Welcome to the latest News Digest the main topic of this week is definitely controlled vocabularies with many presentations from the 4th Ontologies4Chem workshop; therefore the topic got its own chapter. It is a little bit longer today, so let us dive in directly and if you are looking for a way to support me with writing the News Digests, check out the last part. And now, let’s start.

Bridging NFDI’s culture and chemistry knowledge graphs

The following article was already published in October and you probably need some understanding of knowledge graphs and controlled vocabularies, but I highly recommend checking it out. Charles Tapley Hoyt combined the knowledge graphs from NFDI4Culutre and NFDI4Chem. Doing this allows to “connect datasets in Chemotion electronic laboratory notebooks (ELNs) that annotate the instruments used for generation with depictions of those instruments in cultural heritage objects like painting”. And why is this so impressive? Let’s use the words by Charles Tapley Hoyt:

Is this the most practical query? No. But it’s cool, and more importantly, it demonstrates a few things:

1. Even a mundane question might require federating many different resources
2. NFDI has successfully built many detailed resources that support these questions
3. We’re almost at the point where these questions can be operationalized
4. Where the NFDI’s semantic stack has gaps, I am ready to contribute my own technologies. I’m very excited to have recently joined NFDI during summer 2026, and I’m looking forward to helping shape its semantics roadmap

Link to the article on Charles Tapley Hoyt’s website, cthoyt.com 

Classifying, Ontologies and the Semantic Web

On November 11, 2025 the 4th Ontologies4Chem workshop was held in Germany. Which was organized by NFDI4Chem, NFDI4Cat, the Beilstein-Institut and PSDI. Now more and more of the presentations are uploaded in Zenodo. Here I collected the uploads from the last week from this meeting. As you will see, the cooperation on the topics of ontologies and controlled vocabularies is great.

Classifying chemical reactions can be complicated due to the existence of side reaction that should be documented. Here NFDI4Cat is showing a solution, how this problem can be tackled. So if you are looking for a deep dive into chemistry/catalysis and how this situation could be improved by classification via functional groups with the use of SHACL and SAPRQL you should take a look at the presentation by Hendrik Borgelt.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17831171

Interested in how to add domain-specific metadata to a dataset? For chemistry data, NFDI4Chem and NFDI4Cat demonstrate how this can be done with Chem-DCAT-AP, an extension to DCAT-AP. While DCAT-AP allows providing additional metadata in a generic manner. Chem-DCAT-AP adds requirements shared by NFDI4Chem and NFDI4Cat (e.g. Reaction, Yield and more) and standards like Minimum Information Standards (like. MARGARITAS) can be formalized.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17880056

Do you need an introduction into the semantic web? The check-out this presentation by PSDI and NFDI4Chem, they provide a general introduction into the topic and then present more chemistry-specific things like the Chemical Markup Language (CML) and go into details of ontologies best practices, barriers and how collaboration helps to build a better future.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17831367

Need an update on the Galaxy platform and how RO-Crate can helps to publish results? Then this presentation by PSDI is for you:

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17864778

NFDI4Chem

“This is my data, I don’t want to share it.”

There are many reasons why researchers think they cannot share their data. Theo Bender from NFDI4Chem collected some of the reasons (which you have probably also heard a lot) and gave some answers. Maybe this can be useful for your next consultation 😉 So check out the article publish in ChemistryViews, and no worries it is not chemistry-specific so just give it a read. Do you agree with all the answers by Theo Bender?

Link to article on the ChemistryView webpage 

Single files download and Git integration – A new RADAR4Chem version

A new version of RADAR4Chem (repository for chemistry-specific data) was published, most significant changes: single file and folder download is now available and GitHub/GitLab support is now generally implemented, for all updates check the article.

Link to article on the NFDI4Chem webpage

NFDI4Earth

With examples to cultural change in science

I think most people would agree that, if we want to be successful with implementing the FAIR principles and Open Science, we need a cultural change in science. During the CoRDI meeting earlier in 2025 the CC-BY-US@NFDI group gave a presentation on cultural change. One way to introduce this needed cultural change is by demonstrating successful examples. In the presentation, five examples are mentioned and two are shown in more detail. One of their conclusions:

Sustainable cultural change requires aligning technical solutions with researchers’ daily practices while embedding long-term institution commitments and stakeholder buy-in.

If you are interested in the other conclusions as well as the work of CC-BY-US@NFDI check out the presentation and/or visit the website of CC-BY-US.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17628977

Link to website of CC-BY-US@NFDI

AI in Earth System Sciences (ESS)? An update on HPC usage in ESS

Interested in an update on HPC usage in Earth System Sciences (ESS)? Check out the poster by Jonas Eberle et al. newly uploaded in Zenodo. They identified four challenges: 1) Data lakes for data science, 2) Indexes & Catalogues, 3) FAIR AI in ESS, 4) Data/Storage Projects at HPC Centres.

Link to poster in Zenodo with DOI: 10.5281/zenodo.17854324

HPC in ESS – Activity report

A useful summary for people who are eager to know more about HPC in ESS and the activities of NFDI4Earth in this field. You will find useful links for more information and projects like CAPICE (Combined Analysis and Publication of ICE sheet data). One of the most difficult challenges, to no surprise, the large datasets for which the repositories are not ready yet.

Link to the report in Zenodo with DOI: 10.5281/zenodo.17721242

A lasting network of education and training sites

We stay with reports by NFDI4Earth, this time regarding education and training sites of NFDI4Earth. The report seems to be from September 2024, but was recently published. It deals with the “concept for establishing and maintaining a network of NFDI4Earth education and training sites”, so called EduHubs. “EduHubs are partner sites which offer NFDI4Earth-related education and training services on a long-term basis.” The concept sound very interesting to me, specially with the EduPortal which will provide an overview of all events offered by the different EduHubs. If you are active in teaching and training of RDM, then you should definitely take a look at the report. Currently, three of these hubs are established: Hamburg, Munich and Münster.

Link to report in Zenodo with DOI: 10.5281/zenodo.17866245

Questionnaire for training evaluation

Staying with the topic of education and training, it is not only important that trainings are offered, but that they are evaluated and checked for usefulness. NFDI4Earth has now published the results from some of their workshops and developed a general questionnaire they will use from now on. Flagging this for everyone who is looking for a general questionnaire or some insights from other evaluations to boost your own workshops.

Link to report in Zenodo with DOI: 10.5281/zenodo.17860036

NFDI4Earth approved, a label for trusted repositories

Now to a more recent report by NFDI4Earth on their development of a label for “assessing the technical interoperability and trustworthiness of repositories” for ESS. The label should make it easier for researcher to find a trustworthy repository. In the report you can read more about the current developments, discussions about the label, how a repository can get the label as well as check out the current design. What do you think? And could we even think a little bit bigger with labels for the different disciplines, beyond ESS? Or is the CoreTrustSeal enough?

Link to report in Zenodo with DOI: /10.5281/zenodo.17856067

Ensuring quality support

Curious about the support of NFDI4Earth and how it is organized? Then check out the last report by NFDI4Earth is on their Concept for Quality Improvement of the User Support Network. If you are active in an RDM helpdesk or other first level support, then this could be quite helpful/insightful for you. So check it out:

Link to report in Zenodo with DOI: 10.5281/zenodo.15196214

PSDI

The PSDI terminology

One key aspect in this week’s News Digest are controlled vocabularies, and so we are coming back to the topic. In a presentation recently uploaded in Zenodo, PSDI is presenting how they handle metadata, they discuss the PSDI terminology and how it helps to work in a structured way in PSDI. Definitely worth checking out.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17904604

Deep dive into classification systems and their usage in PSDI

If you need an even deeper dive in to classification systems, their differences and how they can help PSDI to describe the resources in their catalogue then check out the following report. I would say this is definitely an insightful report, but aimed at people that are familiar with classification systems and how to benefit from their use.

Link to the report in Zenodo with DOI: 10.5281/zenodo.17867652

Data Stewards, Digital Tools & Ethical AI in Academia

You are a data steward or RDM professional (however you cal yourself) then it is probably worth the time to check out the following presentation on Data Stewards, Digital Tools & Ethical AI in Academia, and if you haven’t heard of CaSDaR (Careers & Skills for Data-driven Research), you definitely should check it out.

Link to presentation in Zenodo with DOI: 10.5281/zenodo.17866517

Electronic Lab Notebooks

How to select the right centralised ELN solution?

Sven Paßmann and Fadwa Alshawaf from the Berlin University Alliance (BUA) published their insights on the evaluation of electronic lab notebook solutions for BUA. The broad spectrum of science in the BUA makes it challenging to offer a centralised software, and a balance between flexibility and specific functions is needed. If you are responsible for establishing an ELN or want to start to offer an ELN, then you should check out this report. It is a great overall resource discussing challenges between having a specialised solution and a more general option. At the end of the report, they also provide collected information about different ELNs, which is always very helpful. So, take a look:

Link to the publication in Zenodo with DOI: 10.5281/zenodo.17876025

Software

FAIRmat

NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems v1.10.7
Link to release notes on GitHub
Link to software in Zenodo with DOI: 10.5281/zenodo.17879394

Outro

Thank you very much for reading this week’s News Digest. Before I close, I want to let you know that I really enjoy working on the overview, but they are taking quite some time to collect and write. So I decided to open a ko-fi page. If you benefit from this weekly overviews, and it is possible for you, I would be deeply grateful if you support me with a tip on ko-fi (follow the button below). Your support allows me to put more time in to the News Digest and improve it each week. Thank you so much.

That is it for today. See you next week.

Benjamin