINC
Uses InChI
Mitch MillerNCATS
Global Substance Registration System: Extending the Concept of
InChiKey to Other Substances
Greg LandrumETH Zurich
Using InChI, and bits of InChI,  from within the RDKit

We hope to see you at the workshop!

Stephen Heller, Ph.D.
Chemistry Group, Information Engineering Branch
National Center for Biotechnology Information, NIH

Marc Nicklaus, Ph.D.
Computer-Aided Drug Design Group
Center for Cancer Research, National Cancer Institute, NIH

Evan Bolton, Ph.D.
Chemistry Group, Information Engineering Branch
National Center for Biotechnology Information, NIH

Noel Southall, Ph.D.
Division of Preclinical Innovation
National Center for Advancing Translational Sciences, NIH




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Re: [Cdk-user] CDK support in chemfp 3.5b1

[Egon Willighagen]

On Wed, Jan 20, 2021 at 10:31 AM Andrew Dalke 
wrote:

> So I'm leaving the supported CDK formats in chemfp to SMILES, SDF, and
> InChI. And if no one asks for other formats then I don't need to do
> anything.
>

I understand that supporting XYZ and PDB here is a "when asked".

Regarding unused formats, it would help if we would have a command line
conversion tool again. We used to have one, but in a retrospectively
questionable decision stopped supporting that, bc we had OpenBabel.

Egon

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Re: [Cdk-user] CDK support in chemfp 3.5b1

[Egon Willighagen]

Yes, I understand that. I think the original workflow was first to
establish the bonds ("single" by default) and then use valency information
and hoping that the structure makes sense (no hydrogens missing), etc. The
book has a follow up section on that second step. But I agree with your
doubt about how well it works. I do not remember if I did a validation like
we would do nowadays. It would be good to do something like this:

1. take 1000 random 3D structures from PubChem (add zeros according to
taste)
2. remove all bond info, and keep only the 3D locations
3. rebond, add missing bond orders
4. compare.

Now, this set would not really be a real world scenario. I could imagine
one would like to repeat this for structures from COD too. Actually, maybe
check out this paper:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0279-6

Egon


On Wed, Jan 20, 2021 at 8:19 AM Andrew Dalke 
wrote:

> On Jan 20, 2021, at 07:37, Egon Willighagen 
> wrote:
> > Jmol had code to deduce bonds (for files which only have coordinates and
> no bond info, like XYZ), which was ported at some point to the CDK. Here's
> some example code:
> https://egonw.github.io/cdkbook/missing.html#reconnecting-atoms
>
> Thanks for the pointer, Egon.
>
> I used your book when trying to figure this out. I was blocked because I
> couldn't figure out how to then identify double and triple bonds.
>
> Eg, quoting part of RebondTool.java where it makes the bond:
>
> /**
>  * Returns the bond order for the bond. At this moment, it only returns
>  * 0 or 1, but not 2 or 3, or aromatic bond order.
>  */
>
> private boolean isBonded(double covalentRadiusA, double
> covalentRadiusB, double distance2) {
>
>
> The book's example uses methane, which of course only has single bonds.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>

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Re: [Cdk-user] CDK support in chemfp 3.5b1

[Egon Willighagen]

On Tue, Jan 19, 2021 at 11:50 PM Andrew Dalke 
wrote:

> BTW, I had to drop support for some of the formats, like XYZ and PDB,
> because I couldn't figure out how to use them to read a structure into a
> form that could be use to generate fingerprints. If anyone needs them and
> can tell me how to handle those cases correctly, do let me know.
>

Jmol had code to deduce bonds (for files which only have coordinates and no
bond info, like XYZ), which was ported at some point to the CDK. Here's
some example code:
https://egonw.github.io/cdkbook/missing.html#reconnecting-atoms

Egon

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Re: [Cdk-user] What are the contents of pom.xml file to install cdk-2.0.jar after installing apache maven?

[Egon Willighagen]

Dear Winod,

On Wed, Dec 30, 2020 at 11:24 AM Winod Dhamnekar
 wrote:
> What should be the contents of pom.xml file in cdk directory?

The pom.xml is the file Maven uses to see how the source code needs to
be compiled. It often also contains metadata about the project, such
as authors, license, etc.

> What are the basics, more project information, build setting, environment 
> setting?

I do not understand that question. Can you explain what you are trying to do?

Egon

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Re: [Cdk-user] CDK 2.4 release date?

[Egon Willighagen]

Yes, half yearly releases would be nice. I second the usefulness of being
able to cite a specific version, ideally one on Zenodo with DOI, and that
-SNAPSHOT is not something I would like in a paper either.

That said, making a release takes a couple of hours and as release manager
I also always had some features in mind that still needed to go in.

Egon

On Mon, Dec 21, 2020 at 8:17 PM Daniel Katzel  wrote:

> Hello,
>   I know we have had many many changes the past year on CDK 2.4-SNAPSHOT.
> Is there a planned timeframe for its eventual release?  I have a couple of
> projects that depend on CDK and I don't want to keep referring to a
> SNAPSHOT.
>
> Thanks and have a safe and happy holidays and new year!
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Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

[Egon Willighagen]

On Thu, Dec 3, 2020 at 12:08 PM Steve Vestal 
wrote:

> Does anyone know of an open source software package that can convert
> SMILES strings into RDF (brass ring) or any sort of attributed graph data
> structure?
>
Oh, that takes me back... yes, I think I wrote an RDF exporter for the CDK
at some point. But I do need to digging up, because I don't immediately see
it in the list [0].

Egon

0.
https://egonw.github.io/cdkbook/appfileformats.html#the-readers-and-writers

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Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

[Egon Willighagen]

Please have a look at:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0282-y

On Tue, Dec 1, 2020 at 4:04 PM Steve Vestal 
wrote:

> Does anyone know of a structure database that can be queried using an
> RDF query language like SPARQL?  PubChemRDF can be accessed in RDF
> format, but it encodes structures as SMILES strings, which cannot be
> queried in this way.
>
> If not, can anyone suggest open source software that might be used to
> construct a modest RDF dataset from an existing structure database for
> the purpose of experimenting?  For example, software that can translate
> SMILES strings into an annotated graph data structure of some sort?
>
> Thanks in advance for any suggestions.
>
>
>
>
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

How will we handle LOD entries for data sets provided by a third party?

For example, Bio2RDF released over time quite a few data sets, each having
a separate entry in the LOD cloud, e.g. Bio2rdf::DrugBank?

Do we create a separate Wikidata item for that? Link it to the Wikidata
item for Drugbank, so that one database can have more than one LOD Cloud ID?

What do you think?

Egon




On Tue, Sep 22, 2020 at 11:02 AM Andy Mabbett 
wrote:

> On Wed, 16 Sep 2020 at 14:53, Lydia Pintscher
>  wrote:
>
> > And we now have the Property \o/
> https://www.wikidata.org/wiki/Property:P8605
>
> Now in Mix'n'match:
>
>https://mix-n-match.toolforge.org/#/catalog/3862
>
> --
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> @pigsonthewing
> http://pigsonthewing.org.uk
>
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

Awesome, thanks!

How was it done? I like to learn a bit more about the steps.

Egon

On Tue, Sep 22, 2020 at 11:02 AM Andy Mabbett 
wrote:

> On Wed, 16 Sep 2020 at 14:53, Lydia Pintscher
>  wrote:
>
> > And we now have the Property \o/
> https://www.wikidata.org/wiki/Property:P8605
>
> Now in Mix'n'match:
>
>https://mix-n-match.toolforge.org/#/catalog/3862
>
> --
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> @pigsonthewing
> http://pigsonthewing.org.uk
>
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

i guess this is the downstream tools still needing to catch up. The
formatter URL is defined: https://www.wikidata.org/wiki/Property:P8605#P1630

Egon

On Thu, Sep 17, 2020 at 8:52 AM Sebastian Hellmann <
hellm...@informatik.uni-leipzig.de> wrote:

> Hi all,
>
> a question here:
>
> P8605 is shown as string, e.g. as "doi" in
> https://www.wikidata.org/wiki/Q5188229  , which is the last path segment
> of the identifier,  shouldn't this be "http://lod-cloud.net/dataset/doi; ?
>
> At least for the LOD Cloud project.
>
> -- Sebastian
>
>
>
> On 16.09.20 15:53, Lydia Pintscher wrote:
> > On Sat, Aug 15, 2020 at 9:06 AM Egon Willighagen
> >  wrote:
> >> Proposed:
> https://www.wikidata.org/wiki/Wikidata:Property_proposal/Generic#Linked_Open_Data_Cloud_identifier
> >>
> >> Egon
> > And we now have the Property \o/
> https://www.wikidata.org/wiki/Property:P8605
> >
> >
> > Cheers
> > Lydia
> >
>
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

All,

On Wed, Sep 16, 2020 at 3:54 PM Lydia Pintscher <
lydia.pintsc...@wikimedia.de> wrote:

> And we now have the Property \o/
> https://www.wikidata.org/wiki/Property:P8605


When approved, a fifth example was added, for a Bio2RDF subset in the LOD
cloud, linked the Bio2RDF entry in Wikidata itself (and not a Wikidata item
for the subset). That would be possible, but then bio2rdf-pubchem (and
many, many more) will be linked to that Wikidata item for Bio2RDF. Is that
what we want? Or should bio2rdf-pubchem be linked to the PubChem entry in
Wikidata? Etc?

What do you think?

Egon

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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

Ah, awesome!

I've been very busy and hope someone will beat me to it, but I was thinking
of doing some webscraping and prepare a Mix'n'Match data set... but we can
all also just do a few more manually :)

Egon


On Wed, Sep 16, 2020 at 3:54 PM Lydia Pintscher <
lydia.pintsc...@wikimedia.de> wrote:

> On Sat, Aug 15, 2020 at 9:06 AM Egon Willighagen
>  wrote:
> > Proposed:
> https://www.wikidata.org/wiki/Wikidata:Property_proposal/Generic#Linked_Open_Data_Cloud_identifier
> >
> > Egon
>
> And we now have the Property \o/
> https://www.wikidata.org/wiki/Property:P8605
>
>
> Cheers
> Lydia
>
> --
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>
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>


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-
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

Proposed:
https://www.wikidata.org/wiki/Wikidata:Property_proposal/Generic#Linked_Open_Data_Cloud_identifier

Egon

On Sat, Aug 15, 2020 at 8:38 AM Egon Willighagen 
wrote:

>
> I'll have a go at it.
>
> Egon
>
> On Fri, Aug 14, 2020 at 3:51 PM Lydia Pintscher <
> lydia.pintsc...@wikimedia.de> wrote:
>
>> On Fri, Aug 14, 2020 at 3:46 PM Lydia Pintscher
>>  wrote:
>> > Hey :)
>> >
>> > Adam got the current numbers for us at
>> https://phabricator.wikimedia.org/P12190
>> > Anyone up for helping put those in?
>>
>> Oh and one thing I forgot: It would be pretty helpful for further
>> automating this if we had the mapping between Wikidata's property and
>> the LODCloud entries. Anyone up for proposing a new property for that?
>>
>>
>> Cheers
>> Lydia
>>
>> --
>> Lydia Pintscher - http://about.me/lydia.pintscher
>> Product Manager for Wikidata
>>
>> Wikimedia Deutschland e.V.
>> Tempelhofer Ufer 23-24
>> 10963 Berlin
>> www.wikimedia.de
>>
>> Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
>>
>> Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg
>> unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das
>> Finanzamt für Körperschaften I Berlin, Steuernummer 27/029/42207.
>>
>> ___
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>> https://lists.wikimedia.org/mailman/listinfo/wikidata
>>
>
>
> --
> Have you heard about Wikidata already? "Use Scholia and Wikidata to find
> scientific literature" is a new tutorial from my colleague Lauren Dupuis.
> https://laurendupuis.github.io/Scholia_tutorial/
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
>


-- 
Have you heard about Wikidata already? "Use Scholia and Wikidata to find
scientific literature" is a new tutorial from my colleague Lauren Dupuis.
https://laurendupuis.github.io/Scholia_tutorial/

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
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PubList: https://www.zotero.org/egonw
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

I'll have a go at it.

Egon

On Fri, Aug 14, 2020 at 3:51 PM Lydia Pintscher <
lydia.pintsc...@wikimedia.de> wrote:

> On Fri, Aug 14, 2020 at 3:46 PM Lydia Pintscher
>  wrote:
> > Hey :)
> >
> > Adam got the current numbers for us at
> https://phabricator.wikimedia.org/P12190
> > Anyone up for helping put those in?
>
> Oh and one thing I forgot: It would be pretty helpful for further
> automating this if we had the mapping between Wikidata's property and
> the LODCloud entries. Anyone up for proposing a new property for that?
>
>
> Cheers
> Lydia
>
> --
> Lydia Pintscher - http://about.me/lydia.pintscher
> Product Manager for Wikidata
>
> Wikimedia Deutschland e.V.
> Tempelhofer Ufer 23-24
> 10963 Berlin
> www.wikimedia.de
>
> Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
>
> Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg
> unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das
> Finanzamt für Körperschaften I Berlin, Steuernummer 27/029/42207.
>
> ___
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> https://lists.wikimedia.org/mailman/listinfo/wikidata
>


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scientific literature" is a new tutorial from my colleague Lauren Dupuis.
https://laurendupuis.github.io/Scholia_tutorial/

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [Wikidata] Wikidata in the LOD cloud

[Egon Willighagen]

Of particular interest is the link counts, based on formatter URI for RDF
resource (P1921).

There are 167 property - P1921 combinations: https://w.wiki/YsV

Calculating the number of links times out when run for all properties:
https://w.wiki/Ysk So, an iterative script is likely more practical.

But basically, the query just counts the number of items with a property,
but limited by the properties that have a P1921 defined. Surely, that can
be done more efficiently.

Egon

On Wed, Aug 5, 2020 at 11:30 PM Andy Mabbett 
wrote:

> On Wed, 5 Aug 2020 at 22:12, Daniel Mietchen
>  wrote:
>
> > the newest version of the LOD cloud is just a week old,[1] but the
> underlying information for Wikidata is out of date by several years.[2]
> >
> > Has anyone looked into streamlining the data submission process?
>
> Yes; here's the discussion from 2018:
>
>https://lists.wikimedia.org/pipermail/wikidata/2018-April/011988.html
>
> Lucas Werkmeister was handing this from the Wikidata Dev Team's side:
>
>https://lists.wikimedia.org/pipermail/wikidata/2018-May/012042.html
>
> --
> Andy Mabbett
> @pigsonthewing
> http://pigsonthewing.org.uk
>
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https://laurendupuis.github.io/Scholia_tutorial/

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [Wikidata] WDQS outage - 2020/07/23

[Egon Willighagen]

See https://phabricator.wikimedia.org/T242453 linked on the report page

On Sun, Jul 26, 2020 at 6:55 PM Kingsley Idehen 
wrote:

> On 7/24/20 3:18 PM, Ryan Kemper wrote:
> > Hi all,
> >
> > We experienced WDQS service disruptions on 2020/07/23. As a result
> > there was a full outage (inability to respond to all queries) for a
> > period of several minutes, and a more extended period of
> > intermittently degraded service (inability to respond to a subset of
> > queries) for 1-2 hours.
> >
> > The full incident report is available here:
> >
> https://wikitech.wikimedia.org/wiki/Incident_documentation/20200723-wdqs-outage
> >
> > Ultimately, we traced the proximate cause to a series of
> > non-performant queries, which caused a deadlock in blazegraph, the
> > backend for WDQS. We have placed a temporary block on the IP address
> > in question and are taking steps to better define service availability
> > expectations as well as processes to make detection of these events
> > more streamlined going forward.
>
>
> What was the problem query?
>
> I ask because I would like to try it against our Wikidata endpoint at:
> https://wikidata.demo.openlinksw.com/sparql .
>
> We have an "Anytime Query" feature designed for these kinds of problems,
> hence the  vested interest in these kinds of problem queries.
>
> --
> Regards,
>
> Kingsley Idehen
> Founder & CEO
> OpenLink Software
> Home Page: http://www.openlinksw.com
> Community Support: https://community.openlinksw.com
> Weblogs (Blogs):
> Company Blog: https://medium.com/openlink-software-blog
> Virtuoso Blog: https://medium.com/virtuoso-blog
> Data Access Drivers Blog:
> https://medium.com/openlink-odbc-jdbc-ado-net-data-access-drivers
>
> Personal Weblogs (Blogs):
> Medium Blog: https://medium.com/@kidehen
> Legacy Blogs: http://www.openlinksw.com/blog/~kidehen/
>   http://kidehen.blogspot.com
>
> Profile Pages:
> Pinterest: https://www.pinterest.com/kidehen/
> Quora: https://www.quora.com/profile/Kingsley-Uyi-Idehen
> Twitter: https://twitter.com/kidehen
> Google+: https://plus.google.com/+KingsleyIdehen/about
> LinkedIn: http://www.linkedin.com/in/kidehen
>
> Web Identities (WebID):
> Personal: http://kingsley.idehen.net/public_home/kidehen/profile.ttl#i
> :
> http://id.myopenlink.net/DAV/home/KingsleyUyiIdehen/Public/kingsley.ttl#this
>
>
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Re: [Wikidata] WDQS status

[Egon Willighagen]

Dear Guillaume,

On Thu, Jul 9, 2020 at 3:23 PM Guillaume Lederrey 
wrote:

> Some very preliminary analysis indicates that less then 2% of the queries
> on WDQS generate more than 90% of the load. This is definitely something we
> need to better understand.
>

Is the data behind that available? I wonder if I recognize any of the top
25 queries.

(I guess the top 2% can be simple queries run very many times, as well as
hard queries rarely run, correct?)

Egon


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Re: [Cdk-user] VolSurf-like molecular descriptors

[Egon Willighagen]

Dear Fleming,

while the methods are different, the CDK does have descriptors for some of
the properties you mention. Some are based on the 3D structure, but not all.

When it comes to interactions, less so. The CDK does not have a lot of
functionality to calculate or map properties onto the molecular surface. I
know that J(S)mol can at least visualize properties onto the surface, but
not sure what surface properties it can calculate.

Others?

Egon

On Fri, Jul 3, 2020 at 4:55 PM Fleming Kretschmer <
fleming.kretsch...@uni-jena.de> wrote:

> Dear all,
>
> We're looking for methods to encode the 3D-Structure of molecules and
> have come across the "VolSurf+" descriptors, used for example in the
> publication https://doi.org/10.1016/j.aca.2016.02.014 :
>
> "[We use] VolSurf + version 1.7.0.l [28]. This software uses GRID
> force fields [29] to characterise molecular interactions, such as
> hydrophilic/hydrophobic and hydrogen bonding donor/acceptor surface
> volumes around the molecules, using a water probe (OH2), a hydrophobic
> probe (DRY), a hydrogen-bonding acceptor carbonyl oxygen probe (O),
> and a hydrogen-bonding donor amide nitrogen probe (N1). Energy maps,
> called Molecular Interaction Fields (MIFs), were then converted into
> molecular descriptors. VolSurf + generates 128 molecular descriptors
> related to molecular shape, volume, polarisability, polar surface
> area, hydrophobic surface area, lipophilicity, molecular diffusion,
> and solubility. It also includes specific descriptors, which refer to
> the volume and relative position of MIFs at given energy values."
>
> Does anyone know whether there is a way to do similar computations with
> CDK or more generally a similar open-source method?
>
> Best regards and thanks,
> Fleming Kretschmer
>
>
>
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Re: [Wikidata] WDQS and SPARQL Endpoint Compatibility

[Egon Willighagen]

On Mon, Mar 30, 2020 at 11:15 PM Maarten Dammers 
wrote:

> Since Stas left last year, unfortunately nobody from the WMF has done
> anything with
> https://www.wikidata.org/wiki/Wikidata:SPARQL_federation_input . I don't
> know if the new SPARQL people are even aware of this page.
>

That's my impression too:


> My bot produces a weekly federation report at
>
> https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service/Federation_report
>

The WikiPathways SPARQL endpoint URL has changed, and I have requested an
update (Jan 2020, [0]), but no update or reply yet.

Maarten, that is causing the simple query in this report to fail.

Egon

0.
https://www.wikidata.org/wiki/Wikidata_talk:SPARQL_federation_input#Updated_URL_for_the_WikiPathways_SPARQL_endpoint

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[Bioc-devel] help with Win10 TSL problem?

[Egon Willighagen]

Hi all,

in the BridgeDbR package I have a TSL issue, just on Windows10 [0]:

> location <- getDatabase("Bacillus subtilis")
Error in function (type, msg, asError = TRUE)  :
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert
protocol version
Calls: getDatabase ... getBridgeNames -> curlPerform ->  -> fun
Execution halted

This method is using the download.file() method (see [1]). I am not sure
what this method uses by default. I have been googling and found a number
of suggestions on how to get RCurl to use other SSL version, such as:

CURL_SSLVERSION_TLSv1_2 <- 1Lopts <- RCurl::curlOptions(  verbose =
TRUE, sslversion = CURL_SSLVERSION_TLSv1_2)download.file(url, file,
mode = "wb", .opts=opts)


But I haven't found something that works. Error messages are very cryptic,
and I'm running out of ideas.

Does someone have a suggestion how to debug this? Maybe even have a
solution?

All feedback is very much appreciated!

Egon



0.
https://bioconductor.org/checkResults/release/bioc-LATEST/BridgeDbR/tokay1-checksrc.html
1.https://github.com/bridgedb/BridgeDbR/blob/master/R/getDatabase.R#L23



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Re: [Cdk-user] Raw fingerprints impossible to calculate

[Egon Willighagen]

Mmm... time to update my book to discuss this :)

Egon

On Fri, Feb 21, 2020 at 10:35 AM John Mayfield 
wrote:

> Hi Maria,
>
> Not all fingerprint support the "RAW" option and Count options.
>
> John
>
> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
> wrote:
>
>> Dear community,
>>
>> It is decidedly substructure search and fingerprinting period of the year!
>>
>> I want to create (to store) raw fingerprints of a range of different
>> fingerprint types for a big number of complex molecules (natural products).
>>
>> For example this:
>>
>> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
>> SilentChemObjectBuilder.getInstance() );
>>
>> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
>>
>> For all my molecules I am getting an" UnsupportedOperationException",
>> which according to the documentation reflects only the fact that the 
>> fingerprinter
>> cannot produce the raw fingerprint.
>> I am using the latest (2.3) version of the CDK.
>> Can anybody help me with this issue?
>>
>>
>> Kind regards,
>> Maria
>>
>>
>> Dr. Maria Sorokina
>> Steinbeck Research Group
>> Analytical Chemistry - Cheminformatics and Chemometrics
>> Friedrich-Schiller-University Jena, Germany
>> http://cheminf.uni-jena.de
>>
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Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

Just for clarity, I am not sure it is a CDK problem. I gave another pom.xml
with the same file, that does not depend on the CDK. Of course, it may
still depend on the same library as the CDK does. I just gave libcdk-java
as one example where I ran into the problem.

I just ran 'mvn clean install' against four other projects, and they *all*
give the file. I think it's Maven itself that depends on this library. I
apologize for the misleading bug report title, but you can also reproduce
it with just this:

mkdir foo
cd foo
mvn archetype:generate

Egon

Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

Just for clarity, I am not sure it is a CDK problem. I gave another pom.xml
with the same file, that does not depend on the CDK. Of course, it may
still depend on the same library as the CDK does. I just gave libcdk-java
as one example where I ran into the problem.

I just ran 'mvn clean install' against four other projects, and they *all*
give the file. I think it's Maven itself that depends on this library. I
apologize for the misleading bug report title, but you can also reproduce
it with just this:

mkdir foo
cd foo
mvn archetype:generate

Egon
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Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

I've just installed the libplexus-utils2-java from Testing and can confirm
that resolves the problem. So, the dep on that package needs a version
upgrade. Simple fix :)

Egon
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Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

I've just installed the libplexus-utils2-java from Testing and can confirm
that resolves the problem. So, the dep on that package needs a version
upgrade. Simple fix :)

Egon

Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

Package: maven
Version: 3.6.2-1
Severity: important

Dear Maintainer,

recently, CDK (libcdk-java) 2.3 hit testing and I have it installed on my 
Stable system. But it depends
on Maven >= 3.6.1 so I installed the version from Testing (see below). But for 
the CDK 2.3 sources
as well as another Maven project [1], the Testing version fails with a 
ClassNotFoundException, not showing
up with Maven 2.6.0-x from Stable:

Exception in thread "main" java.lang.NoClassDefFoundError: 
org/codehaus/plexus/util/xml/Xpp3DomBuilder$InputLocationBuilder
at 
org.apache.maven.model.io.DefaultModelReader.read(DefaultModelReader.java:108)
at 
org.apache.maven.model.io.DefaultModelReader.read(DefaultModelReader.java:85)
at 
org.apache.maven.model.building.DefaultModelProcessor.read(DefaultModelProcessor.java:89)
at 
org.apache.maven.model.building.DefaultModelBuilder.readModel(DefaultModelBuilder.java:552)
at 
org.apache.maven.model.building.DefaultModelBuilder.build(DefaultModelBuilder.java:281)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:448)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:414)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:377)
at 
org.apache.maven.graph.DefaultGraphBuilder.collectProjects(DefaultGraphBuilder.java:414)
at 
org.apache.maven.graph.DefaultGraphBuilder.getProjectsForMavenReactor(DefaultGraphBuilder.java:405)
at 
org.apache.maven.graph.DefaultGraphBuilder.build(DefaultGraphBuilder.java:82)
at org.apache.maven.DefaultMaven.buildGraph(DefaultMaven.java:507)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:219)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:282)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:225)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:406)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:347)
Caused by: java.lang.ClassNotFoundException: 
org.codehaus.plexus.util.xml.Xpp3DomBuilder$InputLocationBuilder
at 
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 26 more

Egon

1.https://github.com/BiGCAT-UM/WikiPathwaysCurator


-- System Information:
Debian Release: 10.2
  APT prefers stable
  APT policy: (1000, 'stable'), (900, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 5.0.0-trunk-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US 
(charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages maven depends on:
ii  default-jre-headless [java7-runtime-headless] 2:1.11-71
ii  libjansi-java 1.17.1-1
ii  libmaven3-core-java   3.6.2-1
ii  libwagon-file-java3.3.1-2
ii  libwagon-http-shaded-java 3.3.1-2
ii  openjdk-10-jre-headless [java7-runtime-headless]  10.0.2+13-2
ii  openjdk-11-jre-headless [java7-runtime-headless]  11.0.5+10-1~deb10u1
ii  openjdk-12-jre-headless [java7-runtime-headless]  12.0.2+9-1
ii  openjdk-8-jre-headless [java7-runtime-headless]   8u212-b01-1
ii  openjdk-9-jre-headless [java7-runtime-headless]   9~b181-4~bpo9+1

maven recommends no packages.

maven suggests no packages.

-- no debconf information

Bug#948286: maven: CDK 2.3 fails to compile with Maven 3.6.2 with ClassNotFoundException

[Egon Willighagen]

Package: maven
Version: 3.6.2-1
Severity: important

Dear Maintainer,

recently, CDK (libcdk-java) 2.3 hit testing and I have it installed on my 
Stable system. But it depends
on Maven >= 3.6.1 so I installed the version from Testing (see below). But for 
the CDK 2.3 sources
as well as another Maven project [1], the Testing version fails with a 
ClassNotFoundException, not showing
up with Maven 2.6.0-x from Stable:

Exception in thread "main" java.lang.NoClassDefFoundError: 
org/codehaus/plexus/util/xml/Xpp3DomBuilder$InputLocationBuilder
at 
org.apache.maven.model.io.DefaultModelReader.read(DefaultModelReader.java:108)
at 
org.apache.maven.model.io.DefaultModelReader.read(DefaultModelReader.java:85)
at 
org.apache.maven.model.building.DefaultModelProcessor.read(DefaultModelProcessor.java:89)
at 
org.apache.maven.model.building.DefaultModelBuilder.readModel(DefaultModelBuilder.java:552)
at 
org.apache.maven.model.building.DefaultModelBuilder.build(DefaultModelBuilder.java:281)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:448)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:414)
at 
org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:377)
at 
org.apache.maven.graph.DefaultGraphBuilder.collectProjects(DefaultGraphBuilder.java:414)
at 
org.apache.maven.graph.DefaultGraphBuilder.getProjectsForMavenReactor(DefaultGraphBuilder.java:405)
at 
org.apache.maven.graph.DefaultGraphBuilder.build(DefaultGraphBuilder.java:82)
at org.apache.maven.DefaultMaven.buildGraph(DefaultMaven.java:507)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:219)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:282)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:225)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:406)
at 
org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:347)
Caused by: java.lang.ClassNotFoundException: 
org.codehaus.plexus.util.xml.Xpp3DomBuilder$InputLocationBuilder
at 
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at 
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 26 more

Egon

1.https://github.com/BiGCAT-UM/WikiPathwaysCurator


-- System Information:
Debian Release: 10.2
  APT prefers stable
  APT policy: (1000, 'stable'), (900, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 5.0.0-trunk-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US 
(charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages maven depends on:
ii  default-jre-headless [java7-runtime-headless] 2:1.11-71
ii  libjansi-java 1.17.1-1
ii  libmaven3-core-java   3.6.2-1
ii  libwagon-file-java3.3.1-2
ii  libwagon-http-shaded-java 3.3.1-2
ii  openjdk-10-jre-headless [java7-runtime-headless]  10.0.2+13-2
ii  openjdk-11-jre-headless [java7-runtime-headless]  11.0.5+10-1~deb10u1
ii  openjdk-12-jre-headless [java7-runtime-headless]  12.0.2+9-1
ii  openjdk-8-jre-headless [java7-runtime-headless]   8u212-b01-1
ii  openjdk-9-jre-headless [java7-runtime-headless]   9~b181-4~bpo9+1

maven recommends no packages.

maven suggests no packages.

-- no debconf information

__
This is the maintainer address of Debian's Java team
.
 Please use
debian-j...@lists.debian.org for discussions and questions.

[Cdk-user] CDK 2.3 now in Debian Unstable

[Egon Willighagen]

Hi everyone,

with great pleasure I can let you know that in the past two month Debian
developers have updated the CDK version in the Debian distribution, and you
can download CDK 2.3 from Debian unstable [0].

Grtz and happy new year,

Egon

0.https://packages.debian.org/search?keywords=libcdk-java

-- 
Hi, do you like citation networks? Already 51% of all citations are
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. Join me in asking the American
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.
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the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

In related news... XOMCML is now distributed as part of Debian GNU/Linux!!!
https://packages.debian.org/sid/libcmlxom-java

It was a dependency for CDK 2.3, that's why.

Egon

On Mon, Dec 30, 2019 at 12:04 PM Peter Murray-Rust  wrote:

>
>
> On Sun, Dec 29, 2019 at 10:00 AM Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>>
>> Dear Oliver,
>>
>>
>
>> BTW2, do we have a critical mass of potential mentor and project ideas to
>> propose the Blue Obelisk as mentoring organization?
>>
>
> It's a really good idea to have projects that drive the definition of the
> languages and packages. I'd be happy to mentor people in this area. My main
> interest is extracting semantic information from legacy - anywhere in the
> domain of chemistry/crystallography/materials/ so happy to react to
> suggestions. Keen to work with spectra and/or reaction schemes. Also
> currently working on phytochemicals.
>
>>
>> --
> "I always retain copyright in my papers, and nothing in any contract I
> sign with any publisher will override that fact. You should do the same".
>
> Peter Murray-Rust
> Reader Emeritus in Molecular Informatics
> Unilever Centre, Dept. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
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Re: Help needed to upgrade cdk

[Egon Willighagen]

Hi Andreas, and other Debian developers,

I saw that CDK 2.3 is now in unstable! Great news! Many thanks for your
time during the BioHackathon, and others for their effort to make this
happen. Very much appreciated.

Egon


On Tue, Nov 19, 2019 at 6:40 PM Andreas Tille  wrote:

> Hi,
>
> I've sat together with Egon Willighagen who is member of CDK upstream
> team to update the cdk package[1].  So far the switch from ant to maven
> seems to have basically succeeded.  However, for some reason it does not
> build modules in the correct sequence and thus we are running into:
>
>
> [INFO] cdk  SUCCESS [
> 0.033 s]
> [INFO] cdk-base ... SUCCESS [
> 0.003 s]
> [INFO] cdk-interfaces . SUCCESS [
> 1.894 s]
> [INFO] cdk-core ... SUCCESS [
> 2.407 s]
> [INFO] cdk-standard ... SUCCESS [
> 1.406 s]
> [INFO] cdk-atomtype ... SUCCESS [
> 0.209 s]
> [INFO] cdk-valencycheck ... SUCCESS [
> 0.240 s]
> [INFO] cdk-misc ... SUCCESS [
> 0.007 s]
> [INFO] cdk-diff ... FAILURE [
> 0.025 s]
> ...
> [ERROR] Failed to execute goal on project cdk-diff: Could not resolve
> dependencies for project org.openscience.cdk:cdk-diff:jar:2.3: Cannot
> access ossrh (https://oss.sonatype.org/content/repositories/snapshots) in
> offline mode and the artifact org.openscience.cdk:cdk-test:jar:tests:debian
> has not been downloaded from it before. -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the
> command
> [ERROR]   mvn  -rf :cdk-diff
>
>
> Egon says cdk-test should be build before cdk-diff and we have no idea
> why its not.  According to Egon the travis build works nicely.  Any idea
> why this is different in a pbuilder chroot?
>
> Any help would be welcome
>
>   Andreas.
>
> [1] https://salsa.debian.org/java-team/cdk
>
> --
> http://fam-tille.de
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

I made a few small edits :)

Egon

On Sun, Dec 29, 2019 at 4:12 PM Mark Williamson  wrote:

>
>
> On 29/12/2019 09:59, Egon Willighagen wrote:
>
> > Within the BlueObelisk-org, I've also created the teams CML and WWMM
> > and assigned the repos to those teams based on their location on
> > Bitbucket.
> > Could someone with higher privileges than myself within the
> > BlueObelisk GH-org add Mark (mjw99) and Peter (petermr) as members,
> > please?
>
> Hi,
>
> I have migrated/corrected the README.md(s) and enabled working Travis CI
> for the following:
>
>https://github.com/blueobelisk/oscar4
>https://github.com/blueobelisk/oscar4-cli
>https://github.com/blueobelisk/chemicaltagger
>
> Thanks,
>
> Mark
>
>
>

-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
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Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

[Egon Willighagen]

Dear Oliver,

On Sat, Dec 28, 2019 at 11:24 PM Oliver Stueker 
wrote:

>   Happy Holidays everyone,
>

Same here.

As discussed a couple of weeks ago, I have today imported the 50
> repositories from the WWMM and CML users/teams on Bitbucket into the Blue
> Obelisk GitHub-org (https://github.com/BlueObelisk; I apologize for the
> flood of emails that I have probably triggered by that).
>

:)


> Within the BlueObelisk-org, I've also created the teams CML and WWMM and
> assigned the repos to those teams based on their location on Bitbucket.
> Could someone with higher privileges than myself within the BlueObelisk
> GH-org add Mark (mjw99) and Peter (petermr) as members, please?
>

Done.


> Next week I'll start experimenting with enabling CI on some select repos
> (using Travis or even the new GitHub Actions - let's see what works better)
> and fixing the markup in the Jumbo-Converters Wiki (
> https://github.com/BlueObelisk/jumbo-converters/wiki).
>

Sounds great!

Do you also have plans to get things moving to Maven Central?

BTW, at the ELIXIR BioHackathon I spoke with a Debian developer to get the
CDK package updated. There is a (partial) dependency on CMLXOM, and I added
a note about that just now: https://github.com/BlueObelisk/cmlxom/issues/2

BTW2, do we have a critical mass of potential mentor and project ideas to
propose the Blue Obelisk as mentoring organization?

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: Help needed to upgrade cdk

[Egon Willighagen]

Awesome! Plz let me know if I can answer any questions around dependencies,
or impact of missing dependencies.

Egon

On Wed, Nov 20, 2019 at 9:35 PM Andrius Merkys  wrote:

> Hi Andreas,
>
> On Wed, 20 Nov 2019, 22:19 Andreas Tille,  wrote:
>
>> I have no idea what restrictions the lack of cmlxom might imply.
>>
>
> I have packaged and uploaded cmlxom today. Will do so with the rest of
> dependencies.
>
> Would you take over and upload your changes?  If not please push and
>> let me know if some further work might be needed.
>>
>
> I can take it for now. I will keep you updated.
>
> Best wishes,
> Andrius
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen

[Wikidata] formatter URL that requires encoding the statement value?

[Egon Willighagen]

Hi all,

for the SMILES (line representation for chemical structures; [0]) there are
currently two properties (P233 and P2017). Each one of them has a formatter
URL to link out to an open source depiction tool (CDKDepict). But statement
values for both properties can have characters that need to be encoded for
the URL (/, +, #).

Some time ago I saw a solution, a separate Wikidata/-media page that did
this, before linking through to the remote service.

Because chemical structures are now not always shown and sometimes wrong, I
really like to see a solution like that implemented. I'm thinking of
working on that during WikidataCon. But I like to ask for your input. What
are the technical solution that could be used to solve the problem? What
are related recommendations? And anything else you like to comment...

Looking forward to hearing from you,

greetings,

Egon

0.https://tools.wmflabs.org/scholia/topic/Q466769

-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [Wikidata] Weekly Summary #384

[Egon Willighagen]

Hi Houcemeddine,

you can just add your article yourself to the "Next" page:
https://www.wikidata.org/wiki/Wikidata:Status_updates/Next

With kind regards,

Egon

On Mon, Sep 30, 2019 at 5:35 PM Houcemeddine A. Turki
 wrote:
>
> Dear Ms.,
> I thank you for your answer. You did not mention our work published in 
> Journal of Biomedical Informatics this week although I have already written 
> an email about it in our mailing list before. It is currently available at 
> https://doi.org/10.1016/j.jbi.2019.103292. You can find the full text of the 
> paper at 
> https://www.researchgate.net/publication/336001723_Wikidata_A_large-scale_collaborative_ontological_medical_database.
>  Please include it to next Wikidata Weekly Summary. I also ask about your 
> opinion about the output of the research paper and the deficiencies of 
> medical information in Wikidata. This will be useful for us to know more 
> about how to continue our project.
> Yours Sincerely,
> Houcemeddine Turki
> 
> De : Wikidata  de la part de Léa 
> Lacroix 
> Envoyé : lundi 30 septembre 2019 16:04
> À : Discussion list for the Wikidata project. 
> Objet : [Wikidata] Weekly Summary #384
>
> Here's your quick overview of what has been happening around Wikidata over 
> the last week.
>
> Discussions
>
> Open request for adminship: Catherine Laurence
>
> Events
>
> Past: Using Wikidata to Provide Visibility to Women in STEM during Dublin 
> Core 2019
> Upcoming: WikiCon, meeting of the German speaking Community from 4th to 6th 
> of October 2019 in Wuppertal (Germany)
> Upcoming: #5 Wikidata tea party/第5回 ウィキデータ茶話会, 18 Oct 2019 in Tokyo, Japan
> Upcoming: Wikidata Zurich Training in Zurich on the weekend of November 2-3. 
> There will be presentations and hands-on sessions on editing, querying and 
> coding for Wikidata.
> Upcoming: Wikidata Zurich Hackathon in Zurich on the weekend of November 
> 23-24.
>
> Press, articles, blog posts
>
> Scottish witches in the press and on TV
> Some witchy history and a very smart woman in data science
> Spoken Conversational Search for General Knowledge - Lina Maria 
> Rojas-Barahona, et al.
> GeneDB and Wikidata, by Magnus Manske
>
> Tool of the week
>
> This Recent changes tool allows to get a list of unpatrolled Wikidata changes 
> with enhanced filters that are more adapted to Wikidata than the standard 
> Recent Changes page. Available actions include mass patroling and easier 
> revert interface.
>
> Other Noteworthy Stuff
>
> The state library of Berlin is using Wikidata to display a map of pictures 
> from their architecture journals: Berlin um 1900 - eine fotografische 
> Zeitreise
> Edit summaries coming from the wbeditentity API (for example from the mobile 
> termbox) will be improved from October 2nd (announcement, ticket)
> You can nominate your favourite Wikidata and Wikibase projects for the 
> WikidataCon Award until October 7th
>
> Did you know?
>
> Newest properties:
>
> General datatypes: regnal ordinal, peer review URL
> External identifiers: GCF Reference, Wi-Fi Certification ID, Rivals.com ID, 
> sixpackfilmdata film ID, sixpackfilmdata person ID, Dirección General de 
> Bibliotecas ID, Elitefootball player ID, The Wind Power farm ID, IGNrando' 
> ID, Fossiilid.info ID, Kivid.info ID
>
> New property proposals to review:
>
> General datatypes: bus, mwnf, Maximum number of playable characters, FIDAL 
> team ID, candidate name string, IP range start, code (image), name in hiero 
> markup, disputed by, name (image), style of karate
> External identifiers: NTS Radio artist ID, Gazetteer for Scotland ID, 
> Gazetteer for Scotland person ID, FootballFacts.ru team ID, 
> FootballDatabase.eu team ID, GENUKI ID, DC Books author ID, LaPreferente.com 
> player ID, Ukrainian Premier League player ID, UEFA team ID, UEFA coach ID, 
> Naver Encyclopedia ID, FAIMER school ID, China Martyrs ID, JournalBase ID, 
> PCEngine Catalog Project ID, PubPeer article ID, memoriademadrid publication 
> ID, doujinshi.org author ID, Beatport label ID, Knesset Law Id, 
> caves.4at.info ID, ADL Hate Symbols Database ID, Amazon Music album ID 2, 
> Qobuz album ID, Plus Music album ID, eska.pl release ID, iHeartRadio album 
> ID, Three Decks people ID, Diccionari de la Literatura Catalana ID, Empik 
> e-book or album ID, identificador GENavarra, Oricon News artist ID, Turkish 
> Football Federation Match ID, Turkish Football Federation Team ID, Turkish 
> Football Federation Referee ID, Turkish Football Federation Stadium ID, 
> Fortuna liga player ID
>
> Deleted properties: P5130 (island of location)
> Query examples:
>
> Civil parishes of Scotland, revealed through their listed buildings (source)
> Scottish civil parishes by county and present-day council area (source)
> Federated SPARQL query from the Swedish National Archive TORA project to 
> Wikidata
> Librairies in Africa (source)
> Most recently dissolved enterprises that were over 200 years old (source)
>
> Newest WikiProjects: 

Re: [Wikidata] Personal news: a new role

[Egon Willighagen]

Dear Houcemeddine,

do you happen to have a preprint for that online?

Egon


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Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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[BlueObelisk-discuss] BODR evolution

[Egon Willighagen]

Hi all,

since this year is the Year of the Period Table, it may be nice to
make a new Blue Obelisk Data Release (BODR) release, our CC0 release
of data on the chemical elements and some simple substances based on
them (https://github.com/BlueObelisk/bodr).

I had some changes in mind. BODR already cites primarily literature as
source, but this is currently at "table" level. However, masses etc,
are typically at element level, which IUPAC type papers appearing
every now and then, with refined standards values.

Now, Wikidata allows citations are reference level, and in fact, allow
multiple values, annotated with deprecated, which could be nice too,
to show the evolution of the accuracy of properties over time (given
each is properly citing to the primary literature).

Then, BODR could harvest the data from there, and then back on the
same route as now.

So, my plans are for the remaining months of this year to migrate more
and more info to Wikidata, set up the aggregation and work towards a
BODR 11 release around x-mas.

To help this work, I have adopted Scholia for data visualization (tho
mostly tables at this moment):
https://tools.wmflabs.org/scholia/chemical-element/

The idea is to write this up as a paper at the end of this year too.

Who like to join this effort?

Egon

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Hi, do you like citation networks? Already 51% of all citations are
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Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [Wikidata] ShEx to validate Medical Wikidata

[Egon Willighagen]

On Sun, Aug 25, 2019 at 12:07 PM Houcemeddine A. Turki
 wrote:
> However, it does not include many schemas. We should develop schemas for 
> medical classes before using ShEx to validate Medical Wikidata statements.

Yes, please do. I have been working on ShEx for other domains. It's a
fairly new effort (great work by the team, IMO), and the more people
adopt this additional way of data validation the better.

Egon

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Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [Wikidata] ShEx to validate Medical Wikidata

[Egon Willighagen]

Dear Houcemeddine,

On Sat, Aug 24, 2019 at 10:57 PM Houcemeddine A. Turki
 wrote:
> I ask if someone is interested in creating shape expressions of Medical 
> Wikidata classes.

Cool, please do!

> As well, I tried to access http://wikidata-shex.wmflabs.org/w/index.php. 
> However, it does not work.

The way I understood it: That link you gave was the test server. It
went "live" earlier this year, and plz check out this now:
https://www.wikidata.org/wiki/Wikidata:WikiProject_ShEx

Grtz,

Egon

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Re: [Wikidata] Important, Critical issues related to Wikidata

[Egon Willighagen]

On Wed, Aug 21, 2019 at 8:44 PM Houcemeddine A. Turki
 wrote:
>
> I thank you for your efforts. It was an honour for me to meet you in 
> Stockholm. Concerning the points you raised, I
> 1. Concerning the problematic use of Instance of and SubClass of, I invite 
> you to see https://tinyurl.com/y29lx9o4. This seems to be not accurate as 
> drugs differ from drug classes from a pharmacological view. For example, 
> Artemisinin, Ibuprofen and Sobosbuvir are drugs. However, drug classes should 
> include antibiotics and antivirals. Concerning WikiProject Ontology, I know 
> it. The project succeeded to solve many matters related to the structure of 
> Wikidata. However, the project is slow.

To me this is actually a nice example of *why* we need to distinction.

Sobosbuvir as in instance is often the active ingredient.
Sobosbuvir as a class is often the formulation, which is not a single
entity, but a class of formulations with different amounts (and
concentrations) of active ingredient

It's just that in street/common language (not wrong, just different!)
we don't use different words for it. Instance-vs-subclass are tools
that help us make this distinction.

Now, related to this, plz have a look at
https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry where
class and instance are both used, for good reasons.

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
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Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [Wikidata] Important, Critical issues related to Wikidata

[Egon Willighagen]

On Wed, Aug 21, 2019 at 1:20 PM Houcemeddine A. Turki
 wrote:
> I thank you for your efforts. I tried to contact Ms. Léa Lacroix and Ms. 
> Lydia. However, I failed due to my participation to many sessions. I saw Ms. 
> Lydia when returning to the hotel on the third day. But, I had to go for the 
> old town. I had nine points to raise:
> 1. Instance of and Subclass of are not well defined for users although they 
> are quite different. I ask if these two properties can be merged as is-a. 
> This will be easier to process by users and developers.

I disagree with this suggestion. To me, the distinction between
classes and individuals is very useful. Removing it will make not make
things easier, but only harder.

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available available for innovative new uses. Join me in asking the
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-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Re: [Wikidata] Virtuoso hosted Wikidata Instance

[Egon Willighagen]

On Wed, Aug 14, 2019 at 1:10 AM Kingsley Idehen  wrote:
> We have loaded Wikidata into a Virtuoso instance accessible via SPARQL [1]. 
> One benefit is helping to understand Wikidata using our Faceted Browsing 
> Interface for Entity Relationship Types [2][3].

Awesome!

I've started seeing how much of Scholia can run on it, and opened a
ticket: https://github.com/fnielsen/scholia/issues/809 It's great the
Wikidata namespaces are loaded. I only had to add the 'bd' prefix to
the Scholia SPARQL. And, the sections that use the WDQS graphical
views, obviously cannot use the VOS instance yet.

So, do you plan to run a WDQS instance on top of your EP? :)

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
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-
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Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [Wikidata] Useful resources for Scholia

[Egon Willighagen]

On Sat, Aug 3, 2019 at 12:10 AM Houcemeddine A. Turki <
turkiabdelwa...@hotmail.fr> wrote:

> I thank you for your efforts. I invite you to use several useful resources
> available in https://shubhanshu.com/awesome-scholarly-data-analysis/ to
> enrich Scholia project.
>

Many of the linked resources are data resources (and at least several of
them not CC0) and are for Wikidata, not Scholia.

For the software in the list, not all is directly suitable for Scholia
either, or is already working with Wikidata. Did you have something
specific in mind?

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [Cdk-user] controlling hydrogen display with DepictionGenerator

[Egon Willighagen]

On Fri, Aug 2, 2019 at 11:28 AM John Mayfield 
wrote:

> Other option You can also use the old *BasicAtomGenerator* which never
> puts hydrogens on anything...
>

Documentation on the old generator stack can be found in this copy of the
Groovy CDK book, "Depiction" chapter:

https://figshare.com/articles/Edition_1_4_1_0_of_Groovy_Cheminformatics_with_the_Chemistry_Development_Kit/2057790

Egon

-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Bug#927056: groovy: Groovy gives warning with OpenJDK 11 about illegal reflective access

[Egon Willighagen]

Package: groovy
Version: 2.4.16-2
Severity: normal

Dear Maintainer,

with OpenJDK 11 (which seems to be the default in Buster) Groovy gives a 
warning at
start up time, for any Groovy script.

$ groovy -e "foo = \"Foo\""
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by 
org.codehaus.groovy.reflection.CachedClass 
(file:/usr/share/groovy/lib/groovy-2.4.16.jar) to method 
java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of 
org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal 
reflective access operations
WARNING: All illegal access operations will be denied in a future release

This is not the case with Java8 and may have to do with classes removed in 
Java11? Setting JAVA_HOME to have it use Java8 removes the warning.
The scripts do seem to run fine otherwise.

With kind regards,

Egon

-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (1100, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-4-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=nl_NL.UTF-8, LC_CTYPE=nl_NL.UTF-8 (charmap=UTF-8), LANGUAGE=en_US 
(charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages groovy depends on:
ii  antlr 2.7.7+dfsg-9.2
ii  default-jre-headless [java7-runtime-headless] 2:1.11-71
ii  ivy   2.4.0-5
ii  junit44.12-8
ii  libasm-java   7.0-1
ii  libbsf-java   1:2.4.0-8
ii  libcommons-cli-java   1.4-1
ii  libcommons-logging-java   1.2-2
ii  libjansi-java 1.17.1-1
ii  libjline2-java2.14.6-3
ii  libqdox-java  1.12.1-3
ii  libservlet3.1-java [libservlet3.1-java]   1:4.0.1-2
ii  libxstream-java   1.4.11.1-1
ii  openjdk-10-jre-headless [java7-runtime-headless]  10.0.2+13-2
ii  openjdk-11-jre-headless [java7-runtime-headless]  11.0.3+1-1
ii  openjdk-8-jre-headless [java7-runtime-headless]   8u212-b01-1
ii  openjdk-9-jre-headless [java7-runtime-headless]   9~b181-4~bpo9+1

Versions of packages groovy recommends:
ii  ant   1.10.5-2
ii  ant-optional  1.10.5-2
ii  libgpars-groovy-java  1.2.1-10
ii  libjcommander-java1.71-3

Versions of packages groovy suggests:
pn  groovy-doc  

-- no debconf information

__
This is the maintainer address of Debian's Java team
.
 Please use
debian-j...@lists.debian.org for discussions and questions.

Bug#927056: groovy: Groovy gives warning with OpenJDK 11 about illegal reflective access

[Egon Willighagen]

Package: groovy
Version: 2.4.16-2
Severity: normal

Dear Maintainer,

with OpenJDK 11 (which seems to be the default in Buster) Groovy gives a 
warning at
start up time, for any Groovy script.

$ groovy -e "foo = \"Foo\""
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by 
org.codehaus.groovy.reflection.CachedClass 
(file:/usr/share/groovy/lib/groovy-2.4.16.jar) to method 
java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of 
org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal 
reflective access operations
WARNING: All illegal access operations will be denied in a future release

This is not the case with Java8 and may have to do with classes removed in 
Java11? Setting JAVA_HOME to have it use Java8 removes the warning.
The scripts do seem to run fine otherwise.

With kind regards,

Egon

-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (1100, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-4-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=nl_NL.UTF-8, LC_CTYPE=nl_NL.UTF-8 (charmap=UTF-8), LANGUAGE=en_US 
(charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages groovy depends on:
ii  antlr 2.7.7+dfsg-9.2
ii  default-jre-headless [java7-runtime-headless] 2:1.11-71
ii  ivy   2.4.0-5
ii  junit44.12-8
ii  libasm-java   7.0-1
ii  libbsf-java   1:2.4.0-8
ii  libcommons-cli-java   1.4-1
ii  libcommons-logging-java   1.2-2
ii  libjansi-java 1.17.1-1
ii  libjline2-java2.14.6-3
ii  libqdox-java  1.12.1-3
ii  libservlet3.1-java [libservlet3.1-java]   1:4.0.1-2
ii  libxstream-java   1.4.11.1-1
ii  openjdk-10-jre-headless [java7-runtime-headless]  10.0.2+13-2
ii  openjdk-11-jre-headless [java7-runtime-headless]  11.0.3+1-1
ii  openjdk-8-jre-headless [java7-runtime-headless]   8u212-b01-1
ii  openjdk-9-jre-headless [java7-runtime-headless]   9~b181-4~bpo9+1

Versions of packages groovy recommends:
ii  ant   1.10.5-2
ii  ant-optional  1.10.5-2
ii  libgpars-groovy-java  1.2.1-10
ii  libjcommander-java1.71-3

Versions of packages groovy suggests:
pn  groovy-doc  

-- no debconf information

Bug#922450: virtualbox: resuming a saved VM state of Linux guest operating systems fails

[Egon Willighagen]

A further update: I just reinstalled Linux Mint 19.1 from scratch (the live
image iso) and that worked.

Bug#922450: virtualbox: resuming a saved VM state of Linux guest operating systems fails

[Egon Willighagen]

Dear Michael,

On Sat, Feb 16, 2019 at 10:43 AM Michael Ott  wrote:

> I believe that you have mounted shared folders?
>

I might have (not sure), because I don't now. They do not show up in the VB
manager and not in the guest host either (when I boot it from scratch).
Also nothing in /etc/fstab in the guest... is there another place where
shared folders are described, or some other way I can see if it tries to
mount anything?


> Try it with the 5.24 version from virtualbox-guest-additions-iso
>

Where do I get that?


> I extract it from the debian package and since then it works again
>

What should I extract? And what then?

Since it was not showing any mapped folders, I created one, and saved the
VM state and tried to restore the saved state, but same error :(

Egon

Bug#922450: virtualbox: resuming a saved VM state of Linux guest operating systems fails

[Egon Willighagen]

Package: virtualbox
Version: 6.0.4-dfsg-5
Severity: normal

Dear Maintainer,

I am running Debian Testing and since recently (1-3 weeks?) an update of 
VirtualBox (I think the version that restored the "Start/Resume" buttons
that got missing some months ago), restoring saved states for Linux guests 
started failing with this error (the first line is in Dutch, and the
translation is below the error message), for example here for a VM with the 
name "My VM":


Het is niet gelukt een sessie te openen voor virtuele machine My VM.

The VM session was aborted.

Resultaatcode:NS_ERROR_FAILURE (0x80004005)
Component:SessionMachine
Interface:ISession {c0447716-ff5a-4795-b57a-ecd5fffa18a4}


The first line says: "It was not possible to restore the virtual machine My 
VM". And
"Resultaatcode" is simply "Result code", or something like that.

It's (sadly) quite reproducible. Linux guess VMs included Linux Mint 19 and 
Debian 6.0.10.
After that, I updated Linux Mint to 19.1, reinstalled the guess additions (I 
tried both
the 5.x deb from Linux Mint 19.1 and the downloaded .iso), but with no
change in behavior. BTW, downloading the .iso for Linux Mint 19 and 19.1 also 
fails at
around 80% with an "Unkown error".

I have run out of ideas on how to resolve the issue, and tried to rule out 
version conflicts.
Of course, what I expect is to guest systems to just restore without this fail.

*** End of the template - remove these template lines ***


-- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (1100, 'testing'), (4, 'unstable'), (2, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-2-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=nl_NL.UTF-8, LC_CTYPE=nl_NL.UTF-8 (charmap=UTF-8), LANGUAGE=en_US 
(charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages virtualbox depends on:
ii  adduser   3.118
ii  iproute2  4.20.0-2
ii  libc6 2.28-6
ii  libcurl3-gnutls   7.64.0-1
ii  libdevmapper1.02.12:1.02.155-2
ii  libgcc1   1:8.2.0-20
ii  libgl11.1.0-1
ii  libgsoap-2.8.75   2.8.75-1
ii  libopus0  1.3-1
ii  libpng16-16   1.6.36-5
ii  libpython3.7  3.7.2-2
ii  libqt5core5a  5.11.3+dfsg-2
ii  libqt5gui55.11.3+dfsg-2
ii  libqt5opengl5 5.11.3+dfsg-2
ii  libqt5widgets55.11.3+dfsg-2
ii  libqt5x11extras5  5.11.3-2
ii  libsdl1.2debian   1.2.15+dfsg2-4
ii  libssl1.1 1.1.1a-1
ii  libstdc++68.2.0-20
ii  libvncserver1 0.9.11+dfsg-1.3
ii  libvpx5   1.7.0-3
ii  libx11-6  2:1.6.7-1
ii  libxcursor1   1:1.1.15-2
ii  libxext6  2:1.3.3-1+b2
ii  libxml2   2.9.4+dfsg1-7+b3
ii  libxmu6   2:1.1.2-2
ii  libxt61:1.1.5-1
ii  procps2:3.3.15-2
ii  python3   3.7.2-1
ii  python3.7 3.7.2-2
ii  virtualbox-dkms [virtualbox-modules]  6.0.4-dfsg-5
ii  zlib1g1:1.2.11.dfsg-1

Versions of packages virtualbox recommends:
ii  libxcb11.13.1-2
ii  virtualbox-qt  6.0.4-dfsg-5

Versions of packages virtualbox suggests:
pn  vde2
pn  virtualbox-guest-additions-iso  

-- no debconf information

Re: [BlueObelisk-discuss] Open Science, not just Open Access

[Egon Willighagen]

Hi all,

a quick update. Thanks to everyone here who signed. We now have a group of
about 40 people together from 12 countries. It hasn't even come close to
going "viral" but the message is simply not as simple as "Too Risky!".
Also, the text is dense and complex.

All help is welcome. There is a lot of Blue Obelisk heritage in this
document, but my social web is also biased. Worse, I am no longer on
platform like Facebook or LinkedIn and cannot share there. Another thing is
that we may want to translate it? Ideas welcome. My social web is getting
exhausted.

Currently, these countries are missing, one which is definitely represented
on this mailing list: Germany. But South-America and Africa are completely
missing too, and being large continents with plenty of countries, let's try
to get representation from there too. Ideas?

The deadline actually is Friday afternoon (CET) giving us two extra days,
but let's try to reach more than 100.

We really need to have Plan S to be about Open Data, Open Source, and Open
Standards, not just CC-BY articles. Plan S and the Guidance actually does a
lot of steps in this direction, and it's important they get support too,
not just complaints. We must fuel the people in cOAlition S that want Open
Science. We must show them there is a significant research community that
wants that too.

Egon









On Sun, Feb 3, 2019 at 8:00 PM Egon Willighagen 
wrote:

>
> Hi all,
>
> I guess most people on this list have heard about Plan S. This Wednesday
> is the deadline for a consultation by cOAlition S on their Guidance on the
> Implementation of Plan S.
>
> Plan S is about Open Access, but that does not mean publishing is
> isolated. Particular our Blue Obelisk community knows that publications are
> not isolated. They feed into open data, open source, open standards, not
> just the other way around. Therefore, Open Access cannot be seen as a
> separate thing. Yet, many arguments against Plan S are only about impact
> factors, money, and personal benefits.
>
> I want to see Open Science as the real goal of Plan S, but for that it
> needs to be improved. The deadline for feedback is *this* Wednesday, so
> help is urgently needed.
>
> Please read what we wrote up this weekend, focusing on the three freedoms
> of open research (reuse, modify, redistribute):
>
> https://goo.gl/forms/jq6ZmnRnjHKBbyCT2
>
> At
> https://docs.google.com/document/d/14GycQnHwjIQBQrtt6pyN-ZnRlX1n8chAtV72f0dLauU/edit?usp=sharing
> you can track who already signed. I hope to see your names soon.
>
> I hope you share my wish to see Plan S put Open Science central and not as
> some collateral benefit. The more people we get to sign, the more impact
> this will have with cOAlition S partners.
>
> So, please sign, and pretty please share with others.
>
> Thanks,
>
> Egon
>
>
> --
> Hi, do you like citation networks? Already 51% of all citations are
> available <https://i4oc.org/> available for innovative new uses
> <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
> Chemical Society to join the Initiative for Open Citations too
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
>  SpringerNature,
> the RSC and many others already did <https://i4oc.org/#publishers>.
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen
___
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Re: [BlueObelisk-discuss] Open Science, not just Open Access

[Egon Willighagen]

Thanks, and also for signing!

Egon


On Mon, Feb 4, 2019 at 2:48 AM Jerome Pansanel 
wrote:

> Hi Egon,
>
> I forward your message to one of my colleague, in charge of Open Science
> at the University of Strasbourg.
>
> Cheers,
>
> Jerome
>
> Le 03/02/2019 à 20:00, Egon Willighagen a écrit :
>
>
> Hi all,
>
> I guess most people on this list have heard about Plan S. This Wednesday
> is the deadline for a consultation by cOAlition S on their Guidance on the
> Implementation of Plan S.
>
> Plan S is about Open Access, but that does not mean publishing is
> isolated. Particular our Blue Obelisk community knows that publications are
> not isolated. They feed into open data, open source, open standards, not
> just the other way around. Therefore, Open Access cannot be seen as a
> separate thing. Yet, many arguments against Plan S are only about impact
> factors, money, and personal benefits.
>
> I want to see Open Science as the real goal of Plan S, but for that it
> needs to be improved. The deadline for feedback is *this* Wednesday, so
> help is urgently needed.
>
> Please read what we wrote up this weekend, focusing on the three freedoms
> of open research (reuse, modify, redistribute):
>
> https://goo.gl/forms/jq6ZmnRnjHKBbyCT2
>
> At
> https://docs.google.com/document/d/14GycQnHwjIQBQrtt6pyN-ZnRlX1n8chAtV72f0dLauU/edit?usp=sharing
> you can track who already signed. I hope to see your names soon.
>
> I hope you share my wish to see Plan S put Open Science central and not as
> some collateral benefit. The more people we get to sign, the more impact
> this will have with cOAlition S partners.
>
> So, please sign, and pretty please share with others.
>
> Thanks,
>
> Egon
>
>
> --
> Hi, do you like citation networks? Already 51% of all citations are
> available <https://i4oc.org/> available for innovative new uses
> <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
> Chemical Society to join the Initiative for Open Citations too
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
>  SpringerNature,
> the RSC and many others already did <https://i4oc.org/#publishers>.
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
>
> ___
> Blueobelisk-discuss mailing 
> listBlueobelisk-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
<https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>.
SpringerNature,
the RSC and many others already did <https://i4oc.org/#publishers>.

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen
___
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Re: [Wikidata] Query on scholarly article fails

[Egon Willighagen]

I round up from DOI/PubMed ID counts on https://tools.wmflabs.org/scholia/

Egon

On Sat, Dec 15, 2018 at 3:03 PM Fabrizio Carrai 
wrote:

> Excellent, I did some tests and with some cycles I already identified and
> classified several articles.
> I will have a look at your script in the  next days but I already have a
> question: the number of iterations is based on the total number of
> articles, how do you know that ?
>
> ---
> Fabrizio
>
> Il giorno sab 15 dic 2018 alle ore 10:18 Egon Willighagen <
> egon.willigha...@gmail.com> ha scritto:
>
>>
>> The approach I use is the following, see this (Bioclipse/Groovy) script:
>> https://gist.github.com/egonw/ca4c348b9a2d1116efcdb55fa85dd158
>>
>> It takes advantage of a combination Blazegraph SPARQL trick and breaking
>> up thing in batches of a certain size:
>>
>> SELECT ?art ?artLabel
>> WITH {
>> SELECT ?art WHERE {
>> ?art wdt:P31 wd:Q13442814
>> } LIMIT $batchSize OFFSET $offset
>> } AS %RESULTS {
>> INCLUDE %RESULTS
>> ?art wdt:P1476 ?artLabel .
>> MINUS { ?art wdt:P921 wd:$conceptQ }
>> FILTER (contains(lcase(str(?artLabel)), "$concept"))
>> }
>> where "$concept" is my search word in the title, and $batchSize and
>> $offset take care of the batching by the script. This script creates
>> QuickStatements.
>>
>> Mind you, I manually check the created statements, because in my domain
>> (biochem) a simple search results of false positives, hence the "blacklist"
>> in the script :)
>>
>> Egon
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Sat, Dec 15, 2018 at 10:13 AM Fabrizio Carrai <
>> fabrizio.car...@gmail.com> wrote:
>>
>>> Thanks Matthias,
>>> that's a pity. Your suggestion relies on the effective characterization
>>> of the item that,  at this writing time, is pretty poor for my interest.
>>> Could it be an idea to download all the "scholary articles", locally
>>> select  for the keyword of interest (e.g. "microgravity") and set the
>>> property P921 for all of them ? Quickstatements may be helpful for the last
>>> step, any suggestions for other tools ?
>>>
>>> Thanks
>>> Fabrizio
>>>
>>> Il giorno ven 14 dic 2018 alle ore 22:16 Matthias Erfurth <
>>> erfu...@gmx.de> ha scritto:
>>>
>>>> Hi Fabrizio,
>>>> unfortunately you can't fulltext search all the scholarly articles
>>>> <https://www.wikidata.org/wiki/Q13442814> , you should better work
>>>> with indexed properties, so
>>>> you can query for other articles with microgravity as main subject ...
>>>> With the ajax based wikidata search
>>>>
>>>> SELECT ?item
>>>> WHERE {
>>>> ?item wdt:P31 wd:Q13442814;
>>>>   wdt:P921 wd:Q48655.
>>>> }
>>>>
>>>> Best regards,
>>>>
>>>> ciao matthias
>>>>
>>>>
>>>> *Gesendet:* Freitag, 14. Dezember 2018 um 18:55 Uhr
>>>> *Von:* "Fabrizio Carrai" 
>>>> *An:* "Discussion list for the Wikidata project" <
>>>> wikidata@lists.wikimedia.org>
>>>> *Betreff:* Re: [Wikidata] Query on scholarly article fails
>>>> Thanks again to Ettore, but I immediately found another timeout problem
>>>> when I just added a FILTER to find all the articles with the word "biokis"
>>>> in the title
>>>>
>>>> SELECT ?istanza_di ?instanza_diLabel WHERE {
>>>>   ?istanza_di wdt:P31 wd:Q13442814.
>>>>   ?istanza_di rdfs:label ?instanza_diLabel.
>>>>   FILTER((LANG(?instanza_diLabel)) = "en").
>>>>   FILTER(CONTAINS(LCASE(?instanza_diLabel), "biokis"))
>>>> }
>>>> LIMIT 100
>>>>
>>>> At least one article should be returned:
>>>> https://www.wikidata.org/wiki/Q57202937
>>>> but I got a timeout.
>>>>
>>>> Thanks to anybody that can help
>>>>
>>>> Fabrizio
>>>>
>>>>
>>>> Il giorno ven 14 dic 2018 alle ore 10:12 Ettore RIZZA <
>>>> ettoreri...@gmail.com> ha scritto:
>>>>
>>>>> Hello Fabrizio,
>>>>>
>>>>> It seems that the problem comes from SERVICE wikibase:label. As said
>>>>> in another discussion, the query executes in less than one second if you 
>>

Re: [Wikidata] Query on scholarly article fails

[Egon Willighagen]

The approach I use is the following, see this (Bioclipse/Groovy) script:
https://gist.github.com/egonw/ca4c348b9a2d1116efcdb55fa85dd158

It takes advantage of a combination Blazegraph SPARQL trick and breaking up
thing in batches of a certain size:

SELECT ?art ?artLabel
WITH {
SELECT ?art WHERE {
?art wdt:P31 wd:Q13442814
} LIMIT $batchSize OFFSET $offset
} AS %RESULTS {
INCLUDE %RESULTS
?art wdt:P1476 ?artLabel .
MINUS { ?art wdt:P921 wd:$conceptQ }
FILTER (contains(lcase(str(?artLabel)), "$concept"))
}
where "$concept" is my search word in the title, and $batchSize and $offset
take care of the batching by the script. This script creates
QuickStatements.

Mind you, I manually check the created statements, because in my domain
(biochem) a simple search results of false positives, hence the "blacklist"
in the script :)

Egon










On Sat, Dec 15, 2018 at 10:13 AM Fabrizio Carrai 
wrote:

> Thanks Matthias,
> that's a pity. Your suggestion relies on the effective characterization of
> the item that,  at this writing time, is pretty poor for my interest.
> Could it be an idea to download all the "scholary articles", locally
> select  for the keyword of interest (e.g. "microgravity") and set the
> property P921 for all of them ? Quickstatements may be helpful for the last
> step, any suggestions for other tools ?
>
> Thanks
> Fabrizio
>
> Il giorno ven 14 dic 2018 alle ore 22:16 Matthias Erfurth 
> ha scritto:
>
>> Hi Fabrizio,
>> unfortunately you can't fulltext search all the scholarly articles
>>  , you should better work with
>> indexed properties, so
>> you can query for other articles with microgravity as main subject ...
>> With the ajax based wikidata search
>>
>> SELECT ?item
>> WHERE {
>> ?item wdt:P31 wd:Q13442814;
>>   wdt:P921 wd:Q48655.
>> }
>>
>> Best regards,
>>
>> ciao matthias
>>
>>
>> *Gesendet:* Freitag, 14. Dezember 2018 um 18:55 Uhr
>> *Von:* "Fabrizio Carrai" 
>> *An:* "Discussion list for the Wikidata project" <
>> wikidata@lists.wikimedia.org>
>> *Betreff:* Re: [Wikidata] Query on scholarly article fails
>> Thanks again to Ettore, but I immediately found another timeout problem
>> when I just added a FILTER to find all the articles with the word "biokis"
>> in the title
>>
>> SELECT ?istanza_di ?instanza_diLabel WHERE {
>>   ?istanza_di wdt:P31 wd:Q13442814.
>>   ?istanza_di rdfs:label ?instanza_diLabel.
>>   FILTER((LANG(?instanza_diLabel)) = "en").
>>   FILTER(CONTAINS(LCASE(?instanza_diLabel), "biokis"))
>> }
>> LIMIT 100
>>
>> At least one article should be returned:
>> https://www.wikidata.org/wiki/Q57202937
>> but I got a timeout.
>>
>> Thanks to anybody that can help
>>
>> Fabrizio
>>
>>
>> Il giorno ven 14 dic 2018 alle ore 10:12 Ettore RIZZA <
>> ettoreri...@gmail.com> ha scritto:
>>
>>> Hello Fabrizio,
>>>
>>> It seems that the problem comes from SERVICE wikibase:label. As said in
>>> another discussion, the query executes in less than one second if you 
>>> rewrite
>>> it in this way
>>> 
>>> .
>>>
>>> Cheers,
>>>
>>> Ettore Rizza
>>>
>>> Le ven. 14 déc. 2018 à 09:59, Fabrizio Carrai 
>>> a écrit :
>>>
 Hello all,
 the following query ends with a timeot:

 SELECT ?istanza_di ?istanza_diLabel WHERE {
   SERVICE wikibase:label { bd:serviceParam wikibase:language
 "[AUTO_LANGUAGE],en". }
   ?istanza_di wdt:P31 wd:Q13442814.
 }
 LIMIT 10

 Can anybody explain why ?
 Thanks in advance

 --
 *Fabrizio*
 ___
 Wikidata mailing list
 Wikidata@lists.wikimedia.org
 https://lists.wikimedia.org/mailman/listinfo/wikidata
>>>
>>> ___
>>> Wikidata mailing list
>>> Wikidata@lists.wikimedia.org
>>> https://lists.wikimedia.org/mailman/listinfo/wikidata
>>
>>
>>
>> --
>> *Fabrizio*
>> ___ Wikidata mailing list
>> Wikidata@lists.wikimedia.org
>> https://lists.wikimedia.org/mailman/listinfo/wikidata
>> ___
>> Wikidata mailing list
>> Wikidata@lists.wikimedia.org
>> https://lists.wikimedia.org/mailman/listinfo/wikidata
>>
>
>
> --
> *Fabrizio*
> ___
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> https://lists.wikimedia.org/mailman/listinfo/wikidata
>


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Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join my in asking the American
Chemical Society to join the Initiative for Open Citations too

Re: [Cdk-user] SMSD and RDT with CDK v 2.x released

[Egon Willighagen]

Thanks, Syed!

Egon


On Sat, Oct 13, 2018 at 3:55 PM Syed Asad Rahman  wrote:

> Dear All,
>
> A quick update- in the past few months I have received several request
> from the CDK community to upgrade SMSD and RDT by making it compatible to
> the CDK v2.0 version.
>
> Finally, I have updated both the tools :)
>
> 1) SMSD (https://github.com/asad/SMSD/releases/tag/2.2.0) and
> 2) RDT (https://github.com/asad/ReactionDecoder/releases/tag/v2.0.0)
>
> Thanks everyone for their feedback and patience.
>
> Best wishes,
> -Asad
>
>
> ___
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> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [Cdk-user] InChi and Docker [solved]

[Egon Willighagen]

Oh, very happy to hear that! Are you going to put it up on DockerHub?

Egon

On Thu, Sep 13, 2018 at 10:42 PM Maria Sorokina 
wrote:

> I managed to make my app function.
>
> The problem comes from the way a Spring Boot application packages the jar
> - internally, the jar is different from plain old Java, so the deployment
> of artefacts is also different. The Jnati library that allows the wrapping
> of the InChi factory is not adapted to that special deployment and is
> simply lost and doesn’t find the artifacts in correct places *if it never
> ran on the system before* (case of a brand new minimal image).
> The trick I found to make a Spring Boot application using InChis run in
> Docker is not very elegant, but functional. In the container, during the
> compilation, or at the execution of the container, before running the main
> Spring Boot jar, run the simples possible mini POJO jar containing the
> InChiGeneratorFactory, that will create the correct environment.
> Now everything works!
>
> This is my Dockerfile:
>
> FROM openjdk:8u171-slim
> EXPOSE 8080
> VOLUME /tmp
> ARG JAR_FILE
> COPY ${JAR_FILE} app.jar
> COPY inchiPet.jar /
>
> RUN java -jar inchiPet.jar
>
> ENTRYPOINT 
> ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]
>
> Where « inchiPet.jar » is the tiny regular jar with only a call to an
> inchiGeneratorFactory, and « app.jar » is my main app.
>
> However, I used a bunch of libraries from CDK and until now, only the
> InChi generator caused this problem within the Spring Boot - Docker
> ecosystem.
>
> Hope this solution could help anybody encountering this kind of problem in
> the future!
>
> Maria Sorokina, PhD
> Steinbeck Research Group
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> http://cheminf.uni-jena.de
>


-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

[Egon Willighagen]

:)

I'm still learning a lot about Docker, which I find a challenge with time I
need to spend on teaching, writing/reading papers, and writing grant
proposals... Fortunately, I increasingly have people around me that can
help...

Chris, yes, Maria's problem should be solved... I know how to deploy a
Docker to DockerHub now but have yet to figure out how to make a
Docker(file) from scratch... my PhD has not had time yet to teach me
that... I split out this thread, because it is interesting to have CDK
microservices... like John's CDKDepict... and how we want to annotated them
with metadata (bioschemas, bio.tools, etc...) so that these services are
FAIR too... that I had in mind of this fork of the Docker discussion...

Egon


On Tue, Sep 11, 2018 at 5:50 PM John Mayfield 
wrote:

> It doesn't use InChI :-).
>
> On Tue, 11 Sep 2018 at 16:43, Egon Willighagen 
> wrote:
>
>> Anyway, I'm quite excited about the idea of a Docker for CDK
>> functionality... (well, excited it triggered here not so much I am entirely
>> sure this is a fantastic platform, but in our OpenRiskNet we use it for
>> workflows, and being able to replace some stuff with CDK functionality in
>> that cloud *is* exciting :)
>>
>> John, how is your CDK Depict docker [0] set up then?
>>
>> Egon
>>
>> 0.https://hub.docker.com/r/simolecule/cdkdepict/
>>
>>
>> On Tue, Sep 11, 2018 at 5:03 PM Maria Sorokina 
>> wrote:
>>
>>> I am building my jar with Maven, but I don’t think that it is the
>>> problem, as I tried tu run the jar on a Centos7 VM having just Java and it
>>> worked without any problem.
>>> I also desperately tried the dirty solution of downloading the manifest
>>> and the jniinchi-1.03_1-LINUX-AMD64.so files the ini-inchi seems to
>>> search for and put them where it seems to search them within the container,
>>> but, of course it failed.
>>>
>>> I’ll try to search for a solution, but for now I’ll just do my thing
>>> without containerizing this part of my app. If I find a solution, I’ll post
>>> it here. Meanwhile, I’m still very open to any suggestion!
>>>
>>
>>
>> --
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: https://www.zotero.org/egonw
>> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
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[Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

[Egon Willighagen]

Anyway, I'm quite excited about the idea of a Docker for CDK
functionality... (well, excited it triggered here not so much I am entirely
sure this is a fantastic platform, but in our OpenRiskNet we use it for
workflows, and being able to replace some stuff with CDK functionality in
that cloud *is* exciting :)

John, how is your CDK Depict docker [0] set up then?

Egon

0.https://hub.docker.com/r/simolecule/cdkdepict/


On Tue, Sep 11, 2018 at 5:03 PM Maria Sorokina 
wrote:

> I am building my jar with Maven, but I don’t think that it is the problem,
> as I tried tu run the jar on a Centos7 VM having just Java and it worked
> without any problem.
> I also desperately tried the dirty solution of downloading the manifest
> and the jniinchi-1.03_1-LINUX-AMD64.so files the ini-inchi seems to
> search for and put them where it seems to search them within the container,
> but, of course it failed.
>
> I’ll try to search for a solution, but for now I’ll just do my thing
> without containerizing this part of my app. If I find a solution, I’ll post
> it here. Meanwhile, I’m still very open to any suggestion!
>


-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
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Re: [Wiki-Medicine] [Wikidata] Please support risk factor Wikidata property

[Egon Willighagen]

Dear Houcemeddine,

interesting proposal, indeed. I left a comment on the page, which basically
says we need qualifiers and references. The references because some claims
will be controversial (even if backed up by literature), while I also see
these links as likely time bound, due to changing health policies (I can
think of a few other reasons), at least for the residence examples (I hope
no one gets any ideas about Q4 'risk factor' 'residence' 'war zone').

With kind regards,

Egon





On Fri, Aug 10, 2018 at 10:05 PM Houcemeddine A. Turki <
turkiabdelwa...@hotmail.fr> wrote:

> Dear Mr. or Ms.,
> I thank you for your efforts. I invite you to support the proposal of risk
> factor as a Wikidata property. The property will be an excellent
> contribution to Wikidata as it can allow this high-scale knowledge base to
> be useful for digital epidemiology purposes. The proposal is available in
> https://www.wikidata.org/wiki/Wikidata:Property_proposal/risk_factor.
> This property is a generalization of the first property proposal I
> developed.
> Yours Sincerely,
> Houcemeddine Turki
> ___
> Wikidata mailing list
> wikid...@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata
>


-- 
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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/
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Re: [Wikidata] You can now query the constraint violations with the Query Service

[Egon Willighagen]

Nice, I put it to use [0,1].

Question, what if the WDQS has a wikisource export format, allowing me to
copy/paste output easily as table in a Wikidata page? Is something like
that already possible? (Alternatively, maybe the Listeria bot can handle
this much better, but I still have to learn how to use that properly...)

Egon

0.https://twitter.com/egonwillighagen/status/1030732574220582912
1.https://twitter.com/egonwillighagen/status/1030737717095788544


On Fri, Aug 3, 2018 at 12:44 PM Léa Lacroix 
wrote:

> Hello all,
>
> We started integrating the constraint violations into the Query Service.
> That means you can build queries using the constraint violations, with the
> predicate wikibase:hasViolationForConstraint. This will hopefully help
> you to watch better the quality of Wikidata content.
>
> Please note that this is a first step. Not all constraint violations are
> exposed yet, only the ones that can be checked fast enough. We're working
> on having more available in WDQS.
>
> You can base your queries on these few examples:
>
> #10 statements with constraint violations that are currently includedSELECT * 
> WHERE {?x wikibase:hasViolationForConstraint ?y.} LIMIT 10
>
> Try it!
> 
>
> #Map/timeline/image grid of items that have a statement with a constraint 
> violation#defaultView:MapSELECT DISTINCT ?item ?itemLabel ?image 
> ?coordinate_location ?point_in_time ?date_of_birth WHERE {
>   ?s wikibase:hasViolationForConstraint ?y.
>   ?item ?z1 ?s.
>   SERVICE wikibase:label { bd:serviceParam wikibase:language 
> "[AUTO_LANGUAGE],en". }
>   OPTIONAL { ?item wdt:P18 ?image. }
>   OPTIONAL { ?item wdt:P625 ?coordinate_location. }
>   OPTIONAL { ?item wdt:P585 ?point_in_time. }
>   OPTIONAL { ?item wdt:P569 ?date_of_birth. }}
>
> Try it!
> 
>
> #Bar chart of statements that have a constraint violation, grouped by 
> instance of the regarding item:#defaultView:BarChart#TEMPLATE={ "template": { 
> "en": "Bar chart of statements that have a constraint violation grouped by 
> ?property the regarding item" }, "variables": { "?property": { 
> "query":"SELECT ?id  WHERE { VALUES ?id {  wd:P31 wd:P17 wd:P571 wd:P361 
> wd:P19 } }" } } }SELECT ?instance_ofLabel (COUNT(?instance_ofLabel) AS 
> ?count) WHERE {
>   ?s wikibase:hasViolationForConstraint ?y.
>   ?item ?z1 ?s.
>   BIND(wdt:P31 AS ?property)
>   SERVICE wikibase:label { bd:serviceParam wikibase:language 
> "[AUTO_LANGUAGE],en". }
>   OPTIONAL { ?item ?property ?instance_of. }}GROUP BY ?instance_ofLabelORDER 
> BY DESC(?count)LIMIT 30
>
> Try it!
> 
>
> The modules included on the property talk pages, Module:Constraints
> ,
> Module:Constraints/SPARQL
>  etc. has been
> updated with a new query link (thanks Matěj!)
>
> 

Re: [Wikidata] Please support risk factor Wikidata property

[Egon Willighagen]

Dear Houcemeddine,

interesting proposal, indeed. I left a comment on the page, which basically
says we need qualifiers and references. The references because some claims
will be controversial (even if backed up by literature), while I also see
these links as likely time bound, due to changing health policies (I can
think of a few other reasons), at least for the residence examples (I hope
no one gets any ideas about Q4 'risk factor' 'residence' 'war zone').

With kind regards,

Egon





On Fri, Aug 10, 2018 at 10:05 PM Houcemeddine A. Turki <
turkiabdelwa...@hotmail.fr> wrote:

> Dear Mr. or Ms.,
> I thank you for your efforts. I invite you to support the proposal of risk
> factor as a Wikidata property. The property will be an excellent
> contribution to Wikidata as it can allow this high-scale knowledge base to
> be useful for digital epidemiology purposes. The proposal is available in
> https://www.wikidata.org/wiki/Wikidata:Property_proposal/risk_factor.
> This property is a generalization of the first property proposal I
> developed.
> Yours Sincerely,
> Houcemeddine Turki
> ___
> Wikidata mailing list
> Wikidata@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata
>


-- 
E.L. Willighagen
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: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [Wikidata] On traceability and reliability of data we publish [was Re: [Wikimedia-l] Solve legal uncertainty of Wikidata]

[Egon Willighagen]

On Sat, Jul 7, 2018 at 5:59 PM mathieu lovato stumpf guntz <
psychosl...@culture-libre.org> wrote:

> I agree this is misconception that a copyright license make any direct
> change to data reliability. But attribution requirement does somewhat
> indirectly have an impact on it, as it legally enforce traceability.
>
I know that "law" has a special corner, but therefore not always the
best... law, in the end, is just a social construct, just like anything we
agree on. First, we all agree (it seems to me) that provenance is valuable.

However, having something in law (or contract) effectively criminalizes if
you fail to add the provenance. Is that what you really wish? Do you want
to be able to legally punish people if the fail to give provenance?
Honestly, that sounds a bit harsh to me... and to me, and this is a
personal opinion and not an argument, I think Wikidata is more open, more
inclusive than that: Wikidata offers carrots, not sticks.

Egon

-- 
E.L. Willighagen
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: https://www.zotero.org/egonw
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Re: [Cdk-user] Question about 3D SDF file from SMILES string

[Egon Willighagen]

Maybe a temporary glitch?
https://cactus.nci.nih.gov/chemical/structure/CCC/sdf works for me right
now...

Egon

On Sun, May 20, 2018 at 4:20 PM Xuan Cao  wrote:

> Hi John,
>
> Thank you for your reply! I will look into that!
>
> BTW, the link is not working (404).
>
> Xuan
>
> On 20 May 2018 at 02:16, John Mayfield 
> wrote:
>
>> There is some support in the *builder3d *modules but there are better
>> options out there. One day I'll find some time to update that code but
>> depending on how many structure you need to convert the NCI resolver uses
>> Corina (via CACTVS) IIRC.
>>
>> https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf
>>
>> John
>>
>> On 20 May 2018 at 06:08, Xuan Cao  wrote:
>>
>>> Hi everyone!
>>>
>>> I am just wondering does CDK have the feature that convert SMILES string
>>> to 3D SDF file, or convert 2D SDF file to 3D SDF file?
>>>
>>> I see that there are some stand-alone programs that do the convert (2D
>>> to 3D), but I prefer using CDK if it has the feature.
>>>
>>> Thank you so much!
>>>
>>> Xuan
>>>
>>>
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>>
>>>
>>
>
> --
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>


-- 
E.L. Willighagen
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: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [Bioc-devel] Best practice on commit

[Egon Willighagen]

Dear James,

I should have mentioned that email... I had seen it. But I mostly read it
as personal experience. However, given that you refer me to that, I will
assume my proposal is acceptable, as it is comparable to Martin's write up.

Thanks,

Egon


On Sun, Mar 11, 2018 at 5:06 PM, James W. MacDonald <jmac...@uw.edu> wrote:

> This was recently discussed:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012875.html
>
> On Sun, Mar 11, 2018 at 4:10 AM, Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>> Hi Nicolas,
>>
>> after doing a bit of work on the BridgeDbR package this weekend, I was
>> wondering exactly the same thing. I prefer small patches, so that I can
>> easily link the change with the commit message and have related changes
>> together (and fairly, it allows me to see when I actually work on what
>> (#academicTimeReporting)... But previously I learned that when you push
>> something to the repository, you should bump the question, so currently I
>> do this for every change I made, leaving a ridiculous number of minor
>> release and really short NEWS entries...
>>
>> Working in a branch and when only bumping the version number just before
>> the merge into master makes a lot of sense to me.
>>
>> Can some senior developer and/or gatekeeper confirm that that is
>> acceptable
>> commit practice?
>>
>> Egon
>>
>>
>>
>> On Fri, Feb 23, 2018 at 8:24 PM, Nicolas Descostes <
>> nicolas.descos...@gmail.com> wrote:
>>
>> >  Dear Bioconductor community,
>> >
>> > When developing further a package, is the best practice to create a
>> branch
>> > and bump the version when a full new feature is merged or to stay on the
>> > master without bumping when committing temporarily? More generally,
>> When do
>> > you usually bump a version?
>> >
>> > Thank you.
>> >
>> > Nicolas
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>>
>> --
>> E.L. Willighagen
>> 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: https://www.zotero.org/egonw
>> ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> <https://maps.google.com/?q=4225+Roosevelt+Way+NE,+%23+100+Seattle+WA+98105=gmail=g>
> Seattle WA 98105
> <https://maps.google.com/?q=4225+Roosevelt+Way+NE,+%23+100+Seattle+WA+98105=gmail=g>-6099
>
>



-- 
E.L. Willighagen
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: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286>
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Re: [Bioc-devel] Best practice on commit

[Egon Willighagen]

Hi Nicolas,

after doing a bit of work on the BridgeDbR package this weekend, I was
wondering exactly the same thing. I prefer small patches, so that I can
easily link the change with the commit message and have related changes
together (and fairly, it allows me to see when I actually work on what
(#academicTimeReporting)... But previously I learned that when you push
something to the repository, you should bump the question, so currently I
do this for every change I made, leaving a ridiculous number of minor
release and really short NEWS entries...

Working in a branch and when only bumping the version number just before
the merge into master makes a lot of sense to me.

Can some senior developer and/or gatekeeper confirm that that is acceptable
commit practice?

Egon



On Fri, Feb 23, 2018 at 8:24 PM, Nicolas Descostes <
nicolas.descos...@gmail.com> wrote:

>  Dear Bioconductor community,
>
> When developing further a package, is the best practice to create a branch
> and bump the version when a full new feature is merged or to stay on the
> master without bumping when committing temporarily? More generally, When do
> you usually bump a version?
>
> Thank you.
>
> Nicolas
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
E.L. Willighagen
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: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen

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[BlueObelisk-discuss] a Blue Obelisk meet up at the 11th ICCS?

[Egon Willighagen]

Hi all,

in May there will be 11th International Conference on Chemical Structures
[0]. I will go and while the program is normally quite packed, I'm sure
there will be an opportunity to come together.

Looking forward to hearing who else is going, and looking forward to
finally be able to join a Blue Obelisk meet up again.

Egon

0.http://www.int-conf-chem-structures.org/

-- 
E.L. Willighagen
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
ORCID: -0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen
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