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

dling 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 f

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

t.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...@gma

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

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

Re: [Cdk-user] Extended Fingerprint: what do the features represent?

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

Re: [Cdk-user] Extended Fingerprint: what do the features represent?

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

Re: [Cdk-user] IUPAC name generation

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

[BlueObelisk-discuss] Fwd: CCL: Call for Papers: Free and Open Source Software symposium at ACS Fall 2023 Meeting

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:

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

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:

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

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

Re: [Cdk-user] Getting warning from AminoAcidCountDescriptor

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:

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

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

Re: [Cdk-user] Generation of FCFP Fingerprint

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 ( >

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

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

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

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

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

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-desk

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

https://bugs.kde.org/show_bug.cgi?id=429408 Egon Willighagen changed: What|Removed |Added CC||egon.willigha...@gmail.com --- Comment #3

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

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. > >

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

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. > >

Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

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 (

Re: [BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

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 -- BiGCaT received a NWO Open Science grant to support our research into interop

[BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

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:

[BlueObelisk-discuss] log4j 2.17.0

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:

Re: [BlueObelisk-discuss] Intro + Possible Member

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

Re: [Cdk-user] Support for chemical standardization

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

[Cdk-user] CDK via Bioclipse/Bacting in Python and on Google Collab with pybacting

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

[BlueObelisk-discuss] CMLXOM 3.2 pushed to Maven Central :)

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

Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

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

Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

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

[BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

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 JUn

[BlueObelisk-discuss] Maven Central (was: WWMM & CML -- sunsetting of Mercurial in Bitbucket)

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, g

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

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.sonatyp

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

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

[BlueObelisk-discuss] Bacting paper published (Bacting is a follow up of Bioclipse)

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:

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

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 >

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

-- 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

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

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

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

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

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

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

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

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,

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

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

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

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

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

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,

Re: [Wikidata] Wikidata in the LOD cloud

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,

Re: [Wikidata] Wikidata in the LOD cloud

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

Re: [Wikidata] Wikidata in the LOD cloud

gt; > > 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 >

Re: [Wikidata] Wikidata in the LOD cloud

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

Re: [Wikidata] Wikidata in the LOD cloud

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.or

Re: [Wikidata] Wikidata in the LOD cloud

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 < > lydi

Re: [Wikidata] Wikidata in the LOD cloud

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

Re: [Wikidata] Wikidata in the LOD cloud

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.

Re: [Wikidata] WDQS outage - 2020/07/23

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

Re: [Wikidata] WDQS status

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

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

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

Re: [Wikidata] WDQS and SPARQL Endpoint Compatibility

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

[Bioc-devel] help with Win10 TSL problem?

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 ->

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

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

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

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'

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

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'

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

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 __ This is the maintainer address of Debian's Java team

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

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

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

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

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

[Cdk-user] CDK 2.3 now in Debian Unstable

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

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

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 Wi

Re: Help needed to upgrade cdk

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

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

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

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

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

Re: Help needed to upgrade cdk

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

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

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

Re: [Wikidata] Weekly Summary #384

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

Re: [Wikidata] Personal news: a new role

Dear Houcemeddine, do you happen to have a preprint for that online? 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.

[BlueObelisk-discuss] BODR evolution

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

Re: [Wikidata] ShEx to validate Medical Wikidata

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

Re: [Wikidata] ShEx to validate Medical Wikidata

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

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

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

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

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

Re: [Wikidata] Virtuoso hosted Wikidata Instance

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

Re: [Wikidata] Useful resources for Scholia

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

Re: [Cdk-user] controlling hydrogen display with DepictionGenerator

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:

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

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:

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

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:

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

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

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

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

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

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

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 t

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

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 2

Re: [Wikidata] Query on scholarly article fails

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: > >

Re: [Wikidata] Query on scholarly article fails

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 {

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

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

Re: [Cdk-user] InChi and Docker [solved]

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

Re: [Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

(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: >

[Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

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*

Re: [Wiki-Medicine] [Wikidata] Please support risk factor Wikidata property

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

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

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

Re: [Wikidata] Please support risk factor Wikidata property

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

Re: [Wikidata] On traceability and reliability of data we publish [was Re: [Wikimedia-l] Solve legal uncertainty of Wikidata]

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

Re: [Cdk-user] Question about 3D SDF file from SMILES string

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). > >

Re: [Bioc-devel] Best practice on commit

. 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, >>

Re: [Bioc-devel] Best practice on commit

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

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

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

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