Version 2.12 of the Chemistry Development Kit has been released. It is the last release with contributions by our NWO Open Science grant.

When I first started writing this post, I started writing up why scientific communication is important, but because I started explaining what needs improving, and what are underlying causes why change is not happening, it got dark pretty quickly. So, I deleted that essay again. Instead, let's just enjoy the awesome and long list of solutions we have for scientific discourse.

I have had this on my todo list for way too long: writing about FAIR Implementation Profiles, or FIPs for short (see also doi:10.1007/978-3-030-65847-2_13): In the early GO FAIR days, people referred to the challenges and choices . FIPs are a formal approach to report the choices.

The number of data and knowledge source relevant to your biological or chemical question increases every year. They all come with different API and different data models. These need to be documented and mapped. What better way to do that than actually do that and then use that. I never asked, but I can imagine that was the original idea of Tooba and Yojana.

Today starts a new project. NWO's Open Science NL awarded Dr Tooba Abbassi-Daloii (Amsterdam UMC) with a grant to work on the interoperability between biomedical databases which all have different scope and design (doi:10.61686/AQNSM35060)). This project will create an open, interoperable framework to connect these databases, enabling efficient access and data use.

Decades of research on environmental, health and safety impacts of nanomaterials have generated large amounts of nanosafety data, but not all data are available online following the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. This lack of FAIR data delays progress in regulatory research, needed by regulators to develop evidence-based policies. In this context, researchers collaborating in the EU NanoSafety Cluster (www.nanosafetycluster.eu) engaged in a discussion on the ethical impacts related to (not) sharing nanosafety data. Screening the potential ethical impacts suggested that openly sharing nanosafety data relevant to risk governance of nanomaterials could give rise to ethical issues related to health and to liberties, and that these data might be misused. On the other hand, not openly sharing such nanosafety data could raise issues related to health, equity, common good, environment, and sustainability. A small-scale Ethical Impact Assessment (EIA) was performed between June 2022 and April 2024 to identify and evaluate more specific ethical issues and to propose recommendations for remediating ethical concerns. Preliminary results were presented in scientific conferences (one poster and three oral presentations), while the comments of the participants were incorporated in the final version of the presented paper. The EIA identified ethical issues and value conflicts related to the following sectors: intellectual property, social justice, public health, dual use, environmental ethics and animal ethics. Some recommendations for remediation are the competence of research organisations. Other recommendations call for societal dialogue and engagement. Yet other recommendations call for political action.

WikiPathways was founded in 2008, in the year I left Wageningen (and we Nijmegen) and moved to Uppsala, Sweden. When we dediced to move back to The Netherlands in 2012, I got to opportunity to join the Department of Bioinformatics (BiGCaT) and work on Open PHACTS. I had visited the group in March 2011 because I had a COST action workshop near Maastricht (about nanoQSAR) and the bioinformatics group did WikiPathways.

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?

Last autumn two TDCC projects started, FAIR4ChemNL (with the PeerTube channel and doi:10.61686/XVYQV45374) and FAIRify for metabolomics data (doi:10.61686/CSGIP04334). But I haven't written much on either yet and what the role is our research group in these projects.

This document describes how you can improve the FAIR-ness of your project report by using compact identifiers. Of course, it can be applied to any other document too, and has been used in, for example, journal articles and online documentation already. Compact identifiers find a balance between compactness in writing and being a persistent, unique, and global identifier.

Thirty years ago, researchers were struggling getting access to literature they wanted to read. I remember PhD candidates visiting friends at nearby universities for a meetup, and while there, for the copying machine in the remote library. Faster and cheaper than inter-library loaning. Scholarly journals were still printed on paper and distributed to university libraries. That was expensive.

About fifteen months ago a new project started: One Million IUPAC names: We started out with using Europe PMC to get JATS XML files for the full texts of open access articles. Parsing the XML is easy and the text paragraphs are passed through OSCAR and OPSIN. That has not changed.

This is a bit of work I did already in March, but with the Zotero 9 release I was reminded that I wanted to blog this. Ideally, it will trigger some further discussion and maybe a future Zotero/Google Docs version supports bibliography-level annotations too. Still, Zotero 8 brought in prefix and suffix support, and I was wondering if this could be used for CiTO citation intent annotations. And it can.

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

Making chemistry more FAIR requires unique identifiers for chemical structures. For organic compounds plenty of solutions exist that do a great job. Last year and last week, I attended two technical InChI meetings, both with organometallic compounds and other molecular inorganics as one of the key topics. Thanks to Sonja (Mastodon bridge) and Gerd for the invitations.

Communication of science is important to me and it comes in many formats. Educational resources, research articles, text books, popular science magazines, blogs, TV shows, podcasts, etc (in no particular order). Somewhere during the pandemic, I started listening to podcasts. I had done that, in the early days, but those early podcasts… well, let's say, the format had not materialized yet.

Motivation Integrating omics data analysis with publicly available databases is crucial for unravelling complex biological mechanisms. However, this integration process is often intricate and time-consuming due to the diversity and complexity of the data involved. Achieving consistent harmonization across data types is challenging when managing disparate formats and sources. To address these issues, we introduce pyBiodatafuse, a query-based Python tool designed to integrate biomedical databases. This tool establishes a modular framework that simplifies data wrangling, enabling the creation of context-specific knowledge graphs (KGs) while supporting graph-based analyses.Results We developed a pipeline for generating context-specific knowledge graphs dynamically, allowing users to create KGs on the fly from a set of gene or metabolite identifiers. pyBiodatafuse features a user-friendly interface that streamlines this process, making it accessible even to researchers without extensive computational expertise. Additionally, the tool offers plugins for widely used platforms such as Cytoscape, Neo4j, and GraphDB, enabling local hosting of resulting property and RDF graphs. This versatility ensures that generated KGs can be efficiently utilized within diverse research workflows. To demonstrate its potential, we used pyBiodatafuse to create a graph for post-COVID syndrome using differential gene expression data, showcasing its ability to build adaptable and context-specific knowledge representations. Thus, pyBiodatafuse sets the stage for streamlined data integration, empowering researchers to focus on discovery and analysis without being hindered by data management complexities.Availability and implementation pyBiodatafuse is open-source, with its source code and PyPi package available at https://github.com/BioDataFuse/pyBiodatafuse and https://pypi.org/project/pyBiodatafuse/. The user interface can be accessed at https://biodatafuse.org/. Additionally, a release has been made on Zenodo at https://doi.org/10.5281/zenodo.18468942.

We need a lot more than diamond open access to really improve the publishing models. That said, but there are examples that diamond open access publishers actually want to improve more just the access to the knowledge dissemination infrastructure. But infrastructure is not only technologies; it also includes the many social aspects that are involved in adoption. And we saw enough of that in the open access transition.

Decades of research on environmental, health and safety impacts of nanomaterials have generated large amounts of nanosafety data, but not all data are available online following the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. This lack of FAIR data delays progress in regulatory research, needed by regulators to develop evidence-based policies. In this context, researchers collaborating in the EU NanoSafety Cluster (www.nanosafetycluster.eu) engaged in a discussion on the ethical impacts related to (not) sharing nanosafety data. Screening the potential ethical impacts suggested that openly sharing nanosafety data relevant to risk governance of nanomaterials could give rise to ethical issues related to health and to liberties, and that these data might be misused. On the other hand, not openly sharing such nanosafety data could raise issues related to health, equity, common good, environment, and sustainability. A small-scale Ethical Impact Assessment (EIA) was performed between June 2022 and April 2024 to identify and evaluate more specific ethical issues and to propose recommendations for remediating ethical concerns. Preliminary results were presented in scientific conferences (one poster and three oral presentations), while the comments of the participants were incorporated in the final version of the presented paper. The EIA identified ethical issues and value conflicts related to the following sectors: intellectual property, social justice, public health, dual use, environmental ethics and animal ethics. Some recommendations for remediation are the competence of research organisations. Other recommendations call for societal dialogue and engagement. Yet other recommendations call for political action.

Nine days ago, the VHP4Safety project (see these posts) held a launch event in Utrecht for the Virtual Human Platform (VHP), a key result of the Dutch Research Agenda (NWA, from the Dutch Nationale Wetenschapsagenda ). Despite the name, the NWA is just one part of the NWO funding mechanisms, but like the NWO Open Science programme it is funding with a specific purpose.