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

The purpose of a web service is that you give it a question or task, and that it returns an answer. For example, we can ask the Open PHACTS platform what compounds it knows with aspirin in the name. We pass the question (with the API key) and get a list of matching compounds. Now, this communication is complex: it happens at many levels, which are spelled out in the Internet Model.

Programming in the Life Sciences #4: communication from within HTML

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used


. CiteULike is currently adding more CiTO more functionality, which they started


doing almost one and a half years ago.

CiTO / CiteULike: publishing innovation

AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).  Agreeing with @citeulike and @abhishektiwari, as a service provider any bad news is good news too: they provide opportunities to improve.

A list of things I miss in CiteULike

During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg. The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be added soon), and allows to use custom evaluation functions.

An R-based genetic algorithm

I value ODOSOS


very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly.

Why ODOSOS is important

CompLife 2007 was held 1.5 weeks ago in Utrecht, The Netherlands. The number of participants was much lower than last year in Cambridge. Ola and I gave a tutorial on Bioclipse, and Thorsten one on KNIME.

CompLife2007, Utrecht/NL. Day 1 and 2

Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.

SMILES to become an Open Standard

Igor wrote a message to the CCL mailing list about OSRA: The email does not give any information on the fail rate, but the demo they provide via the webinterface does show some minor glitches (the bromine is not recognized): The source reuses OpenBabel and uses the GPL license. The value equal to that of text mining tools like OSCAR3


, and together they sounds like the Jordan and Pippen of mining chemical literature.

OSRA: GPL-ed molecule drawing to SMILES convertor

After handing in a new draft of my PhD manuscript with my co-promotors last friday, and a week before we leave for Sweden, it is time to start finishing up the material for my one hour workshop on chemoinformatics in general and QSAR/QSPR in particular for the Bioclipse Workshop. Pierre blogged about this movie.

Preparing a Chemoinformatics workshop

Paul Bracher and Joshua Finkelstein pointed my attention to a nice discussion in Nature on the future of chemistry, in What Chemists Want to Know, by Philip Ball. Paul and Joshua already reviewed it thoroughly, but I could not resist commenting in it too.

Organic chemists can now tune properties without changing the molecular structure??

I plan to do a daily coverage of the Chemistry Development Kit Bug Squash Party (BSP). While Stefan was working hard to get the wiki machine back online after a hard-disc crash, Rajarshi, Miguel and me have been working hard. Miguel started to work on missing JUnit tests for bugs reported on SourceForge and Rajarshi fixed PMD, JavaDoc and other problems.

CDK Bug Squash Party - Day 1

Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse


. Oscar3, however, is capable of more than the name2structure of OPSIN (see also 10.1039/b411033a;

Chemical Archeology: OSCAR3 to NMRShiftDB.org

Peter Corbett from Peter Murray-Rust’s group at the Unilever Cambridge Centre for Molecular Informatics visited Christoph Steinbeck’s junior Research Group on Molecular Informatics at the CUBIC today, and spoke about the status of Oscar3, a chemistry text mining program with the Artistic License.

Text mining for chemistry using OSCAR3

An InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

InChI's in LaTex and CDK News

As of April 3, I will be working as postdoc in the group of Christoph Steinbeck at the Cologne University BioInformatics Center, or simply CUBIC, for a year. Though no exact plans have been decided upon, the work will include CDK, CML, ontologies, Bioclipse, semantic web technologies, Jmol, and other interesting things. Research areas will at least include QSAR, but I hope to touch bits of bioinformatics too.

The Cologne University BioInformatics Center (CUBIC)

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

The Oscar4 paper (CC-BY, just like the screenshots of the paper below) was out already some days now, but the formatting has finished:    I spotted a rogue http:// in the code example b) in Appendix B:    I’ll see what I can do about that, but the API might evolve a bit anyway.

Oscar4 paper: text mining in Bioclipse (and everywhere else, of course)

The meetings in and around Oxford were great! I already wrote that the Predictive Toxicology workshop was brilliant (see Oxford… #1


) and Oxford… #2


), but I also very, very much enjoyed meeting up with Dan and Nico! During the week, someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow; that is, it’s often not clear why I am posting what I am posting.

The Molecular Chemometrics Principles #1: access to data

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta


and wrote a script for it for chemical RDFa


. At this moment, Chemical blogspace and RDF for Molecular Space (see this blog


) are using chemical RDFa to semantically markup molecular information.

Operator 0.8 released: a new Sechemtic user script

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here. The first leaflet is from Chemistry Central, one of the open access publishers.

That big pile of paper...

Deepak blogged about screencasting for bio topics, concentrated at bioscreencast.com


of which he is co-owner. I guess it is like a YouTube for bioinformatics thingies. Jean-Claude picked this up very quickly (seen on Cb? At least I did.), and already uploaded a screencast, demoing JSpecView


written by Robert. I wonder if he will upload the screencasts he made for Bioclipse too?

Screencasts for life science informatics

The second day just started of the Open Source Meets Business, and now actually listening to the PHP talk, but here is a short update on day 1, which was the investment summit. It was not so crowded, but especially the talks from the venture capitalists were interesting. During lunch we actually talked to one in person, which was insightful. I will be putting up links to interesting sites mentioned during this conference on my delicious account.

OSMB2007 Day #1: venture capital, scientific blogger and Kepler

Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.

BioJava 1.5 beta released

I started a spin-off blog earlier this week: kemistry desktop environment. It will deal with integration of chemistry on opensource desktops, with KDE as one of them. Today, it features an overview of earlier blogs on the subject in this new blog.

New chemistry-on-the-desktop blog

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

Yesterday, I struggled some with creating nanopublications with Groovy. My first attempt was an utter failure, but then I discovered Thomas Kuhn’s NanopubCreator and it was downhill from there. On the right, a depiction is given of a compound found in Taphrorychus bicolor (doi:10.1002/JLAC.199619961005). Published in

 Liebigs Annalen

, see this post about the history of that journal. There are two good things about this.

Creating nanopublications with Groovy

CompLife’06 started today in Cambridge, UK. About 80 people are attending the meeting, and topics range from systems biology to QSAR. This evening there was a free software session mostly focussing on opensource software.

CompLife'06 - Day 1

Earlier I already reported that student text books were picking up Jmol as 3D viewer. Now, Nature Structural &amp; Molecular Biology reports (DOI:10.1038/nsmb0206-93) that they picked it up too, using FirstGlance in Jmol (thanx Peter, for reporting this on the Blue Obelisk mailing list!). And, thanx Eric, for acknowledging the hard work of the Jmol developers.

Open source Jmol taking over the world

Some years ago we started the ELIXIR Toxicology Community. It has been an interesting journey, partly covered in this whitepaper). We started with interaction we had in several projects already, but particularly the potential. I see this.

Community activity #2: FAIRsharing

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

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 blogged for about a week now, and been too busy with other things, like finishing my PhD articles/manuscript, my new job at the CUBIC


where I continued the work


on proper protein support in Bioclipse using the CDK and Jmol: The latter involves getting the CdkJmolAdapter


, the interface between the CDK and Jmol, updated for changes


since the Jmol as 3D viewer for CDK


article in CDK News

Protein support in Bioclipse using Jmol and the CDK

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

The announcement of the Panton Principles


is the


big news today, though Peter already spoke about them in May last year


(see coverage on FriendFeed and Twitter). The four principles list in their short versions: When publishing data make an explicit and robust statement of your wishes. Use a recognized waiver or license that is appropriate for data.

Open Data: the Panton Principles

Open source chemoinformatics has become a common phenomenon, though many projects are small in nature: source code is developed by only few developers, or even in a closed manner and released when considered done.

When is open source chemoinformatics successful?

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

Almost a year ago I started a position


with Peter Murray-Rust to work on Oscar for three months (see this overview of results; a paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute bits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately. One thing I did do after that, was write a Bioclipse plugin.

Bioclipse-Oscar4 - Text mining in Bioclipse

Joerg Wegner recently blogged about

 Chemogenomics: structuring the drug discovery process to gene families

by C.J. Harris and A. P. Stevens in Drug Discov Today (DOI: 10.1016/j.drudis.2006.08.013). This review article provides a nice overview of a trend in mathematical modelling of the interaction of small organic molecules with proteins, often referred to as QSAR.

Are chemogenomics and proteochemometrics the same?

As follow up on my Including SMILES, CML and InChI in blogs


blog last week, I had a go at Greasemonkey. Some time ago already, Flags and Lollipops and Nodalpoint showed with two cool mashups (one Connotea/Postgenomic and one Pubmed/Postgenomic) that userscripts are rather useful in science too. I can very much recommend the PubMed/Postgenomic mashup, as PubMed has several organic chemistry journals indexed too!

SMILES, CAS and InChI in blogs: Greasemonkey

I was just about to install Subclipse (for the millionth time), and googled for the update site details:    Does anyone know how you can get Google pick up or how it detects the Download/UpdateSite/etc pages, shown as direct links below the primary hit? Are HTML &lt;link&gt; elements used for that? Or does it use certain meta data, microformats, …?

Tuning Google Results?

I use Google Analytics to analyze the visitors of my blogs and of Planet Blue Obelisk too. Now, for the past couple of weeks, the webpage of the Journal of Chemical Information and Modeling is showing up as refering site: What is going on here ?!?! This is really no fake, but cannot find an actual link when I visit the journal webpage either…

 Update

: When looking at the logs, it becomes even weirder.

The JCIM is linking to Planet Blue Obelisk??

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

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)

The second Programmeerzomer and the second summer of code for me, will end tomorrow with a presentation of Niels on his new JChemPaint code. The summer is over before you know it. One of the goals was making the JChemPaint editor Swing independent and more easy to integrate with SWT widgets. So, I hacked up the last bits of Bioclipse code.

SWT View with the new JChemPaint

Bioclipse 1.0 is to be released in May, and the cartoon on script command is still not working in the Jmol viewer. For those who do not know yet, Bioclipse is a cool Eclipse RCP based Java chemo-and bioinformatics workbench. To have a better idea what goes on inside Bioclipse, I wrote a new BioPolymer tree to show me the strands in the protein.

Getting Jmol's 'cartoon on' to work in Bioclipse

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

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

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

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 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

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

A bit over a year ago I got introduced to Qeios when I was asked to review an article by Michie, West, and Hasting:

 “Creating ontological definitions for use in science”

(doi:10.32388/YGIF9B.2). I wrote up my thoughts after reading the paper, and the review was posted openly online and got a DOI. Not the first platform to do this (think F1000), but it is always nice to see some publishers taking publishing seriously.

Qeios, an open dissemination platform for research output

When last week in a large (and relevant) Dutch research event ChatGPT came up, and that this was going to change the world. Even the critiques came up, but were effectively disregarded with “these methods get better very quickly”. This is not untrue, but not really true either. I murmur “not even wrong”. I know how hard it is to get computers to find meaningful patters; I did a PhD in this in the early 21st century.

Information Retrieval versus ChatGPT

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

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

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another.

Bioclipse git experiences #1: Strip away unwanted plugins

The BridgeDb project (doi:10.1186/1471-2105-11-5) (and ELIXIR recommended interoperability resource) has several aims, all around identifier mapping: provide a Java API for identifier mapping provide ID mappings (two flavors: with and without semantic meaning) provide services (R package, OpenAPI webservice) track the history of identifiers  The last one is more recent and two aspects are under development here: secondary identifiers and dead

Downloading all currently released BridgeDb identifier mapping databases

Bioclipse git experiences #2: Create patches for individual plugins/features

In December I reported about Groovy code to create nanopublications


. This has been running for some time now, extracting nanopubs that assert that some metabolite is found in some species.

What metabolites are found in which species? Nanopublications from Wikidata

It takes effort to move scholarly publishing forward. And the traditional publishers have not all shown to be good at that: we’re still basically stuck with machine-broken channels like PDFs and ReadCubes. They seem to all love text mining, but only if they can do it themselves. Fortunately, there are plenty of people who do like to make a difference and like to innovate. I find this important, because if we do not do it, who will.

Two conference proceedings: nanopublications and Scholia

SWAT4LS was once again a great meeting. I doubt I will find time soon enough to write up notes, but at least I can post the eNanoMapper poster I presented, which is available from F1000Research:

The SWAT4LS poster about eNanoMapper

Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson

 et al.

is balanced.

Slow publishing innovation: SMILES in ACS journals

Adding chemical compounds to Wikidata is not difficult. You can store the chemical formula (P274), (canonical) SMILES (P233), InChIKey (P235) (and InChI (P234), of course), as well various database identifiers (see what I wrote about that [here(http://chem-bla-ics.blogspot.nl/2015/12/new-edition-getting-cas-registry.html)]). It also allows storing of the provenance, and has predicates for that too.

Adding chemical compounds to Wikidata

I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds. The Open PHACTS API support various formats and this JSON is the default format used by the ops.js library.

Programming in the Life Sciences #20: extracting data from JSON

I think the authors of the Open PHACTS proposal made a right choice in defining a small set of questions that the solution to be developed could be tested against. The questions being specific, it is much easier to understand the needs. In fact, I suspect it may even be a very useful form of requirement analysis, and makes it hard to keep using vague terms. Open PHACTS has come up with 20 questions (doi:10.1016/j.drudis.2013.05.008;

Programming in the Life Sciences #17: The Open PHACTS scientific questions

Elsevier’s new ideas on text mining are getting a lot attention now. Sadly, they get it wrong, again. On the bright side, all other publishers, which are expected to follow this year, can learn from this mistake.  Because if done right, the publishers can even help forward science, despite crippling progress. That sound harsh, and surely they have done a lot of good for science. In fact, we would not be where we are now without the publishers.

Elsevier's new text mining initiative is a step sideways

Now that I have wrote out the goals, what they students will practically do, and how to get started with the Open PHACTS platform, I will list how we will assess the students: a presentation on the second day, outlining the project and work plan, working source code at the end of the cour se, a final presentation, showing the results and conclusions. Primarily, they will be judged on their acquired programming skills.

Programming in the Life Sciences #3: the assessment

HTML (HyperText Markup Language), the language of the web, is no longer the only language of the web. But it still is the primary language in which source code of webpages is shared. Originally, HTML pages were always static: the only HTML source of a web page was that was downloaded from a website. Nowadays, much HTML the is visualized in your web browser, is generated on the fly with JavaScript.

Programming in the Life Sciences #11: HTML

I cannot find the bug report just now, but the CDK has an open problem with change even notification, where the nonotify classes still caused change event to be sent around. This was because the nonotify classes extended in a wrong way the data classes. So, I worked today on copying the data class implementations into a new implementation, not extending the data classes, while removing the listener code: the

 silent

module.

Data, Nonotify, or Silent?

Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version


I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules). Kasabi makes the RDF data available via a few APIs, depending on the APIs selected by the uploader. I picked all five of them, just to see how things work.

ChemPedia-RDF #2: Kasabi

Oscar is a text miner. It mines in text for chemistry. Oscar4 is the next iteration of Oscar code that I worked on in the past three months, with Lezan, Sam, and David.

Text mining chemistry from Dutch or Swedish texts

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

Last month I reported a few things I missed


in CiteULike. One of them was support for CiTO (see doi:10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology. I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge.

CiteULike CiTO Use Case #1: Wordles

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

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

JChemPaint history: CML patches in 1999

Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important. The CDK has a few places where atom types are perceived. The HydrogenAdder and ValencyChecker are two examples.

Atom typing in the CDK

Hi all, welcome to this winter solstice challenge! Umm, to not give our southern hemisphere colleagues not a disadvantage, as their winter solstice has already passes, you’re up for a summer solstice challenge! Introduction   So, you know ImpactStory and Altmetric.com (if not, browse my blog); these are wonderful tools to see what people are doing with your work.

Winter solstice challenge: what is your Open Knowledge score?

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"

As part of our Dutch Research Council (NWO) Open Science grant, we organized a Chemistry Development Kit User Group Meeting (#CDK25UGM), of which yesterday was the “conference” day, and today a hackathon. I opened the session with a few slides welcoming everyone at Maastricht University (and our Dept of Translational Genomics, and explaining the NWO grant.

cdk2024 #4: Chemistry Development Kit User Group Meeting - Day 1

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

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.

Niche papers and citation intentions

One-and-a-half years ago I started migration my blog from blogger.com to a Markdown and Git-based blog. It has been a fascinating journey that I do not regret.

Blog updates

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

Lars Willighagen

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

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

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

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"

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

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)

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)

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

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! First, the bad news.

CiTO updates: Wakefield and WikiPathways

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

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"

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

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.