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

This is what Struck wrote in 2018 in a contribution to the 2018 IEEE 14th International Conference on e-Science (e-Science) (doi:10.1109/eScience.2018.00016). I very much agree with this, and the notion is gaining ground in the academic community.

Open Infrastructures #1: Research Software Directory

I have been running automated curation tests for many years now, at least from before 2018. Because it has been done without funding, it has not been as nicely integrated, and depends, for example, first on the RDF generation to be integrated in the GitHub Action. So, I still run them regularly (often in the morning during breakfast). Meanwhile, the curation tests help the project to monitor and maintain the quality of the pathways.

WikiPathways curation reports on profile pages

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

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

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

Linkrot is real and digital preservation problematic. One reason why I have started migrating my blog to a more robust platform. That first step gave me version control. This summer my blog was accepted to Rogue Scholar. That gave me DOIs. And an idea.

FAIR blog-to-blog citations

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

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

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

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)

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 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.

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"

This blog is almost 18 years old now. I have long wanted to migrate it to a version control system and at the same time have more control over things. Markdown would be awesome. In the past year, I learned a lot about the power of Jekyll and needed to get more experienced with it to use it for more databases, like we now do for WikiPathways.

Archiving and updating my blog

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

Making BridgeDb Derby files with Groovy

I am pleased to learn that the Dutch Universities start looking at rankings of a more scientific way. It is long overdue that we take scientific peer review of the indicators used in those rankings seriously, instead of hiding beyond fud around the decline of quality of research.

I am pleased to learn that the Dutch Universities start looking at rankings of a more scientific way. It is long overdue that we take scientific peer review of the indicators used in those rankings seriously, instead of hiding beyond fud around the decline of quality of research.  So, what defines the quality of a journal? Or better, of any scholarly dissemination channel? After all, some databases do better peer review than some journals.

Journal Rankings

The Internet Journal of Chemistry (IJC, issn:1099-8292) was one of the first scientific journals to get published on the world wide web (part of the Internet), see doi:10.1080/00987913.2000.10764578. Issues were published from 1998 to 2004. But because it predates systematic archiving of webpages by libraries, a lot is lost.

The Internet Journal of Chemistry (IJC, issn:1099-8292) was one of the first scientific journals to get published on the world wide web (part of

 the Internet

), see doi:10.1080/00987913.2000.10764578. Issues were published from 1998 to 2004. But because it predates systematic archiving of webpages by libraries, a lot is lost.

The Internet Journal of Chemistry

Mike Taylor wrote up a post about the various things a journal article is doing, the first being a scientific report. We put a lot of money in establishing a scientific track record. In the past 30 years how we publish our research and how we archive it has changed significantly. If you read my blog more often, you know I have been critical of the performance of many publishers.

Mike Taylor wrote up a post about the various things a journal article is doing, the first being

 a scientific report

. We put a lot of money in establishing a scientific track record. In the past 30 years how we publish our research and how we archive it has changed significantly. If you read my blog more often, you know I have been critical of the performance of many publishers.

Archiving, but not really

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

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 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"

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

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

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

While this was not the primary hack project during the ELIXIR BioHackathon Europe last autumn, but I really like BioHackrXiv and I got the question if I could have a look at getting the ORCID logo in generated PDF. The ORCID was already in the YAML metadata of report markdown, so it sounded easy.

New preprint: "BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports"

Every day a child is born with an inherited metabolic disorder, and many do not grow old. MetaKids is a Dutch foundation that collects money and raises awareness and the charity selected this year for the NPO (Dutch national radio/tv) 3FM Serious Request. This has become a Dutch tradition. Serious Request will play music on the radio, when people contributed to the fundraiser, and the more money, the more often the music gets played.

Serious Request: "WikiPathways in actie voor MetaKids"

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

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

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

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

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

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

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).

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

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

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

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

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"

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)

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

Okay, the Pilot is over ending with 17 papers, 16 of which have CiTO annotations (and so far 4 J.Cheminform. papers after the pilot), but my interest in the Citation Typing Ontology continues and we just need more adoption.

Okay, the Pilot is over ending with 17 papers, 16 of which have CiTO annotations (and so far 4 J.Cheminform. papers after the pilot), but my interest in the Citation Typing Ontology continues and we just need more adoption.

 Datasets as source of annotations

So, here’s a quick Wikidata update.

CiTO updates #4: annotations in datasets

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

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

And just like that, without a warning, Twitter changed policies again, and you now need a Twitter account and be logged in to see public tweets: Twitter has started blocking unregistered users (The Verge). Though I learned it first via Mastodon, of course.

And just like that, without a warning, Twitter changed policies again, and you now need a Twitter account and be logged in to see public tweets: Twitter has started blocking unregistered users (The Verge). Though I learned it first via Mastodon, of course.  For example, this is what happens when you go to twitter.com/wikipathways:    Fortunately, WikiPathways does have a Mastodon account, that anyone can see without having a Mastodon account.

Twitter exits FAIR and is no longer a dissemination solution

Sometimes I think back about how Scholia started, and then I think I remember a Twitter discussion. Twitter was a social platform that was unable to fight hate speech. I left it last year in favor of Mastodon.

Sometimes I think back about how Scholia started, and then I think I remember a Twitter discussion. Twitter was a social platform that was unable to fight hate speech. I left it last year in favor of Mastodon. Anyway, I did some digging today and found this thread


from October 8-9 2016.

Scholia timeline

Doing the "Open Science Challenge"

There are multiple initiatives to support the migration from Twitter to Mastodon (see also this blog post ). But Wikidata should not be forgotten here which has been tracking Mastodon accounts of things in their database:

There are multiple initiatives to support the migration from Twitter to Mastodon (see also this blog post


). But Wikidata should not be forgotten here which has been tracking Mastodon accounts of things in their database: So, here are some Wikidata SPARQL queries to see the uptake: Universities with Mastodon All Mastodon accounts in Wikidata (or subset with also a Twitter account) Nobel Prize winners with Mastodon Academic journals

Finding Mastodon accounts with Wikidata (a few SPARQL queries)

In August I reported about 2D depiction of (CX)SMILES in Wikidata via linkouts (going back to 2017). Based on a script by Magnus Manske, I wrote a Wikidata gadget that uses the same CDK Depict (VHP4Safety mirror) to depict the 2D structure in Wikidata itself:

In August I reported about 2D depiction of (CX)SMILES in Wikidata via linkouts (going back to 2017). Based on a script by Magnus Manske, I wrote a Wikidata gadget that uses the same CDK Depict (VHP4Safety mirror) to depict the 2D structure in Wikidata itself:    Note the depiction of the undefined (CIP) stereochemistry on two atoms. Thanks to Adriano and John for working that out.

Wikidata script for SMILES, SMARTS, and CXSMILES depiction

Yeah, it has been hard to miss it (see e.g. Should I join Mastodon? A scientists’ guide to Twitter’s rival). Twitter is experiencing some turbulence and Mastodon has become a very attractive, open source, community-driven, inclusive alternative. It’s been around since 2016 and there is some research literature about it already. I got my account in 2018, but did not start actively using it until earlier this year.

s/Twitter/Mastodon/g

Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before the start of the pandemic.

Biology, ACPs, lipids, cheminformatics, and Dagstuhl

Part of the scientific program of the ICCS 2022.

The International Conference on Chemical Structures scientific program is online!

In the end it was a very simple change today (huge thanks to Nikki!), but Wikidata now escapes SMILES and CXSMILES (P10718) with the formatter URL (P1630)!

In the end it was a very simple change today (huge thanks to Nikki!), but Wikidata now escapes SMILES and CXSMILES (P10718) with the formatter URL (P1630)!    That means that the link to CDK Depict now also works for SMILES (P233 and P2017) with a triple bond in it :) And because Adriano created the so far missing formatter URL for CXSMILES, it also works for lipid classes (see my post yesterday), polymers, etc :)   CXSMILES for a group of

Wikidata now escapes SMILES and CXSMILES!

Open Science is happening. The merits are no longer theoretical or idealistic but tangible. Research is faster than ever, more vetted than ever (think PubPeer), more cited than ever. Fairly, not just because of Open Science, but open access causes readership causes impact causes citations. When new people and organizations start adopting Open Science this warms my hearth.

new: "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community"

I am a bit behind with tweeting about new published papers, but let that not reflect that these papers are not very exciting. The first paper is by Marvin an almost-finished PhD candidate in our group and now working as postdoc on the VHP4Safety project. He has been working on linking adverse outcome pathways (AOPs) with molecular pathways, such as in WikiPathways.

new: "Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content"

Last month I reported on the start of the NWO Open Science grant and it is time for an update. First, our grant now has a grant number, 203.001.121. For a project that is about identifiers, having a project identifier is a big deal.

Last month I reported


on the start of the NWO Open Science grant and it is time for an update. First, our grant now has a grant number, 203.001.121. For a project that is about identifiers, having a project identifier is a big deal.

BridgeDb NWO grant update #2: building up momentum

Last year, Denise, Tina, Marvin, and I received an NWO Open Science grant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel (see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work part-time on this grant.

BridgeDb NWO grant update #1: first steps

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong.

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong.  Long story short: it worked!

BioHackathon Europe 2021 #1: CiTO annotations in BioHackrXiv

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

Please find below the presentation I gave today at SWAT4LS :

Please find below the presentation I gave today at SWAT4LS


:

SWAT4LS: "Linking Open Drug Data to Cheminformatics and Proteochemometrics"

I am happy that I got my first research grant awarded (EU FP7), which should start after all the contracts are signed, etc, somewhere early 2014. The project is about setting up data needs for the analysis of nanosafety studies. And for this, I have the below two position vacancies available now.

Looking for a PhD and a Postdoc to work on Open Science Nanosafety

Update 2021-02: this post is still the second-most read post in my blog. Welcome!

Update 2021-02

: this post is still the second-most read post in my blog. Welcome! Some updates: Ammar Ammar in our BiGCaT group has set up a new SPARQL endpoint. Please use and tweet. blog, or otherwise let others now how you use the ChEMBL RDF. Since this post I have blogged a lot more about ChEMBL.

 Update

: this work is now written down in this paper. I’m having a really bad month, as you can see from the number of posts.

ChEMBL 09 as RDF

Say, you have your own dictionary of chemical compounds. For example, like your company’s list of yet-unpublished internal research codes. Still, you want to index your local listserv to make it easier for your employees to search for particular chemistry you are working on and perhaps related to something done at other company sites. This is what Oscar is for.

Say, you have your own dictionary of chemical compounds. For example, like your company’s list of yet-unpublished internal research codes. Still, you want to index your local listserv to make it easier for your employees to search for particular chemistry you are working on and perhaps related to something done at other company sites. This is what Oscar is for. But, it will need to understand things like UK-92,480.

Adding a new dictionary to Oscar

With the general framework set up for editing and validation of CML documents , it was fairly easy to support the PubChem XML file format schema too.

With the general framework set up for editing and validation of CML documents


, it was fairly easy to support the PubChem XML file format schema too. With the upcoming Bioclipse2 beta (scheduled next Friday), all you need to install on top of the Bioclipse2 core is the new XML feature.

Editing and Validation of PubChem XML documents

CDK 1.1.x releases are well in progress, but a recent commit broke a number of unit tests. Here comes git-bisect.

Finding the commit that causes the regressions...

Some time ago Noel ran a poll on

 chemoinformatics

and

 cheminformatics

, so I set up a poll too in part #1 of this series


. The outcome is clear: The Obernai meeting


strongly suggested

 chemoinformatics

[1], but the start of the open access Journal of Cheminformatics is the killer.

Chemoinformatics p0wned by cheminformatics... #2

The reason why I have not been able to blog much lately, is that my family and I have been moving to Uppsala/Sweden, where I’ll start a postdoc in the group of Jarl Wikberg @ BMC @ Uppsala University, where I’ll work on chemoinformatics in drug design, and the use of CDK and Bioclipse in particular.

Moved to Sweden: Post-doc in the Bioclipse group of Prof. Jarl Wikberg

The great thing about open source is that… it’s open.

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

I added a Bioclipse plugin for JOELib (GPL, by Joerg) which comes with many QSAR descriptors, several of which are now available in the QSAR feature of Bioclipse :

I added a Bioclipse plugin for JOELib (GPL, by Joerg) which comes with many QSAR descriptors, several of which are now available in the QSAR feature of Bioclipse


: Meanwhile, the Bioclipse team in Uppsala has set up the obligatory scatter plot functionality, but leave that screenshot for them to show. Therefore, time for integration with R.

More QSAR in Bioclipse: the JOELib extension

Back on October I presented Everything you always wanted to know: plant pathway modelling in WikiPathways (doi:10.5281/zenodo.18149988) at the Knowledge Graphs for Plant and Microbiome Multiomics symposium (see this archived LinkedIn post) on 14th October 2025 (youtube recording). I had not found time yet to post about this meeting, but it was an awesome list of speakers, regrettable absense of some others, but resulting in new contacts and some

Back on October I presented

 Everything you always wanted to know: plant pathway modelling in WikiPathways

(doi:10.5281/zenodo.18149988) at the

 Knowledge Graphs for Plant and Microbiome Multiomics

symposium (see this archived LinkedIn post) on 14th October 2025 (youtube recording). I had not found time yet to post about this meeting, but it was an awesome list of speakers, regrettable absense of some others, but resulting in new

PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge

Three weeks ago, I wrote a the post Rescuing Scholia: will we make it in time?, where I sketched a future without Scholia. Scholia, started almost 10 years ago and I think it is worth keeping around longer.

Rescuing Scholia #2: getting closer

My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider:

My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider:    I uploaded the source to MyExperiment, so anyway can play with it. There is much to improve, such as using CDK-Taverna for further analysis of the results.

Metabolomics workflows in Taverna

I have been wanting to blog about this since this summer, but with everything going on, I never really got around to it. What is this Cited In feature of WikiPathways and where does that information come from?

I have been wanting to blog about this since this summer, but with everything going on, I never really got around to it. What is this

 Cited In

feature of WikiPathways and where does that information come from?

Where does the WikiPathways Cited In information come from?

Just a few new blogs since #13 in July


: Chemical Abstracts Service Committee (CCAS) (entry in Cb


) Agilemolecule’s Blog (entry in Cb


) The Allotrope (entry in Cb


) If you know good chemistry blogs, please contact the author and ask them to email me for inclusion.

Cb: New Blogs #14

The Cb software is still holding… I jettinsoned the old post cache, which speeded up the processing of blogs considerably, but the system just doesn’t scale right. Yet, Euan has done a great job, and the Cb site has now been online for some three years!

Cb: New Blogs #13

Dear lazyweb! I have been trying to figure out which Eclipse 3.4 feature I must install from the update site to get the

 org.eclipse.zest

plugin in my environment. I installed the Zest feature (which I am going to use to visualize an RDF network


), but my workspace still complained that I did not have the plugin.

Which feature must I install for org.eclipse.zest?

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

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.

chem-bla-ics

Chem-bla-ics