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

Re: [Wikidata] Recoin2: New version of relative completeness status indicator for all entities

On Wed, Dec 6, 2017 at 10:01 AM, Simon Razniewski wrote: > More information can be found on the tools page at > https://www.wikidata.org/wiki/User:Ls1g/Recoin2. > > Interesting! At the moment the colored indicator refers to

Re: [Wikidata] An answer to Lydia Pintscher regarding its considerations on Wikidata and CC-0

Dear Mathieu, On Thu, Nov 30, 2017 at 2:28 PM, mathieu stumpf guntz <psychosl...@culture-libre.org> wrote: > Le 30/11/2017 à 10:13, Egon Willighagen a écrit : >> On Wed, Nov 29, 2017 at 10:45 PM, Mathieu Stumpf Guntz >> <psychosl...@culture-libre.org> wrote: >&

Re: [Wikidata] An answer to Lydia Pintscher regarding its considerations on Wikidata and CC-0

Dear Mathieu, On Wed, Nov 29, 2017 at 10:45 PM, Mathieu Stumpf Guntz < psychosl...@culture-libre.org> wrote: > I forward here the message I initially posted on the Meta Tremendous > Wiktionary User Group talk page >

Re: [BlueObelisk-discuss] website / migration to Markdown+git ?

Hi Chris, I think it's time to update the redirect of blueobelisk.org to the new website... Egon On Sun, Oct 1, 2017 at 12:14 PM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > > Hi all, > > On Mon, Sep 11, 2017 at 7:05 PM, Egon Willighagen > <egon.willigha...@g

[Cdk-user] initial Java9 observations

Hi all, this weekend I installed Java9 and did a bit of initial testing... for the CDK the following seems to have changed: 1. it compiles without issues 2. the compiling seems faster (N=3): 19 seconds instead of the old 66 seconds 3. the tests seem to run *slower* (N=3)... 134 seconds instead

Re: [BlueObelisk-discuss] Does anyone on this list own the blueobelisk (one word) repository on GitHub?

Geoff, thanks! I've moved the stub index.md to the new "organization" and removed the hyphened one. Egon On Tue, Sep 12, 2017 at 5:44 AM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > So, can you grow the number of admins with people from this list? Then > we ca

Re: [BlueObelisk-discuss] website / migration to Markdown+git ?

On Mon, Sep 11, 2017 at 9:22 PM, Christoph Steinbeck wrote: > Please remind me of the new wiki location and I’ll redirect the domain for > now. My ageing neural network had forgotten about it, otherwise I would have > fixed the problem a while ago.

Re: [Cdk-user] Atom Signatures with stereo-info

Hi Staffan, some years ago we looked at exactly this with AZ (Lars) and Gilleain (EBI)... I need to look up that code... Egon On Fri, Jul 21, 2017 at 10:39 AM, Staffan Arvidsson < staffan.arvids...@gmail.com> wrote: > Hi all, > > I wonder if there is any way of producing atom signatures with

Re: [Cdk-user] Computing the LogD

Hi Yannick, I don't think we have a LogD model. Egon On Sun, Jul 9, 2017 at 11:08 PM, Yannick .Djoumbou wrote: > Hey all, > > I am looking for a tool to compute the LogD for various compounds. I could > not find any function/module that computes this property. Is there

Re: [Cdk-user] Title line for MDL formats

Mmm... I'd consider that a regression, as that was the intended behavior... John, do you agree we should restore that behavior, or do you have a better solution? Egon On Sat, Jun 24, 2017 at 4:23 PM, Tim Dudgeon wrote: > Hi All, > > I'm needing to write the title line

[Cdk-user] Third CDK paper is out

Hi all, https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4 Thanks to everyone who contributed to the project, both (part-time) developers but also all users, for whom we are doing this. Happy reading! Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht

Re: [Wikidata] Improve Wikidata links to Dutch municipalities

On Sat, May 20, 2017 at 6:47 PM, Andy Mabbett <a...@pigsonthewing.org.uk> wrote: > On 19 May 2017 at 11:49, Egon Willighagen <egon.willigha...@gmail.com> > wrote: > > > I am not sure I see how you want to achieve that beyond Wikidata at > > this moment? > &g

Re: [Wikidata] Improve Wikidata links to Dutch municipalities

On Thu, May 18, 2017 at 8:45 PM, Andy Mabbett wrote: > I'm ambivalent as to which is the ideal solution; but using both, > inconsistently, and on an arbitrary basis, is certainly not it. I agree, but we're in a mixed world right now... semantic web is being picked up,

Re: [Wikidata] Improve Wikidata links to Dutch municipalities

On Wed, May 17, 2017 at 4:09 PM, Wouter Beek wrote: > Wikidata currently includes links to the Kadaster, but these do not point to > the proper IRIs. For example, Dutch municipalities in Wikidata currently > link to an HTML viewer of Kadaster [1], but they should point to our >

[Wikidata] [update] Re: Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

Hi all, here's a quick update below... (in case you missed it: there is this event page: https://www.wikidata.org/wiki/Wikidata:Events/NPOS2017) On Mon, Apr 24, 2017 at 9:36 AM, Léa Lacroix wrote: > Thanks Egon for letting us know. > Feel free to add the event on

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

Dear Arne, On Tue, Apr 25, 2017 at 11:18 AM, Arne Wossink wrote: > Thank you for taking on the role of coordinator! I'm happy to present > anything if necessary, but that depends on the format of the day, I guess. This Friday we will likely finalize the program of the full

Re: [Cdk-user] n way-bonds

On Thu, Apr 27, 2017 at 9:54 AM, John Mayfield wrote: > I was wondering does anyone use n-way bonds in CDK (a bond with more than > two atoms)? > > IAtom atom1 = object.getBuilder().newInstance(IAtom.class, "C"); >> IAtom atom2 =

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

On Mon, Apr 24, 2017 at 12:33 PM, Arne Wossink wrote: > Sounds good. How do we proceed from here? Are you going to propose a session > for this day and invite attendees? Do we need to sign up anywhere? Yes, we need to register. But we don't need a proposal: 1. it will be an

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

On Mon, Apr 24, 2017 at 10:19 AM, Arne Wossink wrote: > Interesting opportunity! I would be interested in attending and/or helping > out as WMNL representative, but I don't have a case study or anything else I > could contribute. Yes, of course, Wikidata is just part of

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

t; Feel free to add the event on https://www.wikidata.org/wiki/Wikidata:Events > :) > > On 23 April 2017 at 11:24, Egon Willighagen <egon.willigha...@gmail.com> > wrote: >> >> Hi Wikidata community, >> >> on May 29 in Delft, The Netherlands, the first nation

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

Maarten > > > > On 23-04-17 12:34, Egon Willighagen wrote: >> >> Dear Amit, >> >> you make me painfully aware of something I should have mentioned (my >> apologies for haven forgotten that; still tired from the science march >> yesterday): it is not

Re: [Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

doing few competitions on Kaggle : > https://www.kaggle.com/amitkumarjaiswal. > > Please let me know how can I join/participate in this meeting. > > Regards > > Thank you > Amit Kumar Jaiswal > > On 4/23/17, Egon Willighagen <egon.willigha...@gmail.com> wrote: >> Hi Wiki

[Wikidata] Joining May 29, National Plan Open Science meeting in Delft, The Netherlands

Hi Wikidata community, on May 29 in Delft, The Netherlands, the first national meeting is planned for researchers (at a various stage of their career) about the Dutch National Plan Open Science. There will be a large session where organisations and individuals can present their experiences with

Re: [BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson wrote: > Just thought I would let people know that Jmol/JSmol now can calculate R/S > chirality for any carbon atom. I've been working with Jmol for 10 years and > only yesterday realized it was pretty trivial to write this. Well,

Re: [Cdk-user] Rendering 3D mols

> Pass the molfile to what? To JMol? > Is there an example anywhere? > > Tim > > > > On 07/03/2017 16:42, Egon Willighagen wrote: >> >> On Tue, Mar 7, 2017 at 5:31 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: >>> >>> What's the state of

Re: [Cdk-user] Rendering 3D mols

On Tue, Mar 7, 2017 at 5:31 PM, Tim Dudgeon wrote: > What's the state of play with rendering 3D structures with CDK? > I see some mention of this in the 2006 paper, but it seems to say that > 3D rendering is done using JMol? Yes, correct. We have had 3D viz in the CDK,

Re: [Cdk-user] 'neutralizing' a molecule

;>> 1(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(2 >>> 5)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H >>> ,30,31)(H2,17,18,19)/ >>> >>> You'd also be surprised how far a very simple approach gets you: >>> Neutralize.java &g

Re: [Bioc-devel] RMassBank (almost) builds ...

Hi all, including all BioC developers, On Thu, Oct 13, 2016 at 4:32 PM, Zach Charlop-Powers wrote: > When I initially submitted to CRAN I did NOT check the Java version and > therefore users would be able to use Java 7 and would encounter errors only > when using

Re: [Bioc-devel] RMassBank (almost) builds ...

cc: Rajarshi Hi Emma, On Wed, Oct 12, 2016 at 10:18 PM, Schymanski, Emma wrote: > Thanks to Laurent and Jo for updating MSnbase and thanks to the BioC team for > getting the email updates working again! The good news is that RMassBank now > builds on most

Re: [Cdk-user] [Cdk-devel] CDK III paper: software using CDK 1.4 or 1.5?

Dear Todd, On Tue, Aug 16, 2016 at 9:05 PM, Martin, Todd wrote: > The web link is fine for referencing T.E.S.T. I still use 1.0 release of CDK > so not to break the JChemPaint linkage. In the web services version we will > probably use a newer CDK version since we wont need

[Cdk-user] CDK v1.5.15 and v2.0-SNAPSHOT

Hi all, over the last few months we have been working on finalizing a third paper about the CDK library. You can find the result here: https://github.com/cdk/cdk-paper-3 (including a PDF) This paper picks out a number of changes in the library and describes changes in the development model, since

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

> > 2016-10-08 11:33 GMT+02:00 Egon Willighagen <egon.willigha...@gmail.com>: > >> >> >> On Sat, Oct 8, 2016 at 11:28 AM, Lydia Pintscher < >> lydia.pintsc...@wikimedia.de> wrote: >> >>> On Sat, Oct 8, 2016 at 11:23 AM, Egon Willighagen >&g

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

On Sat, Oct 8, 2016 at 11:28 AM, Lydia Pintscher < lydia.pintsc...@wikimedia.de> wrote: > On Sat, Oct 8, 2016 at 11:23 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: > > Ah, those numbers are for https://www.wikidata.org/wiki/Property:P234 > ... > &g

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

On Sat, Oct 8, 2016 at 11:19 AM, Lydia Pintscher < lydia.pintsc...@wikimedia.de> wrote: > On Sat, Oct 8, 2016 at 11:14 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: > > For small compounds this is answered by Sebastian's analysis... 5K would > > c

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

On Sat, Oct 8, 2016 at 11:07 AM, Lydia Pintscher < lydia.pintsc...@wikimedia.de> wrote: > > Based on this my proposal is to increase string and URL and > potentially external identifier if you request it. One open question > is still what the new limit should be. > For small compounds this is

Re: [Wikidata] signing license declarations

On Wed, Oct 5, 2016 at 9:55 PM, Benjamin Good wrote: > How do you plan to handle updates ? Bug the upstream author when they make a release... like in the other part of the thread, it's upstream should make it clearly available under CCZero from their site... but we

Re: [Wikidata] signing license declarations

On Wed, Oct 5, 2016 at 7:44 PM, Benjamin Good wrote: > When negotiating the import of data from resources that are not CC0, it > would be very valuable to have a somewhat formal process to allow them to > declare that some portions of their databases may be imported into

Re: [Bioc-devel] unit test results not showing up for BridgeDbR?

sen > <l.eijs...@maastrichtuniversity.nl> > -Maintainer: Anwesha Bohler <anweshaboh...@gmail.com> > +Maintainer: Egon Willighagen <egon.willigha...@gmail.com> > Depends: R (>= 3.3.0), rJava > Imports: RCurl > Suggests: testthat > > > More on

[Bioc-devel] unit test results not showing up for BridgeDbR?

Hi all, I have pushed a newer version of BridgeDbR to the repository, which includes tests with 'testthat', but when looking at the package homepage [0], it does not seem the test results are being picked up... I looked at the documentation, and did not find anything that could explain it (e.g.

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

e information here: http://jcheminf.springeropen.com/articles/10.1186/1758-2946-5-7 Egon > On Fri, Sep 23, 2016 at 3:27 AM Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> >> Sebastian, great you found time for it! I didn't :/ (Stats are worth a >> tweet, IMHO :) >

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

rall > slightly shorter. > > Best, > Sebastian > > On Sun, Sep 18, 2016 at 9:19 PM, Denny Vrandečić <vrande...@gmail.com> > wrote: > > Can you figure out what a good limit would be for these two use cases? > I.e. > > what would support 99%, 99.9%, and 10

Re: [Wikidata] Greater than 400 char limit for Wikidata string data types

Hi all, sorry for joining the party late... On Tue, Sep 13, 2016 at 11:39 AM, Sebastian Burgstaller wrote: > I think this topic might have been discussed many months ago. For > certain data types in the chemical compound space (P233, canonical > smiles, P2017

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

g 30, 2016 at 8:13 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: >> >> >> Rajarshi, Ola, >> >> where is the code base? Then I can look at updating the code. The QSAR >> stack has not changed a lot, neither has the SMILES parsing API.

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

s I teach right now, so no course material development time :( Egon > On Tue, Aug 30, 2016 at 7:13 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: >> >> >> Rajarshi, Ola, >> >> where is the code base? Then I can look at updating the code. Th

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

Rajarshi, Ola, where is the code base? Then I can look at updating the code. The QSAR stack has not changed a lot, neither has the SMILES parsing API. I think I can fix it without much trouble, if there is a git repository and build instructions... Then Ola and I can look at updating the

[Cdk-user] wedge bonds from SMILES?

John, how do I create wedge bond info for 2D depiction after starting with a (chiral) SMILES? 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:

Re: [Cdk-user] Complex Molecule Rendering

Dear Steve, On Mon, Aug 15, 2016 at 7:32 PM, Steve Roy wrote: > [Cu+].CC#N.CC#N.CC#N.CC#N.F[P-](F)(F)(F)(F)F > with the latest CDK version (1.5.x) I get something that more resembles what you expect:

Re: [Cdk-user] [Cdk-devel] Reaction Agents

No objections. Egon On Sat, Aug 13, 2016 at 5:20 PM, John M wrote: > Hi All, > > Lots of the ReactionManipulator methods don't consider agents. Guessing they > may have been written before an API change. > > Is there any objection to me updating the semantics such

existing semantic models for normal conditions of metabolites in bodily fluids?

Hi all, I'm extracting some metabolite-disease relationships and the book I'm reading also lists normal concentrations metabolites in various bodily fluids for various age groups. For example, for Phe 0-1 years in serum it lists <80 micromolar ("newborns" is another age group, but most are like

Re: [Wikidata] Op-ed on Wikipedia Signpost regarding Wikidata licensing

All, first, thanks for your reply blog, Gerard. On Sat, Jun 18, 2016 at 1:00 PM, Markus Kroetzsch wrote: >> I have written my opinion on the licensing of Wikidata data.. [1] > > I agree with your position there. So do I. The original article ends with: "Among

Re: [Wikidata] SQID evolved again: references

Super! Egon On Thu, Jun 2, 2016 at 11:26 PM, Markus Kroetzsch wrote: > Dear all, > > By popular demand, SQID now also shows references for most statements > (collapsed by default, of course). You can see it, e.g., here: > >

Re: [Wikidata] Ontology

On Sat, May 14, 2016 at 5:36 PM, Gerard Meijssen wrote: > We are talking DSM. When the DSM had never called something a disease and > never had a consistent presentation. When there is a lot of literature > showing how that something is NOT a disease, why persist on

Re: [Wikidata] Ontology

On Sat, May 14, 2016 at 3:39 PM, Gerard Meijssen wrote: > When an external ontology says that something is a disease and the DSM-5 > says it is not. There is a huge problem. How is DSM-5 not an ontology itself? Why is this a huge problem? Isn't this just two sources

Re: [Cdk-user] Interest in metabolic reaction depictions.

On Thu, May 12, 2016 at 5:54 PM, John M wrote: > > Thoughts? > Yes, this is very useful indeed! And it looks so much better than that stuff I did when with Peter and Janet Thornthon (OK, that was only 3 months)! That double arrow would be very cool, but doing this

Re: [Wikidata] Multiple properties/identifiers for the same resource

Hi Jerven, all On Fri, Apr 29, 2016 at 3:29 PM, Jerven Tjalling Bolleman wrote: > Could I be so bold to suggest that in Wikidata we should strive > to use external URI's for identifiers not Strings. > > For example in Wikidata, there are a lot of UniProt accessions. >

Re: [Bioc-devel] updated BridgeDbR package

to the repo. If > you don't have credentials we can request them for you. That would be nice. Please let me know if I need to make steps or if you need information. Egon > If you want the changes in quickly you could ask the maintainer to push > them. > > Valerie > > > On 04/29/2

[Bioc-devel] updated BridgeDbR package

Hi all, I am one of the upstream developers of BridgeDbR and like to see newer version of the package included in Bioconductor. After the pull request I created was closed [0], I realized that was not the right approach. But I also do not have SVN write access, and therefore can not push it like

Re: [Cdk-user] create amino acide

Something like this (in Groovy, from my CDK book)? import org.openscience.cdk.tools.*; crambin = ProteinBuilderTool.createProtein( "TTCCPSIVARSNFNVCRLPGTPEA" + "ICATYTGCIIIPGATCPGDYAN" ); println "Crambin has " + crambin.atomCount + " atoms." Grtz, Egon On Thu, Apr 28, 2016 at 1:24 AM,

Re: [Wikidata] Wikidata to search chemical compound names

On Mon, Apr 25, 2016 at 7:23 PM, Sebastian Burgstaller wrote: > A way to achieve this could be to fetch all labels and aliases for all > chemical compounds in one query and store them locally in your web > application. This certainly is only feasible if the number

Re: [Cdk-user] [Cdk-devel] CDK Release 1.5.14

On Mon, Apr 25, 2016 at 11:23 AM, John M wrote: > Also, I'm planning on removing the front page link to CDK 1.4.19 from > SourceForge (https://sourceforge.net/projects/cdk/). I understand this is > the most recent "stable" version but I think it would be better to

[BlueObelisk-discuss] soon: BODR 11 release

://github.com/egonw/bodr Grtz, Egon 2016-03-28 Egon Willighagen <egon.willigha...@gmail.com> * elements/symbols.bibxml: added two references for recently confirmed elements 2014-10-09 vaitkus <antanas.vaitku...@gmail.com> * elements/elements.xml: fixed the element symbol for Lv * elements/

Re: [Wikidata] Status and ETA External ID conversion

I think the predicate may need depend on the type of thing we're linking, and on what is being linked. A strong predicate, like owl:sameAs, requires a (very) strong similarity between concepts... this is often not the case... mind you, this applies also to the things being linked... there are

Re: [BlueObelisk-discuss] List of chemical names and identifiers

Peter, On Tue, Mar 8, 2016 at 7:43 PM, Peter Murray-Rust wrote: > I am now enhancing contentmine.org to search the daily literature and need > dictionaries to match names. I don't mind false negatives so am simply > matching names, but they should have identifiers. > > The

[BlueObelisk-discuss] Twitter account

Hi all, with all the Open storms around now, which is good, it's important that the Blue Obelisk stays on the radar. It's doing important things and if not well-known it will be easily overlooked. And there remains so much to be done in chemistry... (BTW, anyone among us going to the upcoming

Re: [Wikidata] Status and ETA External ID conversion

On Mon, Mar 7, 2016 at 9:13 AM, Lydia Pintscher wrote: > Ok. I think we're making this much more complicated than necessary. The > question you should ask yourself is: Does this identify a concept in another > database/website/...? Nice to have: a website to link to.

Re: [Wikidata] Status and ETA External ID conversion

Never mind. I found these in already done. Egon On Sat, Mar 5, 2016 at 3:42 PM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > Mmm... I previously added a few chemical identifiers, like KEGG, > ChEBI, DrugBank, but I cannot find them anymore... :/ > > Egon > > On

Re: [Wikidata] Status and ETA External ID conversion

Mmm... I previously added a few chemical identifiers, like KEGG, ChEBI, DrugBank, but I cannot find them anymore... :/ Egon On Sat, Mar 5, 2016 at 3:16 PM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > Hi Lydia, all, > > On Sat, Mar 5, 2016 at 2:54 PM, Markus Krötzsch >

Re: [Wikidata] Status and ETA External ID conversion

On Sat, Mar 5, 2016 at 3:25 PM, Lydia Pintscher <lydia.pintsc...@wikimedia.de> wrote: > On Sat, Mar 5, 2016 at 3:17 PM Egon Willighagen <egon.willigha...@gmail.com> >> What is the exact process? Do you just plan to wait longer to see if >> anyone supports/contradicts my

Re: [Wikidata] Status and ETA External ID conversion

Hi Lydia, all, On Sat, Mar 5, 2016 at 2:54 PM, Markus Krötzsch wrote: > On 05.03.2016 14:45, Lydia Pintscher wrote: >> Give it another 2 to 3 weeks and it'll get there. More and more editors >> are exposed to the separation in the UI now and start noticing the ones

Re: [Cdk-user] [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

that students can see the ideas too! Egon On Tue, Mar 1, 2016 at 7:06 PM, Greg Landrum <greg.land...@gmail.com> wrote: > I can probably help with that Egon, at least as far as the RDKit bit is > concerned. > > > On Tuesday, 1 March 2016, Egon Willighagen <egon.willig

Re: [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

that students can see the ideas too! Egon On Tue, Mar 1, 2016 at 7:06 PM, Greg Landrum <greg.land...@gmail.com> wrote: > I can probably help with that Egon, at least as far as the RDKit bit is > concerned. > > > On Tuesday, 1 March 2016, Egon Willighagen <egon.willig

Re: [Cdk-user] [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

Geoff, thanks for the suggestions. I need to look at the HTML code that uses $foo.js and create an SVG image... emscripting looks nice, but also harder to easily integrate... I need to see how much you can rip out, to just have the core content... Egon On Tue, Mar 1, 2016 at 4:55 PM, Geoffrey

[BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

Hi all, the NRNB is an USA-based organization around Cytoscape and WikiPathways, the latter involving PathVisio. You may know that Cytoscape has a plugin that used the CDK (by Scooter Morris et al., UCSF) and here in Maastricht we have been working on PathVisio plugins for metabolites also using

[Jabref-devel] GSoC project idea for citation management

Hi all, the NRNB is a mentoring organization in this years Google Summer of Code (like a few times before), and has one project idea I like to put in your attention: https://github.com/nrnb/GoogleSummerOfCode/issues/28 PathVisio is written in Java, and JabRef has been explicitly mentioned as a

Re: [Wikidata] WDQS stability

On Fri, Feb 5, 2016 at 10:57 AM, Markus Kroetzsch wrote: > Thanks for the update. Maybe this is a good opportunity to say that you and > everybody involved in WDQS are doing a tremendous job in maintaining this > service. Even with the small glitches in the last

Re: [Cdk-user] inconsistency in ready molfiles

On Wed, Jan 20, 2016 at 10:44 AM, John M wrote: > Ultimately it's silly that V2000 and V3000 are considered different but > haven't had time to put them in a single 'MolfileReader' yet. The formats *are* different, but that does not mean the readers must be too! The

Re: [Wikidata] Help with SPARQL queries

Daniel, On Sun, Jan 10, 2016 at 3:53 AM, Daniel Mietchen wrote: > What I want now is a list of (ideally) statements (or - less ideally - > items with such statements) that have references of one of the types > given in (1) and (2). It would look something like:

[Wikidata] query.wikidata.org and wikibase:Statement ?

Hi all, after a tweet from Magnus [0] we talked a bit about entries without statements (about 2.5M) and on the question if SPARQL could list all entries in Wikidata that do not have statements. I played a bit with combinations of OPTIONAL and FILTER-BOUND and FILTER NOT EXIST... something like:

Re: [Wikidata] query.wikidata.org and wikibase:Statement ?

Dear Stas, thanks for your reply! On Sat, Jan 9, 2016 at 7:29 AM, Stas Malyshev wrote: >> statements (about 2.5M) and on the question if SPARQL could list all >> entries in Wikidata that do not have statements. I played a bit with > > Technically, it could, but since

Re: [Cdk-user] Dear CDK, QUESTIONS of standard data set to evaluate ligand-based models

Dear Yu, On Wed, Dec 16, 2015 at 1:19 PM, 杜宇 wrote: > I just achieved a ligand-based model with ChEMBL data. Is there any standard > data set to evaluate models against other models? > By comparison, I could depict a ROC curve to validate my model and convince > others.

[Cdk-user] CDK code migration guides

let me know if you have upgrade questions, happy new year, and may the CDK be with you! Egon 0.http://www.lulu.com/shop/egon-willighagen/groovy-cheminformatics-with-the-chemistry-development-kit/paperback/product-22051359.html (CDK 1.5.10, 240 pages) 1.https://figshare.com/articles

Re: [Cdk-user] [Cdk-devel] Preserving public API

On Thu, Dec 31, 2015 at 8:16 PM, Rajarshi Guha wrote: > On Thu, Dec 31, 2015 at 6:21 AM, John M wrote: > As to Egons concern regarding maintenance burden - I think it's a safe to > state that deprecated API's will not be maintained. That

Re: [Cdk-user] [Cdk-devel] Preserving public API

John, all, On Thu, Dec 31, 2015 at 12:21 PM, John M wrote: > Is the approach of adding new API and deprecate the old sound acceptable? Or > are public API changes acceptable? In general I think keeping APIs is a good thing, also for development branches. I think

[Wikidata] property value max lenght? (aka: why doesn't this InChI fit??)

Hi all, I just discovered that there seems to be a limit on the length of property values... some properties for compounds, however, are longer, the InChI being a good example... 400 chars is not enough for some compounds in Wikipedia, like teixobactin (Q18720369) This length is not defined

[Cdk-user] Free (old) copy of Groovy Cheminformatics with the CDK

Hi all, excuse me my x-mas spam, but I just wanted to let everyone know that I have placed an 2011 copy of the "Groovy Cheminformatics with the CDK" book as CC-BY on Figshare (that's edition 1.4.1-0). https://dx.doi.org/10.6084/m9.figshare.2057790.v1 Please grab a copy! Egon -- E.L.

Re: [Cdk-user] Feedback about CDK 1.4 to 1.5 Migration

On Tue, Nov 10, 2015 at 4:23 PM, Till Schäfer wrote: > Long story short: Thank you for the good work! I'm happy to hear John's work is working out well for you! Grtz, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University

Re: [Cdk-user] Fingerprints in 1.4 und 1.5

Oh, sorry the CDK 1.4 identical to 1.5... No, they are typically not, as they depend on an aromaticity model. This is why I introduced the SP2-based fingerprinter, which also takes into account hybridization, but does not depend on definitions of aromaticity... and should be more stable. (But

Re: [Cdk-user] Fingerprints in 1.4 und 1.5

ing for > something else: if the different CDK versions would produce the same > fingerprint for the same molecule. > > Regards, > Till > > Am Mittwoch, 4. November 2015, 14:37:03 schrieb Till Schäfer: >> thx for the fast answer. >> >> Viele Grüße >> Till

Re: [Cdk-user] CDK Depict

On Sat, Oct 24, 2015 at 8:26 PM, John M wrote: > Anyways, just deployed one to OpenShift running the latest CDK SnapShot with > some improvements to layout: http://cdkdepict-openchem.rhcloud.com/depict.html Nice! > Are there any objections to distributing source/war

Re: [Cdk-user] CDK Depict

On Sun, Oct 25, 2015 at 5:02 PM, John May wrote: > GitHub can attach binaries to releases, we do it already: > https://github.com/cdk/cdk/releases/tag/cdk-1.5.11. Given the whole > SourceForge Gimp fiasco I’m wary of using it. Oh, nice! I seem to have

Re: [Wikidata] Units are live! \o/

On Tue, Sep 15, 2015 at 10:12 PM, Michael Peel wrote: > It seems to assume a default uncertainty on values, though: I just added > the elevation above sea level to: > https://www.wikidata.org/wiki/Q1513315 > just specifying the central value, and it assumes that this value is

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

. On Tue, Jul 7, 2015 at 5:03 PM, Egon Willighagen egon.willigha...@gmail.com wrote: Dear Zheng Shi, I think what you are looking for is isomorphism checking. If the chemical graph of two structures is the same, they are called isomorphic. The following Groovy code shows a very basic example

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

Dear Zheng Shi, I think what you are looking for is isomorphism checking. If the chemical graph of two structures is the same, they are called isomorphic. The following Groovy code shows a very basic example: butane = MoleculeFactory.makeAlkane(4); isomorphismTester = new

[Cdk-user] Metabolomics 2015

Hi all, I'm attending the Metabolomics 2015 meeting starting today, and already noted some CDK uses. Anyone else at this conference? Maybe meet up? We could discuss CDK 1.5, or I could help with upgrading to this version? I already had one question about stability of 1.5. At this moment, that

Re: [Cdk-user] Regarding IteratingMDLReader in Cdk1.5

Dear Siva, It was renamed to IteratingSDFReader. See http://chem-bla-ics.blogspot.com/2014/04/changes-in-cdk-16-2-iteratingmdlreader.html Grtz. Egon On Mon, Jun 29, 2015 at 4:59 PM, T. V. Siva Kumar tvsivaku...@gmail.com wrote: I was porting my code from Cdk1.4 to Cdk1.5. The class

Re: [Wikidata] Help needed for Freebase to Wikidata migration

On Wed, Jun 17, 2015 at 4:01 PM, Andy Mabbett a...@pigsonthewing.org.uk wrote: On 16 June 2015 at 19:43, Thomas Pellissier-Tanon thoma...@google.com wrote: I've just added to the page properties for chemistry: https://www.wikidata.org/wiki/Wikidata:WikiProject_Freebase/Mapping#Chemistry It

Re: [Wikidata] Help needed for Freebase to Wikidata migration

Dear Thomas, I am personally interested in the chemistry bits, and checked the list, but did not see the chemistry domain from Freebase: https://www.freebase.com/chemistry/chemical_compound?schema= Is that just a matter of timing, or is it left out because WP/WD already has a good coverage?

Re: [Wikidata-l] next 2 rounds of arbitrary access coming up

Dear Lydia, On Wed, May 13, 2015 at 5:20 PM, Lydia Pintscher lydia.pintsc...@wikimedia.de wrote: The rollout of arbitrary access on Dutch Wikipedia Is there an overview of Dutch WP pages where it is being used? The Berlin/Germany use case experienced resistance, needed further discussion and

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