Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.

Maastricht University

Egon Willighagen

During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on the topic.

Open Science Retreat #2: CiTO Nanopublications

This paper got published in July already, but I had not had the time yet to blog about this exciting work by Irini Furxhi and Ammar Ammar:

 A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability

(doi:10.1016/j.impact.2023.100475) The study has two sides to it: first, it looks into how far we

Using FAIR to select data for reuse

Last week I attended the Open Science Retreat (#osr24nl) in a quite and relaxing region in North-Holland. The meeting was how I like all meetings to be (and I count myself lucky many of my meetings are like this): open, welcoming, constructive, diverse, and intellectually challenging. Not all scientific meetings are like this and it is easy to end up going to obligatory meetings where the discussions are of a different level.

Open Science Retreat #1: impressions

2023 has been a long year in which a lot happens. Two EU projects ended (RiskGONE and NanoSolveIT; more about that in a later post), our group leader Chris Evelo will retire this year, the ELIXIR Toxicology Community started (see this post), the new WikiPathways website launched (see this post), and a lot, lot more.

PhD Defences: Andra Waagmeester and Marvin Martens

A New Descriptor for Structure−Property and Structure−Activity Correlations

A New Class of Molecular Shape Descriptors. 1. Theory and Properties

The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies

4D-Fingerprints, Universal QSAR and QSPR Descriptors

Whole-Molecule Calculation of Log P Based on Molar Volume, Hydrogen Bonds, and Simulated13C NMR Spectra

For the past few weeks I have been working on a review article, which will contain a section with new QSAR/QSPR descriptors published in the period 2000-now.

Novel QSAR and QSPR descriptors?

If you have read my previous post and visited that other blog, you might have noted the Technorati keywords . Or tags, really, as explained in this rel=“tag” microformat. Adding them to blog items, will enable indexing by Technorati, one of the bigger blog search engines. So, from now on, you’ll see these tags in my items too, hoping they don’t get annoying.

Tagging blog items

This is the best news I heard in weeks! The US Patent and Trade Offfice spoke with open source representatives about ways to deal with open source software as prior art. Apparently, their problem was how to be sure about release dates of open source, and authoritative sites like SourceForge.net, FreshMeat.net help a lot here, which extensive logging of releases.

USPTO considers open source software prior art

Tobias commited Jumbo 5.0 to CDK CVS, so that the CDK is now again up to date with the latest CML library. Note that Jumbo 5.0 requires Java 5.0.  At first all JUnit tests seems to work, but apparently the CML2Writer tests were skipped because they were only run when Java 1.4 was found. I updated the test for the a appropriate Java version, and then it turned out that most tests fail.

Jumbo 5.0 and CML support in CDK

I reported earlier  that the CDK has been updated in CVS to use CML from the new Jumbo 5.0. The transition actually involved a lot of changes in the CDK, some I would like to address in the following comments. One thing is that CML write support (not reading!) uses the new Jumbo library which requires Java 1.5. Thus, if Java 1.5 is not available, then CML writing should not be compiled. This is how this is done.

Jumbo 5.0 and the CDK

Some weeks back there was the CDK5AW , the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden. It was then decided to generalize their work resulting in Bioclipse:  https://www.bioclipse.net/  It’s heavily using the Eclipse Rich Client Platform , making additional plugins trivial.

Bioclipse: the chemo-/bioinformatics workbench

I just read that the Kubuntu team wants to include Kat in the dapper release (scheduled for April 2006). Kat is (to be) the KDE equivalent of Google’s desktop search bar.  This is great news for us chem-bla-icians, as Kat has support for full text searching of chemistry files! Let’s see if I can get the Kubuntu team to package up kfile_chemical too, which will extend Kat (and KDE in general), with extraction of meta data from chemical documents.

Ubuntu Dapper will include chemistry features

Just finished applying the latest spelling error fixes to CDK News 2.3 . Took me some three hours to finish it up the 12 pages, which has mostly to the need to recompile the PDF after each change to make sure that nothing in the layout got broken.

CDK News

Stefan has done an excellent debugging week on JChemPaint, while I have been late with a 2.1 release. Anyway, I’ve just uploaded a Java 1.4 compiled JChemPaint 2.1 series release. I was told the (reported) bug count is down to one, so I expect to see the next stable branch to be released soon (2.2 series).  But what after JChemPaint 2.2 gets released? Will a 2.3 developers branch be opened?

About JChemPaint's future and todays 2.1.5 release

We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit

One of the things I had not fully figured out up to today, was how to configure my Kubuntu system to easily view DVDs on our TV, using my NVIDIA’s TV-OUT. I’ve seen xorg.conf files that define a X11 server for the monitor and a second for the TV, and files that use TwinView. Now, I did not really like the way first option worked, so tried the second.

Kubuntu, XRandR and TV-OUT

OK, just back from the first German Chemoinformatics Conference, which I enjoyed very much. A rather interesting program, and lots of interesting posters too. You can read the programme online, and will not spend too many words on that (at least not now). But what I will do is point out some interesting posters here. One poster was on the Molecular Query Language (MQL) by Ewgenij Proschak from Frankfurt.

Back from the 1st GCC

Not so long ago, it was decided that KDE 4.0 will use SCons as a configuration and building tool, instead of the autotools and make: the common ./configure &amp;&amp; make &amp;&amp; make install which has served the open source community very well for so long. SCons is different in several ways.

Scons and bksys for kfile_chemical

I was very pleased to read today that Kalzium, one of the projects that participate in the Blue Obelisk, got awarded! Cheers, Carsten!

Kalzium Wins Award; Carsten Niehaus Interviewed

Today I received news on the Jmol user list that Lubert Stryer’s Biochemistry  replaced the proprietary Chime  with the open source Jmol. The third edition from which I learned biochemistry in my first year at the university did not feature a CD with live figures, but I am very thrilled to see a program on which I have actively programmed hit a text book I used myself in the past.

Open source Jmol hits student text book Biochemistry

I never got around to mentioning this blog, but YAKAFOKON is a nice blog about, as the titel already says, bioinformatics, the semantic web and social networks. Nice to read, and interesting comments on the function and features of the internet and how they relate to bioinformatics, and science in general. Recommended!

A blog about bioinformatics, semantic web, comics and social networks.

Most Dutch chemists have their annual Lunteren meeting, so do I. Lunteren is a small village on the Veluwe where nothing much can be done, except for listening to the presentations. I participate in the Lunteren meeting for analytical chemists, i.e. HPLC, MS, GC and all their combinations upto and including HPLC/MS/MS, and since a few years the Lab-on-a-Chip stuff.

The annual Lunteren meeting

I just want to drop this here. There are various ways to make BridgeDb identifier mapping files.

Making BridgeDb Derby files with Groovy

This week there was an interesting article in the Dutch Intermediar about viagra. They cite an article in Environmental Conversation and state that it saves the environment as it greatly reduced the market for animal parts from the traditional chinese medicine that address the same problem as viagra does.

 Viagra: good for the environment, good for you! ;)

You don’t see this often, though.

Viagra saves the environment

On the Use of 1H and 13C 1D NMR Spectra as QSPR Descriptors

About two years ago a student started with me to work on the use of 1D NMR and IR spectra in quantitative structure-activity relationship (QSAR) work, with the goal to show that these spectra contain 3D information relevent to QSAR models. It is known that these spectra depend on the 3D conformation of the molecule.

1D NMR Spectra do not work in QSPR

CDK News  2.3 is scheduled for this month, and origanally planned to be distributed on the CDK5AW event. So, it’s a bit late. But the editorial process is converging… I realized that I forgot to mention the requirement for InChI’s whenever molecules are given.

CDK News 2.3 and InChI's

This week the next WikiPathways NAR Database issue paper was published (doi:10.1093/nar/gkad960). It is the next paper in a series of papers about the evolution of the Open Science project for making biological pathways available in a Open and FAIR way. This year, it described that significant move away from MediaWiki.

New paper: “WikiPathways 2024: next generation pathway database”

My research is about the interaction of (machine) representation and the impact on the success of data analysis (matchine learning, chemometrics, AI, etc). See the posts about molecular chemometrics. This got me into FAIR: making data interoperable and being able to (really) reuse data is the starting point of doing research.

Reusing data: two new papers

This is my last post on blogger.com. At least, that is the plan. It has been a great 18 years. I like to thank the owners of blogger.com and Google later for providing this service. I am continuing the chem-bla-ics on a new domain: https://chem-bla-ics.linkedchemistry.info/  I, like so many others, struggle with choosing open infrastructure versus the freebie model.

Last post there / the Freebie model online

I drop in on the #classpath channel of freenode.net IRC network, where the #cdk channel runs too. The #classpath channel is for the Classpath project which is developing the free Java libraries used by most open source virtual machines. A Slashdot.org item was mentioned “Java Is So 90s”. It lead to a funny discussion about what that would make C/C++ and Fortran.

Math libraries for Java?

The great thing about open source is that… it’s open. When I was browsing the internet just now, I dropped in on KDE Dot News. In the rightside column, there is a feed of new KDE software from KDE-apps.org. A new version of my favoriate music player, amarok, lured me to the KDE-apps website, where I saw rkward is latest announcement.

A R GUI: rkward

Jerome Pansanel contributed new patches for kfile_chemical; on Monday actually, but I have been busy with other things, among which a presentation I have to give next Monday for some 100+ analytical chemists. The patch adds support to KDE for five new chemical MIMEs: XYZ, Mol2, SMILES, VMD and GenBank. Therefore, I just released a new version (0.10), and added an announcement to Freshmeat.net.

kfile_chemical gets XYZ, Mol2, SMILES, VMD and GenBank support

Less then three months before the end of my contract of my PhD project. And not nearly done yet. Weekends are now spend on wrapping up bits of experimental research into something like a coherent article. And even lot’s of calculations to do to answer the open questions. FreeMind is helping me organize thoughts. Opensource chemoinformatics is a welcomed diversion now and then.

Wrapping up...

The Jmol FAH team  has just entered the Top 800 of most active Folding@Home  teams. And they started monitoring contributions on a user level. Thus, I can now see how active I am within the team. And so can you! Join the team, and let’s get into the Top 500!

Jmol's FAH team in Top 800

This week was the CDK5AW  event, a workshop for users and developers of the Chemistry Development Kit (CDK). After talking with other developers we agreed on creating PDF and HTML versions of single articles that appeared in the CDK News  newsletter. Well, I haven’t figured out how to create nice HTML (the latex2html does not give nice results, anyone ideas?), but for the PDF version I now have a pipeline.

Single PDFs for CDK News articles

While waiting for a Dragon calculation to finish (it does not work for molecules with more than 300 atoms!), I updated CDK’s build.xml to support gjdoc. The build script is now able to compile the custom doclets we use for creating the src/*.javafiles and others from the Java source files. And using gij I could also run CDK’s 1688 JUnit tests!

Open Source Java tool chain: CDK compiles and JUnit tests run

Because I am still looking forward to testing CDK against the latest Classpath 0.20, I downloaded cacao 0.94-1 for Debian sid, then tried to compile CDK with it: JAVA_HOME=/usr/lib/jvm/cacao ant -Dbuild.compiler=gcj clean test-all  But that hangs at some point with zero load. I have no idea what is going on there.

Trouble running the CDK JUnit tests with Cacao and Kaffe

The code clean up after CDK’s interfaces transition is in progress, and two CDK modules are now independent of the

 data

module. After doing the

 core

module , the standard was next, and I finished this yesterday. The dependencies in CVS now look like (click it to get a larger view): IMAGE LOST This UML diagram was made with Umbrello, and the source is in XMI in CVS.

UML diagram of CDK module dependencies

After requests I added yesterday more visible the RSS and Atom feeds for the Planet Blue Obelisk. They are linked in the menu on the right, and as alternative links to the document. These should show up in most recent webbrowsers as feed icon in the lower right corner of the browser window. It is often an orange icon. I also added a ‘Leave a comment’ link to encourage people to leave comments on items.

Planet Blue Obelisk website updates

Getting Started with Eclipse and the SWT is a very nice set of introductory tutorial on working with SWT and Eclipse in general. The tutorials cover the basic, advanced SWT widgets, SWT layout, and several other interesting topics. Now that Bioclipse is gaining speed, it is a must-read.

Getting Started with Eclipse and the SWT

After asking about it, Tom explained me how Taverna can pick up the apiconsumer.xml file from jars: just copy it into the root directory of the jar package. Easy as that.  So, users now only need to copy the cdk-taverna.jar into the taverna-workbench-1.3/lib/ directory and have a nice chemoinformatics workbench environment. I’ll upload the jar to CDK’s project page right now.

CDK-Taverna fully recognized

Because I wanted to test internet telephony I downloaded Skype and tried to get it to work on my Kubuntu system. Unfortunately, the Skype version is only 1.2.0.18, and it does not work well with arts :( That is, using artsdsp it crashes with segfaults whenever I start even a chat, let alone a phone call. This could be worked around by disabling sound in my KDE session, and then the /dev/dsp is open again.

Skype on Kubuntu using a Tiptel USB telephone

KDE 3.5 was released with lots of changes. SuperKaramba is now a standard KDE application and is neatly integrated. It allows embedding themelets on your desktop background. It shows several themelets: the weather, a calender, a toolbar with applications, a FoldingAtHome monitor , the contents of the clipboard, the music that is playing (Cake) and a simple todo list. All customizable up to the pixel.

KDE 3.5 is out

This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I’ve setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.

The goal: a live chemblaics CD

Two weeks ago the write up of a week-long scientific discussions around artificial intelligence for natural product drug discovery in Leiden at the Lorentz Center got published (doi:10.1038/s41573-023-00774-7, free PDF).    Sadly, the meetings was still during the (partial) lockdown, and I think my contribution could have been more extensive.

Artificial intelligence for natural product drug discovery

Just before the end of the year, the

 Wikidata subsetting: approaches, tools, and evaluation

paper by Seyed Amir Hosseini Beghaeiraveri

 et al.

got published (doi:10.3233/SW-233491). I am really excited our group (i.e. Ammar and Denise) has been able to contribute to this. I think it also is a great example of the power of hackathons to bring together people.

New paper: “Wikidata subsetting: approaches, tools, and evaluation”

About four weeks ago the Fall 2023 American Chemical Society meeting (#ACSFall2023). I have attended a few ACS meetings in person and even organized a symposium at the 2010 ACS meeting in Boston. This time too, I did not participate in person, tho visiting San Francisco again would have been nice. I gave two presentations (slides doi:10.5281/zenodo.8255394), but have not uploaded my slides of the first presentation to Zenodo yet.

American Chemical Society Fall 2023 meeting

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide’s ‘a CRC quick reference handbook’ from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements.

Boiling points in Wikidata

Just a quick note: I just love the level of detail Wikidata allows us to use. One of the marvels is the practices of named as, which can be used in statements for subject and objects. The notion and importance here is that things are referred to in different ways, and these properties allows us to link the interpretation with the source.

History, provenance, detail

Earlier I reported about postgenomic.com , and needed some diversion from my manuscript work (could no longer think straight about the article I’m working on). So time for some reading up on new technologies. Timing was perfect, because the source code of postgenomic.com got just uploaded to SourceForge SVN.

Hacking InChI support into postgenomic.com

The Blue Obelisk—Interoperability in Chemical Informatics

OpenSource, OpenData and OpenStandards are not as strong in chemoinformatics as they are in bioinformatcs, where it is common knowledge that sharing is a good. Today, the JCIM published on the web an article about the Blue Obelisk movement, which promotes these three idealogies. Several open source projects participate, amongst which the CDK, Jmol, JOELib, OpenBabel, Chemical Markup Language, Bioclipse and Kalzium.

BlueObelisk: OpenSource, OpenData and OpenStandards

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators

You might have read earlier posts in this blog on CMLRSS, and received a question today on how to integrate CMLRSS with blogs on blogspot.com. Now, current CMLRSS feeds are normally generated with customized scripts, often directly from a database. So, here’s my attempt to include CML in a blogspot.com blog. OpenBabel 2.0 can create good CML, for example for acetic acid:  Nothing much to see, right?

Blogging chemistry on blogspot.com

Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions

MACiE: a database of enzyme reaction mechanisms

Gemma Holiday’s article on CMLReact was published in the january issue of the JCIM (doi:10.1021/ci0502698), which seems to be marked as sample issue right now. She used CMLReact as data format for MACiE  (see doi:10.1093/bioinformatics/bti693), a database of 100 enzyme reactions, with fully annotated reaction mechanisms, making this an remarkable and insightfull database.

Chemical reactions in CML

Recently, a Dutch version of Google News was started, and might mean a replacement for nu.nl. I do not like the verbose layout much, because it makes it more difficult to scan headlines. I do like the themes. Except for one. The English theme ‘Sci/Tech’ is Wetenschap in the Dutch version, or plain Science. And it annoys me to read IT headlines when looking up scientific news.

Dutch Google News themes messed up

Gene-function wiki would let biologists pool worldwide resources

Roland Krause  discussed today in his blog Notes from the Biomass an interesting website: postgenomic.com . This website, still marked BETA, mines blogs in the field of genomics and extract noteworthy statistics from it: which articles are cited in those blogs. For example, the most discussed article is Kai Wang’s Gene-function wiki would let biologists pool worldwide resources  in Nature.

Hot articles; mining the semantic web

This weekend I continued my work on getting the CDK and Jmol run with free, open source JVMs. Really, a lot works fine, as reported earlier in this blog: JChemPaint works and Jmol almost works (see the Classpath’s FreeSwingTestApps wiki page), and well over 95% of the CDK JUnit tests run without trouble too. So it comes down to identifying what does not run properly, and file bugs for this. For example, 26101 and 26108.

An test suite for free, open source JVMs

Free at last! Well, not quite yet, but close enough anyway: my PhD contract has ended; last friday was my last working day, which my collegues and I celebrated with a visit to Nijmegen oldest bar, In de Blauwe Hand . But I still have my manuscript to finish. This formally ends a period of almost 12.5 years at the Radboud University Nijmegen. Starting last monday I’m at home, trying to get things finished as soon as possible.

Free at last!

Derek Lowe is the author of the blog In the Pipeline  which is really fun to read. Derek works in pharmaceutical industry and gives a great insight in how things work in that field of molecular sciences. Yesterday he blogged about What Makes an Ugly Molecule? , and touches the Rule-of-Five, the hydrochloric acid bath (aka stomach), and other reasons that make molecules ugly.

The good, the bad and the ugly molecules

After the three obligatory days of christmas holidays (fun, especially with two children, but very exhausting), it is time to get back to business again. I’m still at my father-in-laws place with only XP installed, so booted the Knoppix 4.0.2 DVD I burned last friday. Eclipse is not working, but being able to use Kmail to read my email again is just what you need as in internet-junkie.

Knoppix saves the day...

Relationships between Molecular Complexity, Biological Activity, and Structural Diversity

In a recent JCIM article, Schuffenhauer compares a few subset selection methods, and notes that some of them reduce the average complexity of the molecules. They put this in relation to other research that states that lead compounds with high complexity have higher activities. Recommended reading material for the holidays.

Subset selection: mind the complexity

One of the Classpath developers pointed me to their CVS statistics when I asked them how actively their project is currently developed, i.e. the number of active developers. The pages are generated with StatCVS, and I ran it one the CDK too. I knew I did a lot of work on the CDK, but never realized that 62.7% of the commits were mine! Keep in mind, though, that a lot of these commits are for code maintainance!

StatCVS on CDK

For some weeks now I have been thinking about bug 1309731: “ModelBuilder3D overwrites Atom IDs”. The ModelBuilder3D is a complex piece of source code, reusing many other parts of the CDK, including atom type perception. Somewhere in October, however, I found that Taverna could not create 3D models and convert these into reasonable CML because the Atom ID’s were messed up. So the question is, where did the ModelBuilder3D do this?

CDK Debug classes and fixing the ModelBuilder3D bug

Today I setup a blog planet for Blue Obelisk members. First I tried Chumpologica but it did not read Atom feeds. Next in line was Planet , which turned out to be used by many big planet sites, like Planet Debian . It also works with Atom feeds in general, but not well with Atom 1.0 feeds, like that of Carsten. After some googling I found a patched version  which did the job.

A Blue Obelisk blog Planet

Where I was able to mention earlier  that JChemPaint now runs with free (as in open source) Java virtual machines, I just tried to run the core Jmol renderer, using the Integration.java  which comes as an example. Sadly, the original screenshots got lost there were made with jamvm 1.3.3 and classpath 0.19.  It is very slow, however. I have not tried it with other free virtual machines, which are supposedly faster.

Open Source Swing: Jmol renderer runs!

Doesn’t happen often, but my machine crashed two hours ago. Not a big deal, because I have my important files in SVN. Oh wait, SVN had a commit in progress during the crash. So, svn recover. Mmmm… doesn’t work either. OK, SVN FAQ: try db_recover. That worked. No, it did not: svn commit still not working for the files I was trying to commit.

Machine crash; SVN went along

On the 7th International Conference on Chemical Structures Jeroen Kazius has a poster on finding discriminative substructures, that is, molecular fragments which can be discriminate between two acitivity classes. The software is released as Gaston, is written in C++ and has the GPL license. Later I encountered MoSS which has the same goal, but uses a different algorithm. MoSS is written in Java and uses the LGPL license.

Open Source data mining in chemoinformatics

Thanx to Mark’s encouragements, I tried to run Jmol and JChemPaint with jamvm. Jmol fails with an NullPointerException , but JChemPaint runs! And note that this was not even running with the latest of the latest; just recent packages from Kubuntu! Yes, there are some glitches, but I’m happy nevertheless!

Open Source Swing: JChemPaint runs!

Method for the computational comparison of crystal structures

This sunday starts the first German Chemoinformatics Conference  in Goslar. It’s an interesting programme , with presentations on the InChI, PubChem, 25 years of chemoinformatics, the chemical semantic web, and much more. Among these presentations is mine, on comparing crystal structures (PDF ) and deducing cell parameters. But I’m having a poster on QSAR too.

Going to the German Chemoinformatics Conference

Yesterday I reviewed an article which published a QSPR model which looked something like:  \y = 151 + 50p1 - 12p2 - 0.006p3\  with quite OK prediction results (R=0.9880). But I was not quite comfortable with the coefficient for the \p3\ variable. The article did not calculate significances for the coefficients, so it was not obvious from the article wether is was useful to include them. I then looked at the range for p3, which was 110-150;

When to stop including QSAR model variables...

Some time ago Rajarshi Guha introduced R bindings for the CDK (see his CDK News articles), and today I tried to install his rcdk package that makes it happen. However, it requires SJava which compiled fine on other machines, but not on my AMD64 machine. The problem seems to be related to the GNU GCC 4.0 compiler I have installed.

R/CDK install fails on GCC 4.0 systems

Yesterday I had some spare time before going to a meeting about the Woordenboek Organische Chemie, so I was boldly going where no one has went before: getting the CDK module core independent of the data module.

More cdk.interfaces updates

Today is my 31st birthday, nearing half-point now (statistically seen). Also, by now I should have had my scientific moment of glory, otherwise I can forget that Nobel prize. Oh well, forget it.  Have you seen those small advertisements on this page (RSS users, please visit the website :)? Funny links they give. The system is very nice btw: it awaits google indexing of the blog and then decides which ads are relevant.

My birthday (31) and the Adsense

A good functional molecular editor is of much important to the chemical web. There are a few small download sized editors around. JChemPaint has been available as applet for some time now, but the download size has been large. The situation has improved considerable over the past months, and the download size upon which the applet now shows up in your webbrowser is down to 538kB. A live demo is available from www.chemistry-development-kit.org.

JChemPaint applet download size: 538kB

I’ve just uploaded kfile_chemical 0.9 . It has new translations for ES and DA, and plugins for InChI files. It will extract the InChI string as meta data (and will thus be used by the KDE desktop search Kat , and the InChI version number. Thinking about this, it might be useful to extract all layers as meta data, so that one can search on chemical formula and even connectivity, and find all matching structures.

InChI meta data with kfile_chemical

This new blog will deal with chemblaics in the broader sense, and will not be restricted to research in this field in which I am involved personally. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to address and possibly solve problems in the area of chemistry, biochemistry and related fields. The general denomiter seems to be molecules, but I might be wrong there.

Chem-bla-ics

I have just enabled CIA  statistics for the Blue Obelisk SVN : /stats/project/cdk/blueobelisk .  It’s done by using the ciabot_svn.py  client script and hooked into the $REPOS/hooks/post-commit hook on the SVN server. The client script is slightly hacked to hard code the module name, which otherwise did not show up on the chat channel.

CIA statistics for Blue Obelisk

chem-bla-ics

During the [Open Science
Retreat](http://chem-bla-ics.linkedchemistry.info/2024/03/31/open-science-retreat-1.html)
I organized a short session where we looking into typing citation
intentions using a new nanopublication template. First, let's describe
nanopublications (originally used in
doi:[10.3233/ISU-2010-0613](https://doi.org/10.3233/ISU-2010-0613)) a
bit. Scholia gives [a nice overview of (macro?)publications on the
topic](https://scholia.toolforge.org/topic/Q57814310). The
[nanopub.net](https://nanopub.net/) website describes that *\[a
nanopublication is a small knowledge graph snippet with metadata that is
treated as an independent (scientific) publication.\]*. The knowledge
graph, it continues, can be anything from an opinion to the link between
a disease and a gene
(doi:[10.1109/ESCIENCE.2018.00024](https://doi.org/10.1109/ESCIENCE.2018.00024)).

Now, in this post I will document an update of how we can use
nanopublications for citation intention annotation, and compare this to
existing solutions. I have been collecting and indexing the CiTO
intention annotations in Wikidata and visualizing the corpus with
Scholia at
[scholia.toolforge.org/cito/](https://scholia.toolforge.org/cito/).
There are currently 22 journal articles with explicit CiTO annoation,
largely thanks to a [Journal of Cheminformatics
pilot](https://www.biomedcentral.com/collections/cito) (e.g. see
doi:[10.1186/s13321-023-00683-2](https://doi.org/10.1186/s13321-023-00683-2)).
Recently, the preprint/report server
[BioHackrXiv](https://biohackrxiv.org/discover) started [CiTO
support](https://github.com/biohackrxiv/publication-template) too, also
visible in the statistics on Scholia with another 17 papers. A third
source is data sets from bibliometric-like studies, as explained in
[this
post](https://chem-bla-ics.blogspot.com/2023/04/cito-updates-4-annotations-in-datasets.html).
Nanopublications would be a fourth solution.

So, why another solutions? Like the datasets, assuming DataCite
approaches, have clear provenance, but the overhead of and needed time
for creating a dataset with citation intent annotations can be limiting.
And because nanopublications can be linked to ORCID identifiers, we can
even discover which citation intent annotations are created by the
original authors of articles. Another advantage is that nanopubs are
basically RDF and we can query them easily, allowing the citation
intentions to migrate to Wikidata. Scholia already saw an update to
recognize nanopublications as a unique kind reference (see the new
Wikidata property [Nanopublication identifier
(P12545)](https://www.wikidata.org/wiki/Property:P12545)).

# NanoDash template

So, if we can make it easy for people to define nanopublications with
CiTO citation intent annotations, than we can start formalizing intent
annotations from a much wider range of use cases. For example, we can
annotate historically important discussions. Anyone can retrospectively
annotate all their own articles, making them more FAIR. And if we use
DOI links, then it no longer is limited to journal articles, but we can
use of for software and data citations too. This is where [a recent
template](https://w3id.org/np/RAX_4tWTyjFpO6nz63s14ucuejd64t2mK3IBlkwZ7jjLo)
comes in created by [Tobias
Kuhn](https://orcid.org/0000-0002-1267-0234), one of the main nanopub
developers:

![](/assets/images/citoPub.png)

This nanopublication template defines the minimal needs of the
assumptions, along with useful provenance and nanopub info. Basically,
the assertion defines that one DOI is a ScholarlyWork and using the
CiTO, defines that it cites one or more article works (with DOI). For
each citations, one can select any of the known CiTO intent types, e.g.
'extends' or 'uses method' in, as in [this
nanopublication](https://w3id.org/np/RA6Rxk1sSOSWxM7A6gW4SjJZRVt4fbY6nShPTAbQ8kce8)
created with this template:

![](/assets/images/citoPub2.png)

## SPARQL-ing CiTO annotations

Besides the template, Tobias also started a SPARQL query to which I
added restrictions that the citing and cited resources needs to have a
DOI, giving us [this
query](https://query.np.trustyuri.net/tools/type/2c1cce3f3152738c1009d59251409392aaaa3b0324bcb5fdfb4b7b944b8f0c18/yasgui.html#query=prefix+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0Aprefix+np%3A+%3Chttp%3A%2F%2Fwww.nanopub.org%2Fnschema%23%3E%0Aprefix+npa%3A+%3Chttp%3A%2F%2Fpurl.org%2Fnanopub%2Fadmin%2F%3E%0Aprefix+npx%3A+%3Chttp%3A%2F%2Fpurl.org%2Fnanopub%2Fx%2F%3E%0Aprefix+xsd%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0Aprefix+dct%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A%0Aselect+%3Fnp+%3Flabel+%3Fsubj+%3Fcitationrel+%3Fobj+%3Fdate+where+%7B%0A++graph+npa%3Agraph+%7B%0A++++%3Fnp+npa%3AhasValidSignatureForPublicKey+%3Fpubkey+.%0A++++%3Fnp+dct%3Acreated+%3Fdate+.%0A++++%3Fnp+np%3AhasAssertion+%3Fassertion+.%0A++++optional+%7B+%3Fnp+rdfs%3Alabel+%3Flabel+.+%7D%0A++++filter+not+exists+%7B+%3Fnpx+npx%3Ainvalidates+%3Fnp+%3B+npa%3AhasValidSignatureForPublicKey+%3Fpubkey+.+%7D%0A++++filter+not+exists+%7B+%3Fnp+npx%3AhasNanopubType+npx%3AExampleNanopub+.+%7D%0A++%7D%0A++graph+%3Fassertion+%7B%0A++++%3Fsubj+%3Fcitationrel+%3Fobj+.%0A++++filter(regex(str(%3Fcitationrel)%2C+%22%5Ehttp%3A%2F%2Fpurl.org%2Fspar%2Fcito%2F.*%24%22))%0A++++filter(regex(str(%3Fsubj)%2C+%22doi.org%2F10%22))%0A++++filter(regex(str(%3Fobj)%2C+%22doi.org%2F10%22))%0A++%7D%0A%7D%0A++&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql-results%2Bjson&endpoint=%2Frepo%2Ftype%2F2c1cce3f3152738c1009d59251409392aaaa3b0324bcb5fdfb4b7b944b8f0c18&requestMethod=POST&tabTitle=Query&headers=%7B%7D&outputFormat=table):

:::: {.language-sparql .highlighter-rouge}
::: {.highlight}
``` highlight
prefix rdfs: 
prefix np: 
prefix npa: 
prefix npx: 
prefix xsd: 
prefix dct: 

select ?np ?label ?subj ?citationrel ?obj ?date where {
  graph npa:graph {
    ?np npa:hasValidSignatureForPublicKey ?pubkey .
    ?np dct:created ?date .
    ?np np:hasAssertion ?assertion .
    optional { ?np rdfs:label ?label . }
    filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . }
    filter not exists { ?np npx:hasNanopubType npx:ExampleNanopub . }
  }
  graph ?assertion {
    ?subj ?citationrel ?obj .
    filter(regex(str(?citationrel), "^http://purl.org/spar/cito/.*$"))
    filter(regex(str(?subj), "doi.org/10"))
    filter(regex(str(?obj), "doi.org/10"))
  }
}
```
:::
::::

This includes 6 citation intentions defined by 4 nanopublications added
during the Open Science Retreat:

- [RAUjZE1JMu](https://w3id.org/np/RAUjZE1JMu1GAvUQ_fZ4yc9-7sOSCT9xbeS0wYznkKtYk)
  by
  [me](https://nanodash.knowledgepixels.com/explore?id=https%3A%2F%2Forcid.org%2F0000-0002-7192-1486)
  for a paper by Marija Purgar
- [RAXgI--5gc](https://nanodash.knowledgepixels.com/explore?id=RAXgI--5gcKskgrnOI1XZoA4b3hu9RbNj3bcc2Zxeos7c)
  by [Christian
  Meesters](https://nanodash.knowledgepixels.com/explore?id=https%3A%2F%2Forcid.org%2F0000-0003-2408-7588)
- [RATZNhd3l_j](https://nanodash.knowledgepixels.com/explore?id=RATZNhd3l_jN0y8GEi8mLIqy-uVV8tiUZIq2RJtkq6G8A)
  by [Taichi
  Oichi](https://nanodash.knowledgepixels.com/explore?id=https%3A%2F%2Forcid.org%2F0000-0003-4285-690X)
- [RA6Q6wxSYy](https://nanodash.knowledgepixels.com/explore?id=RA6Q6wxSYyWfA3XwpOBqSNFKgQpM7ZgdVBoU2kSD-CFjw)
  by [Niklas
  Hohmann](https://nanodash.knowledgepixels.com/explore?id=https%3A%2F%2Forcid.org%2F0000-0003-1559-1838)

# From nanopublications to Wikidata

Now, this query also provides me with enough information to propagate
the citation intent (a fact?) to Wikidata and cite the original
nanopublication as reference. With a variation of the above SPARQL
query, I can get the five most recent new nanopublications, convert them
to QuickStatements, and then enjoy them in Wikidata. This is written up
in [this Bacting
script](https://github.com/egonw/ons-wikidata/blob/main/Nanopubs/createQS.groovy).

The script needs to handle some situations. For example, it will not add
items for DOIs not already in Wikidata. So, if neither of the two DOIs
are known in Wikidata, then nothing gets added. If they both are, then
it will add the citation intent. There are alternative solutions, but in
practice that doesn't matter and the QuickStatements is in all
situations the same, and QuickStatements will only add the new
information.

This is what it will [look like in
Wikidata](https://www.wikidata.org/wiki/Q113312162#P2860):

![](/assets/images/citoPub3.png)

And this is [what it
looks](https://scholia.toolforge.org/cito/#articles) (yellow) when we
compare the contributions from nanopublications now with the other
sources:

![](/assets/images/citoPubs4.png)


Last week I attended the [Open Science
Retreat](https://openscienceretreat.eu/)
([\#osr24nl](https://hashtags-hub.toolforge.org/osr24nl)) in a quite and
relaxing region in North-Holland. The meeting was how I like all
meetings to be (and I count myself lucky many of my meetings are like
this): open, welcoming, constructive, diverse, and intellectually
challenging. Not all scientific meetings are like this and it is easy to
end up going to obligatory meetings where the discussions are of a
different level. Therefore, great thanks to the organizers, but also to
all participants, that showed not just to have a hearth for open science
(getting pretty common), but also a drive to advocate for open science.
Finally, I like to thank the people that joined me in creating
nanopublications for CiTO annotations (will blog about that later), and
[to Sadik and
Marija](https://twitter.com/marija_purgar/status/1773745895508451573)
with whom we worked on exploring using Wikibase for capturing knowledge
about research waste in ecology (more about that later too).


OpenSource, OpenData and OpenStandards are not as strong in
chemoinformatics as they are in bioinformatcs, where it is common
knowledge that sharing is a good. Today, the
[JCIM](http://pubs3.acs.org/acs/journals/toc.page?incoden=jcisd8)
published on the web an [article](http://dx.doi.org/10.1021/ci050400b)
about the [Blue Obelisk](http://www.blueobelisk.org/) movement, which
promotes these three idealogies.

Several open source projects participate, amongst which the
[CDK](http://cdk.sf.net/), [Jmol](http://www.jmol.org/),
[JOELib](http://joelib.sf.net/), [OpenBabel](http://openbabel.sf.net/),
[Chemical Markup Language](http://cml.sf.net/),
[Bioclipse](http://bioclipse.net/) and [Kalzium](http://cdk.sf.net/).

#### References

- [10.1021/CI050400B](https://doi.org/10.1021/CI050400B)


This is the best news I heard in weeks! The [US Patent and Trade
Offfice](http://www.uspto.gov/) spoke with open source representatives
about ways to deal with open source software as prior art. Apparently,
their problem was how to be sure about release dates of open source, and
authoritative sites like [SourceForge.net](http://www.sf.net/),
[FreshMeat.net](http://freshmeat.net/) help a lot here, which extensive
logging of releases.

Quoting from there website:

:::: {.language-plaintext .highlighter-rouge}
::: {.highlight}
``` highlight
The Department of Commerce’s United States Patent and Trademark Office (USPTO)
has created a partnership with the open source community to ensure that patent
examiners have access to all available prior art relating to software code
during the patent examination process.
```
:::
::::

It also indicates that releasing open source software with, or
announcing it on, such an authoritative website is important! Otherwise,
patent offices will not be able to decide wether our open source art is
really prior.

#### References
