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

Ola has released the second beta for Bioclipse 2.0. Things are getting along, and I will not go into details on the molecules table Arvid is working on, the 1GB+ SD file support, the validating CML editor , the support for XMPP services , or the brand new welcome page which will guide new users around in what Bioclipse has to offer.

Ola has released the second beta for Bioclipse 2.0. Things are getting along, and I will not go into details on the molecules table Arvid is working on, the 1GB+ SD file support, the validating CML editor


, the support for XMPP services


, or the brand new welcome page which will guide new users around in what Bioclipse has to offer. This blog will focus on what Bioclipse has to offer CDK developers.

Bioclipse for CDK Developers #1

This autumn I will end my current post-doc position at Plant Research International in the Applied Bioinformatics group and at Biometris (both part of Wageningen University) funded by the Netherlands Metabolomics Center (lot’s of vacancies), where I had a good time, and collaborated in several projects within the NMC with much pleasure.

Moving to Sweden: Improving CDK support in Bioclipse

Two working days left before I’m off to two conferences. First, next Thursday/Friday, the two day CompLife2007 in Utrecht/NL, with sessions on genomics, systems biology, medical information and data analysis. And, on the second day tutorials on KNIME and CDK/Bioclipse. I will try to orient as much as possible around MS-based metabolomics, and metabolite identity in particular. Last year the conference was very interesting.

Two working days left before I’m off to two conferences. First, next Thursday/Friday, the two day CompLife2007 in Utrecht/NL, with sessions on genomics, systems biology, medical information and data analysis. And, on the second day tutorials on KNIME and CDK/Bioclipse. I will try to orient as much as possible around MS-based metabolomics, and metabolite identity in particular. Last year


the conference was very interesting.

CompLife2007, Utrecht/NL; Taverna, EBI/Hinxton/UK

Now, the DOI ubiquity scripts I just blogged about, was just the beginning of things. Me exploring the environment and learning the JavaScript language.

Now, the DOI ubiquity scripts


I just blogged about, was just the beginning of things. Me exploring the environment and learning the JavaScript language. I start to become really interesting when we use these technologies to improve things. I am still not sure people will like the command line nature, but at least I will be a happy user.

Ubiquity fun: entering semantic markup as easy as running a Ubiquity command

One of the goals of my project in Cambridge is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.

One of the goals of my project in Cambridge


is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.

Oscar text mining in Taverna

Later this year the ninth International Conference on Chemical Structures (ICSS) conference will be held in the Netherlands. I had the pleasure of joining this meeting, I think, eight years ago, when I was doing my PhD in Nijmegen. Mind you, I did not

 attend

the conference;

The 9th International Conference on Chemical Structures (ICCS)

Publishing habits changes very slowly, too slowly. The whole industry is incredibly inert, which can lead to severe frustration as it did for me . But sometimes small changes can do so much.

Maastricht University

Publishing habits changes very slowly, too slowly. The whole industry is incredibly inert, which can lead to severe frustration as it did for me


. But sometimes small changes can do so much.

Scholarly journals should use "Archived on" instead of "Accessed on"

Peer review is an important component of open source development, and recently there was the discussion the other way around, if open source is required for peer review.

Peer reviewed Cheminformatics #2: Code review for the Chemistry Development Kit

Yesterday’s blog about Who says Java is not fast?!? caused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper (see also the comments in the blogs by Noel (the author) and Rich). Many things determine why the CDK might be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading;

Yesterday’s blog about Who says Java is not fast?!?


caused quite some feedback (thanx to all commenters!) with several good points. Of course, a table like that in the cinfony paper (see also the comments in the blogs by Noel (the author) and Rich). Many things determine why the CDK might be fastest in that table for SDF iterating. Suggestions have been that OpenBabel and RDKit may be doing much more than simple reading;

Cheminformatics Benchmark Project #1

One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility.

Editing and Validation of CML documents in Bioclipse

Recently, I have been blogging about Git:

Recently, I have been blogging about Git: GitToDo support for Freemind


Git mirror for the CDK


CDK development with branches using Git


Offline CDK development using git-svn


One concern expressed by people was the lack of integration with IDEs. Now, an Eclipse plugin seems well on its way: With a experimental update site (http://www.jgit.org/update-site), the plugin is just an Eclipse reboot away.

Git-Eclipse integration

… a source code reviewer nightmare. The must-read lwn.net ran a nice open letter to a Linux kernel developer.

… a source code reviewer nightmare. The must-read lwn.net ran a nice open letter to a Linux kernel developer. I’d like to cite this bit about code review (see also Re: Open Source != peer review


): This is important indeed! This is also why CDK quality assurance tends to complain about short variables.

Short variables and lack of comments...

The Blue Obelisk mantra ODOSOS, Open Data, Open Source, Open Standards, is well known, and much cited too. Jean-Claude Bradley popularized the Open Notebook Science (ONS). This has always been nagging me a bit, because the CDK, Jmol, JChemPaint and other chemistry projects have done that for much longer, though we did not use notebooks as much, so called it just an open source project.

Open{Data|Source|Standards} is not enough: we need Open Projects

While slowly merging with Sweden , and ADSL which should reach my house in some two weeks, I am enjoying my new office space and Git to upload patches to the CDK. Christoph wondered if we should switch CDK from SVN to Git. A few developers objected, for various reasons: no native Windows clients (though msysgit might be the solution), no (stable) plugins for Eclipse, IDEA(?), etc.

While slowly merging with Sweden


, and ADSL which should reach my house in some two weeks, I am enjoying my new office space and Git to upload patches to the CDK. Christoph wondered if we should switch CDK from SVN to Git. A few developers objected, for various reasons: no native Windows clients (though msysgit might be the solution), no (stable) plugins for Eclipse, IDEA(?), etc.

Git mirror for the CDK

Just updated Bioclipse2 with Jmol 11.6 RC 18:

Just updated Bioclipse2 with Jmol 11.6 RC 18: Now working in Uppsala


makes Bioclipse my default life sciences platform, and I’ll be porting older Bioclipse1 plugins to Bioclipse2, which has a much better architecture.

Jmol 11.6 RC 18 in Bioclipse

Mark pointed me to the embed functionality of Gist, product on GitHub where I host some todo software and a git mirror of CDK 1.2.x .

Mark pointed me to the embed functionality of Gist, product on GitHub


where I host some todo software


and a git mirror of CDK 1.2.x


. So, the other day, when I blogged about Bioclipse2 scripts


, I should have embedded the script like this:

Embedding Gists in blogs

Christoph pointed me to a video on Git by Linus. CDK is now using branches extensively in development, and just set up a branch for the upcoming 1.2.0 release later this year (end of October, see cdk-1.2.x). Christoph has just reviewed the branch containing the API move to Iterable.

CDK development with branches using Git

The nice thing about a hacksession, is that you have something to write about. Below a screenshot of a Ugi reaction in Bioclipse… note the source tab of the editor, which holds the CML.

The nice thing about a hacksession, is that you have something to write about. Below a screenshot of a Ugi reaction in Bioclipse… note the

 source

tab of the editor, which holds the CML.

UgiChem2CML

Rajarshi has patched trunk last night with his work to address a few practical issues in the molecular descriptor module of the CDK (and I peer reviewed this work yesterday ). One major change is that the IMolecularDescriptor calculate() method no longer throws an Exception, but returns Double.NaN instead. The Exception is stored in the DescriptorValue for convenience.

Rajarshi has patched trunk last night with his work to address a few practical issues in the molecular descriptor module of the CDK (and I peer reviewed this work yesterday


). One major change is that the IMolecularDescriptor calculate() method no longer throws an Exception, but returns Double.NaN instead. The Exception is stored in the DescriptorValue for convenience.

Molecular QSAR descriptors in the CDK

As promised yesterday , here’s the pretty visualization of the mass spectrum, using JavaScript from the PRIDE project:

As promised yesterday


, here’s the pretty visualization of the mass spectrum, using JavaScript from the PRIDE project: Note the manual adding of peaks at 10 and 100 m/z to get the real peaks somewhere in the middle instead of on the left and right border of the graph.

MetWare screenshot: spectrum support #2

Not visually attractive, but that will be solved when Steffen gets his hands on it. For now, I’m happy with a table formatting.

MetWare screenshot: spectrum support

Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm parameter setting is somewhat inappropriate. As seen yesterday , it works fine for larger peaks, but fails for low intensity peaks.

Steffen reminded me over email that the particular machine only has a 1 dalton accuracy, and that the 150ppm parameter setting is somewhat inappropriate. As seen yesterday


, it works fine for larger peaks, but fails for low intensity peaks.

Recovering full mass spectra from GC-MS data #2

CDK QSAR descriptors are not allowed to change the input [molecule|atom|bond], and I recently added a unit tests (rev 11138) for that to the abstract class AtomicDescriptorTest.

Finding differences between IChemObjects #2

Days after the release of OSRA last week, I saw the optical chemistry structure recognition on the front page of my favorite Dutch /. equivalent, Tweakers.net, Duitsers leren computer chemische structuren herkennen, written by René Gerritsen.

Days after the release of OSRA


last week, I saw the

 optical chemistry structure recognition

on the front page of my favorite Dutch /. equivalent, Tweakers.net,

 Duitsers leren computer chemische structuren herkennen

, written by René Gerritsen. The article discusses the Fraunhofer Institute’s ChemoCR, which was, IIRC, presented as poster at last year’s German Conference on Chemoinformatics (to be held again this year).

Optical Chemical Structure Recognition

Neil wondered “what a Nature Chemistry paper should look like”, and asked the following questions. Below are my answers.

Neil wondered

 “what a Nature Chemistry paper should look like”

, and asked the following questions. Below are my answers.

 1. HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?

I typically read the HTML to scan if a paper is interesting for me. But because electronic paper is still too expensive, I typically make a print of the PDF.

Re: What should a Nature Chemistry paper look like?

Today starts the MetWare developers meeting, hosted by Steffen Neumann, at the Leibniz-Institut für Pflanzenbiochemie. Steffen’s group and the Applied Bioinformatics group where I now work, are co-developing an opensource platform for metabolomics data management.

The MetWare developers meeting in Halle

I reported earlier on how to compare unit test results between CDK trunk and a branch . Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added.

I reported earlier on how to compare unit test results between CDK trunk and a branch


. Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added.

Comparing JUnit test results between CDK trunk/ and a branch #2

I normally do not do these kinds of blog items, but, in reply to Christoph’s blog, here’s an overview of the ceremony (see also T-26 and T+18 ):

I normally do not do these kinds of blog items, but, in reply to Christoph’s blog, here’s an overview of the ceremony (see also T-26


and T+18


): This is the doctorate certificate Christoph mentioned, with also Karin and our kids: And, here (map) was the dinner in the evening:

T plus 51 hours: a short photo impression

Twenty five years ago the Chemistry Development Kit (CDK) was founded. The Chemistry and Internet (ChemInt2000) had just ended (it ran from 23 to 26 September) and my friend and I had taken the Amtrak night train from Washington to South Bend. At that time there were two leading Java applets for chemistry, JChemPaint and Jmol.

25 years of the Chemistry Development Kit

This is a bit of an administrative post and historic, but keep coming back to the question, where are all the deliverable of the (past) project. Now, since many eNanoMapper project deliverables were public, we were able to release most of them on Zenodo. This post makes an overview.

This is a bit of an administrative post and historic, but keep coming back to the question, where are all the deliverable of the (past) project. Now, since many eNanoMapper project deliverables were public, we were able to release most of them on Zenodo. This post makes an overview. To former partners and collaborators, thanks for this awesome journey!

The eNanoMapper project deliverables

A lot is happening. If you have been following this project more closesly, you may have already seen some interesting updates, but I will post it here too. First, a quick recap. In March I started a new Blue Obelisk project to collect CCZero IUPAC names from primary literature (paper still pending). It turned out we can automate that, while legally not violating any laws or licenses.

One Million IUPAC names #4: a lot is happening

I could not find the time earlier to report (reason), but three weeks ago we passed the fourth milestone release of the CCZero IUPAC names found in literature collection. This release contains 200026 IUPAC names, 168702 unique names, reflecting 116207 unique InChIKeys. Time for an update of the One Million IUPAC names project.

One Million IUPAC names #3: the 200 thousand milestone and 1 million IUPAC names

A recent report by the Dutch RIVM, PFAS in the blood of the Dutch population (doi:10.21945/RIVM-2025-0094), writes that seven PFAS compounds are found in blood samples of all tested people. Another nine compounds are found in at least 1-in-10 people. Because there is relevant data in the report on the 28 studied PFAS compound, I wanted to have the report more FAIR than it is on the website. Why this report?

A recent report by the Dutch RIVM,

 PFAS in the blood of the Dutch population

(doi:10.21945/RIVM-2025-0094), writes that seven PFAS compounds are found in blood samples of all tested people. Another nine compounds are found in at least 1-in-10 people. Because there is relevant data in the report on the 28 studied PFAS compound, I wanted to have the report more FAIR than it is on the website. Why this report?

PFAS in the blood of the Dutch population

Depending on your exact definition of doing science, keeping track as precise as possible of your observations is an essential part of doing science. The precision should be high enough that mistakes are obvious. This pattern is, of course, not limited to doing science and we see this in open source development too. Unfortunately, in the modern way of doing science, this is not getting the attention it should get.

Curation is an essential part of doing research

Last week, the Wikidata and Sister Projects event tooks place. The presentations are recorded, and I strongly encourage you to check the schedule. One presentation I liked (there are more), was the one by Mike Peel with the title “Best practices for reusing Wikidata’s data in the Wikimedia Projects”. At some point he walks us through the {{Cite Q}} template, around 26:07.

Last week, the Wikidata and Sister Projects event tooks place. The presentations are recorded, and I strongly encourage you to check the schedule.

Retracted articles cited in Wikipedia

One reason to move my blog from Blogger to a git-backed repository is that I can update links but that the version history shows exactly what change was made.

Updating links to blogs: Peter Murray-Rust

Names of chemicals are part of the human user experience when browsing a chemical database. And literature too, of course. Chemical names are also not easy to use, and what a chemical name means is not always clear. This is why the IUPAC started a standardizing nomenclature in chemistry, the IUPAC names. Each IUPAC name uniquely defines the chemical structure it defines. For example, methane is the IUPAC name for the chemical CH4.

Names of chemicals are part of the human user experience when browsing a chemical database. And literature too, of course. Chemical names are also not easy to use, and what a chemical name means is not always clear. This is why the IUPAC started a standardizing nomenclature in chemistry, the

 IUPAC names

. Each IUPAC name uniquely defines the chemical structure it defines.

One Million IUPAC names

This week the 13th International Conference on Chemical Structures took place (see also this Scholia overview or this overview of the full ICCS history). This is the conference I first joined 20 years ago as a PhD student presenting a poster (see these past blog posts). Of course, I am actually co-organizer nowadays (actually, co-treasurer). Organizing a meeting with just over 200 participants, and I like to thank Gerard and Willem in

ICCS2025: back in Noordwijkerhout

Two and a half month into the One Million IUPAC Names project, we passed the third milestone, the one for 100 thousand IUPAC names (doi:10.5281/zenodo.15266459). Time for an update.

Two and a half month into the One Million IUPAC Names project, we passed the third milestone, the one for 100 thousand IUPAC names (doi:10.5281/zenodo.15266459). Time for an update. This milestone release took a bit longer. Going from 50 to 100 thousand is a bigger step than from 10 to 50 thousand, but the open access chemistry literature was already done by then. Basically, I ran out of open access chemistry publications.

One Million IUPAC names #2: the 100 thousand milestone

Two week ago I uploaded a paper that has been in the works for some time. In fact, I first mention it as conference paper for the special issue of the 11th International Conference on Chemical Structures, you know, the meeting held in 2018, of which the 13th edition starts in 7 days. I had a poster at that conference which I described in this blog post.

New preprint: "Scholia Chemistry: access to chemistry in Wikidata"

INTOXICOM is an ELIXIR Toxicoloy Community (doi:10.12688/f1000research.74502.2) implementation study, organizing five workshops, each one with a different topic. The first three workshops were in Utrecht (doi:10.37044/osf.io/un2rw), Basel, and Uppsala.

INTOXICOM Workshop #4: Training Materials for Toxicology

Where the first workshop day had several talks about new and old features of the Chemistry Development Kit (CDK), the second day was a hackathon day. We hacked and we talked.

cdk2024 #5: Chemistry Development Kit User Group Meeting - Day 2

I wish I could say I remember the first citation to one of my research articles. I do not. But I do remember the excitement to see why someone was citing my research. What I do remember is that I got a comment around the same time along the lines of this: “why would anyone cite your article if they can download the results for free?” (about open science cheminformatics research). Other times.

I wish I could say I remember the first citation to one of my research articles. I do not. But I do remember the excitement to see why someone was citing my research. What I do remember is that I got a comment around the same time along the lines of this:

 “why would anyone cite your article if they can download the results for free?”

(about open science cheminformatics research). Other times.

Niche papers and citation intentions

This is the third weekend I am working on Scholia, the first two part of the April 2025 hackathon. It follows the hackathons last year October and November hackathons. There is some urgency for this unpaid work, because Wikidata is splitting the RDF into two SPARQL endpoints (see this The Signpost and this post by Finn). This split has happened, but there is a legacy server for tools that have not been upgraded.

This is the third weekend I am working on Scholia, the first two part of the April 2025 hackathon. It follows the hackathons last year October and November hackathons. There is some urgency for this unpaid work, because Wikidata is splitting the RDF into two SPARQL endpoints (see this The Signpost and this post by Finn). This split has happened, but there is a

 legacy

server for tools that have not been upgraded.

The April 2025 Scholia hackathon

Tomorrow is already the last day of the NWO Open Science grant for the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more to finish up the reporting.

Tomorrow is already the last day of the NWO Open Science grant for the Chemistry Development Kit. We are wrapping up, but I am happy we have a few weeks more to finish up the reporting. We held a user group meeting earlier this month (btw, check out the slides by Jonas), and I did a few more JUnit testing updates last week:    Actually, you see one pull request here that I closed. I accidentally included a circular dependency.

cdk2024 #6: wrapping up already

Two weeks ago, the Beilstein Institute announced Bioschemas support in their journals:

Two weeks ago, the Beilstein Institute announced Bioschemas support in their journals:  The idea is far from new and has been around for two decades. But the two Beilstein journals (both diamond Open Access), actually integrated into their active publishing model. That has been trialed and put in action before.

Beilstein journals contain Bioschemas

With a year of preparation and two years of thinking, on September 1st 2024 the Department of Bioinformatics, aka BiGCaT, merged with two other departments to form the Department of Translational Genomics (see also this LinkedIn announcement). This merger creates many new opportunities while it strenghtens our bioinformatics research.

s/BiGCaT/Translational Genomics/g

This is mostly a test, but if it turns out the way I hope it will, likely after a few iterations, it adds support in my blog for CiTO intent annotations to the DOIs I cite. I pondered about the earlier.

CiTO for blog citations

If you are into openscience chemistry or chemistry blogging, then you probably heard of Rich Apodaca’s Depth-First blog. Rich started blogging in 2006 but this is not how I discovered his work originally. I know that we at least already had contact in 2005, because that is when he wrote about an integration between his Octet library and the Chemistry Development Kit in the CDK News (volume 2, issue 2), CDKTools: The CDK-Octet Bridge.

If you are into openscience chemistry or chemistry blogging, then you probably heard of Rich Apodaca’s Depth-First blog. Rich started blogging in 2006


but this is not how I discovered his work originally.

Richard L. Apodaca

The last week before the winter break Serious Request took place. We started an action around WikiPathways and we collected 877 euro for the MetaKids Foundation. In total there were 2612 actions, many of which brought in a lot more. We ended up in position 928.

Serious Request: the results

In 2022 I had my first experience with the ISAAC database by the Dutch NWO research funding organization. ISAAC is where you apply for funding and where grants get tracked. As such, research output is recorded in this database.

ISAAC Chrome Extension

Blogs come and go. Sometimes they move from one location to another. However, blogs have not been systematically archived, perhaps for work by efforts by OpenLaboraty.

Archiving blogs

Before we go into the learning bit, let’s just revisit what a version of record is. Wikipedia describes it as “the fully copyedited, typeset and formatted copy of a manuscript as published” (with two references). Basically, in the whole scheme of research output, it is a release.

Before we go into the learning bit, let’s just revisit what a

 version of record

is. Wikipedia describes it as “the fully copyedited, typeset and formatted copy of a manuscript as published” (with two references). Basically, in the whole scheme of research output, it is a

 release

. It is a tagged version of the output, allowing people to discuss that version specifically, so that we do not run into endless “oh, but I meant

Version of record, and what Open Access must learn from Open Science

Jerven Bolleman et al. recently published a great preprint about how to use RDF to give SPARQL queries context by linking it (semantically) with metadata. The context includes keywords, the SPARQL endpoint the query can be run against, and a human-oriented description of the query.

Jerven Bolleman

 et al.

recently published a great preprint about how to use RDF to give SPARQL queries context by linking it (semantically) with metadata. The context includes keywords, the SPARQL endpoint the query can be run against, and a human-oriented description of the query.

SPARQL examples: SIB model, software, and patches

The x-odus continues and there is a wave of researchers moving from X to another walled-garden called Bluesky. This is good and bad. First, it is good that people are leaving X (imho) and it is good that they move to a platform that supports open standards, the AT Protocol. But I am less sure, about moving to another closed source platform. I prefer Mastodon.

Mastodon, RSS, BlueSky

Diabetes was already discussed in literature back in 1838-1839 (doi:10.1016/S0140-6736(02)96038-1, doi:10.1016/S0140-6736(02)96066-6, and doi:10.1016/S0140-6736(02)83966-6). These three papers show a short discussion. Papers were a lot shorter back in the days, and the discussion actually shows why papers are longer now (tho I am not sure they really got sufficiently more reproducible, but that’s another discussion).

Diabetes was already discussed in literature back in 1838-1839 (doi:10.1016/S0140-6736(02)96038-1, doi:10.1016/S0140-6736(02)96066-6, and doi:10.1016/S0140-6736(02)83966-6). These three papers show a short discussion.

Scholarly discussions through the eyes of CiTO (and Wikidata)

Open Science doesn’t make publishing easier. That that’s all for the better: our research efforts are complex, so why should the publishing be. Sure, I am not talking about references formatting or moving the Methods section to the right location, or some silly statement that all authors agree with the manuscript when you are the only author.

Open Science doesn’t make publishing easier. That that’s all for the better: our research efforts are complex, so why should the publishing be. Sure, I am

 not

talking about references formatting or moving the Methods section to the right location, or some silly statement that all authors agree with the manuscript when you are the only author. No, let’s talk about data. What should you publish? How, and when?

Additional files, data, datasets, databases, and published data

I have not posted a lot about our Virtual Human Platform for Safety Assessment (VHP4Safety) project yet. Actually, more generally I do not post frequently about the funded projects. This is likely that few of them are Open Science by contract and often they have some formal process in place to approve output. That makes open notebook science-style posting about these projects hard. One is restricted to previously cleared material.

New paper: The Virtual Human Platform for Safety Assessment (VHP4Safety)

Division 1 of our Institute of Nutrition and Translational Research in Metabolism (NUTRIM) held a meeting last week which had a panel discussion on the use of patents to bring research to the market, aimed at PhD candidates of the institute. Patents are one of the routes to make research output more sustainable. For example, the research output into a new method to study something or make something often needs the development into a product.

Patents, societal impact, and sustainability

It was on my radar for some time already, but did not get around to finishing it. But I completed all five modules of the NASA Transform to Open Science (TOPS) Open Science 101 (doi:10.5281/zenodo.10161527). This Open Science 101 consists of several modules, starting with The Ethos of Open Science, via Open Tools and Resources, Open Data, and Open Code, to Open Results.

It was on my radar for some time already, but did not get around to finishing it. But I completed all five modules of the NASA Transform to Open Science (TOPS) Open Science 101 (doi:10.5281/zenodo.10161527). This Open Science 101 consists of several modules, starting with

 The Ethos of Open Science

, via

 Open Tools and Resources

,

 Open Data

, and

 Open Code

, to

 Open Results

. Now, since I have been

NASA Transform to Open Science (TOPS) Open Science 101

If you read my blog, it should not surprise you that I have long experimented with technologies to improve knowledge dissemination, for example in HTML. And I have blogged about publishing from an author and researcher, and editor perspective, for many years (see this longer list on my old blog). Also, in the Journal of Cheminformatics we pushed for innovation, including ORCID and GitHub adoption and Citation Typing Ontology adoption.

Better Publishing

Scholarly articles provide context to the factualness of statements in Wikidata, similar to the [citation needed] in Wikipedia. And just like the cited references in each scholarly article itself. The citation network is general seen as an essential part of (doing) science, even without citation intention annotation.

Adding citations between existing articles in Wikidata

About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago.

About a year ago I started migrating my blogger.com blog to a git-version-controlled, Markdown-based blogging platform. I have to say, it has been a happy year. It actually is awesome to port old blog posts (follow that here) and to see what I have been working on some 17, 18 years ago. I do have a nasty bug to fix that causes the conversion of the Markdown to HTML is scaling badly.

GoatCounter, Rogue Scholar and more new things

Scholia is a visual layer on top of Wikidata providing a rich user experience for browing scholarly research related knowledge. I am using the combinatie for various things, including exploring new research topics (a method, compound, or protein I do not know so much about yet), indexing notable research output (including citations), progress of Citation Typing Ontology uptake, etc.

Scholia configurability

Kasabi was an innovative RDF publishing platform from around 2011. Shortlived, and maybe just too early. I published two open datasets there. One was ChEMBL-RDF (see these posts). The second was a small data sets called ChemPedia, a open science effort to crowdsource chemical names. This is still very much needed, and possibly Wikidata could fill that gap, but it would first need to be able to handle all labels as statements itself.

Kasabi archive at the Internet Archive

This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an update on my Citation Typing Ontology use cases. And I have to say, a mention by Silvio Peroni is pretty awesome, thanks!

This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an update on my Citation Typing Ontology use cases. And I have to say, a mention by Silvio Peroni is pretty awesome, thanks! First, the bad news.

CiTO updates: Wakefield and WikiPathways

I am still catching up with a lot of work, and found out I actually had forgotten to blog about this cool article by Denise Slenter: “Discovering life’s directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool” (doi:10.1039/D3DD00069A). This paper explains how various open science resources (Wikidata, Reactome, WikiPathways) are used to visualize the biological story of the data from two metabolomics experiments

New paper: "Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool"

In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The Groovy Cheminformatics with the Chemistry Development Kit book is a project that has run since 2009.

In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The

 Groovy Cheminformatics with the Chemistry Development Kit

book is a project that has run since 2009.

cdk2024 #3: an unexpected downstream project

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore.

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore. But in the past two weeks I did attend two workshops.

Two meetings: ELIXIR Toxicology and FAIR4ChemNL

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

Ammar is finishing up his PhD thesis with his research on the use of FAIR towards predictive toxicology. Or, “AI ready”, as the term FAIR is now sometimes explained. Any computational method needs good data, and just FAIR is not enough. It needs to meet community standards, as formalized in R1.3. To me, this includes meeting community standards like minimal reporting standards.

New paper: FAIR assessment of nanosafety data reusability with community standards

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

cdk2024 #2: publishing grant proposals

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

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

Making BridgeDb Derby files with Groovy

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.

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

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.

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

The role of a university is manifold. Being a place where people can find knowledge and the track record how that knowledge was reached is often seen as part of that. Over the past decades universities outsources this role, for example to publishers. This is seeing a lot of discussion and I am happy to see that the Dutch Universities are taking back control fast now.

Universities and open infrastructures

I think that if you want to make your knowledge FAIR, you should use an open license and RDF. Simple. Now, not everything is knowledge. A lot of data is, but a lot more is not, think raw data. Using RDF to explain a protein sequence is still something that makes me feel uneasy.

I think that if you want to make your knowledge FAIR, you should use an open license and RDF. Simple. Now, not everything is knowledge. A lot of data is, but a lot more is not, think raw data. Using RDF to explain a protein sequence is still something that makes me feel uneasy. However, first, you need to make RDF, you need to make assumptions explicit, you need to decide on meaning. Making RDF is not easy.

Paper: The FAIR Cookbook - the essential resource for and by FAIR doers

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a blog planet. Blog planets aggregate blogs from many people around a certain topic. It’s like a forum, but open, free, community driven. It’s exactly what the web should be.

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a

 blog planet

. Blog planets aggregate blogs from many people around a certain topic. It’s like a forum, but open, free, community driven.