Happy New Year and welcome to the News Digest 2025. Your overview of news, updates and more in the field of research data management in natural sciences. In 2024, I posted the News Digest each Friday with an overview of the past week. From now on, I will post the News Digest of the past week on Monday. So you can start your week right!

I am very much looking forward to all the great things in 2025. So let us dive in directly.

Paper on Chemical Data Extraction

How can we get data out of a scientific paper? In a new article published by members of the FAIRmat consortium, it is shown how large language models (LLMs) can help with this task. I have to say, it is an excellent introduction for someone like me, who has no idea how LLMs actually work. The best thing is, that they not only provide the article, but they also added a Jupyter notebook, so you can follow along, and there is a short recording published on YouTube to help get the Jupyter notebook running. Great work, and if you are interested in LLMs and how we can use them to get data out of scientific publications: check it out!

Article: https://pubs.rsc.org/en/content/articlelanding/2025/cs/d4cs00913d
Online book: https://matextract.pub/
Jupyter notebook: https://hub.nfdi-jupyter.de/hub/login?next=%2Fhub%2Fshare%2Fuser_options%2F5DsDAINJwu4
YouTube: https://www.youtube.com/watch?v=l-5QNUo1fcU

Zenodo

New versions of the NOMAD Measurement Plugin as well as the software NOMAD CAMELS were published. At the end of last year, we saw already quite some activity for the NOMAD plugin, as well as CAMELS. If you would like to know more about the changes here, you can find the changelogs:
NOMAD Measurement Plugin – https://github.com/FAIRmat-NFDI/nomad-measurements/releases
NOMAD CAMELS – https://github.com/FAU-LAP/NOMAD-CAMELS/releases

If you are unfamiliar with NOMAD, a tool to “manage and share your material science data”, then you should definitely check out the last new upload. These are slides from a lesson dealing with research data management in material science, FAIRmat and NOMAD with great examples and use cases. It is definitely worth checking out. You can also check the webpage (https://nomad-lab.eu/nomad-lab/). There, you can also find more information about NOMAD CAMELS (https://nomad-lab.eu/nomad-lab/nomad-camels.html), an “open-source measurement software targeted towards the requirements of experimental physics” that allows implementing “instrument communication without programming skills”.

NOMAD Measurements Plugin [Software]
https://doi.org/10.5281/zenodo.14628577

NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems [Software]
https://doi.org/10.5281/zenodo.14615231

Revolutionizing Materials Science through Data-Driven Approaches and FAIR Principles [Lesson]
https://doi.org/10.5281/zenodo.14551614

3rd Ontologies4Chem Workshop Recordings available

In the last News Digest of 2024, we looked at the report by NFDI4Chem on the 3rd Ontologies4Chem workshop (see here for the report: https://www.nfdi4chem.de/3rd-ontologies4chem-workshop-2024/). In the report, it was promised that the recordings of the talks will be shared on YouTube. These recordings are now available. You can check out the first video of the playlist right here, or go to YouTube for the complete playlist: https://www.youtube.com/playlist?list=PLlTKDYkC1Ls9wZYRUKW0b743EMOkbWucD

Zenodo

If you want to or need to publish your data, there is always the question of which repository to choose. For chemistry, the NFDI4Chem has a list of core repositories that can help you to easier find the right one for you. The uploaded presentation goes into more detail about these repositories and highlights the more general repository RADAR4Chem. It goes into detail on how to use it, the advantages and much more. If you work in the field of chemistry and looking for the right repository, you check out this presentation.

HeFDI Data Talk: NFDI4Chem Core Repositories and RADAR4Chem [Presentation]
https://doi.org/10.5281/zenodo.14184982

Zenodo

Two reports were published by NFDI4Earth, the first one is on the software architecture in the NFDI4Earth project and the second one is the documentation of a workshop discussing data management plans (DMPs) in earth system science. The later one not only has the results of the workshop, but also the slides from intuitions that participated in the workshop. Very interesting, especially regarding the point of how to integrate the DMP4NFDI Basic Service into a consortium.

NFDI4Earth Software Architecture Documentation [Report]
https://doi.org/10.5281/zenodo.14534839

NFDI4Earth x DMP4NFDI Basic Service Online Workshop 2024 Report [Report]
https://doi.org/10.5281/zenodo.14534702

Zenodo

PSDI participated in the 3rd Ontologies4Chem workshop by NFDI4Chem and NFDI4Cat (https://www.nfdi4chem.de/event/3-workshop-ontologies4chem-ontologies-for-chemistry/). The slides from the workshop are now available and show how PSDI deals with metadata and how they handle their vocabulary. You can find a recording of the talk in the provided playlist in the section for NFDI4Chem.

Introduction to PSDI Metadata [Presentation]
https://doi.org/10.5281/zenodo.14609504

Zenodo

A new version of the Python tool collection for analyzing physics data was published. You can find the changes listed on Zenodo and in the change log on GitHub: https://github.com/LatticeQCD/AnalysisToolbox/releases.

LatticeQCD/AnalysisToolbox: v1.2.3 [Software]
https://doi.org/10.5281/zenodo.14538126

Outro

That was is for today and the first News Digest in 2025. Thanks for reading and see you next week!

Benjamin