Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management

In the age of scientific digitization, ensuring data is Findable, Accessible, Interoperable, and Reusable (FAIR) is crucial for machine-processable data. Ontologies play a vital role in achieving data FAIRness by representing knowledge in a machine-understandable format. Catalysis research data is often complex and diverse, requiring a broad collection of ontologies. While existing ontology portals aid in ontology discovery, they lack deep classification, and quality metrics specific to catalysis research ontologies are absent.

This work from Alexander Behr, Hendrik Borgelt and Prof. Dr. Norbert Kockmann from our partner TU Dortmund proposes a systematic approach for collecting ontology metadata focused on the catalysis research data value chain. Ontologies are classified by subdomains of catalysis research, enabling efficient comparison. A workflow and codebase are provided to represent metadata on GitHub, along with a method to automatically map ontology classes, offering insights into relatedness. The methodology is designed for reusability and can be adapted to other ontology collections or knowledge domains. The ontology metadata and code developed are available in a GitHub repository: https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat.

If the summary has piqued your interest, you can find the paper here.

A vocabulary for all areas of catalysis initiated in NFDI4Cat. Starting with photocatalysis we add more and more terms from other areas of catalysis and related disciplines like chemical enineering or material science.

With the help of Susanne Arndt from the Leibniz Information Centre for Science and Technology University Library, we have succeeded in publishing this great tool.

You can find it here.

 

In the field of catalysis research, microkinetic modelling is an important tool for understanding surface kinetics and developing efficient catalysts. However, its development traditionally requires expertise, resources and time.

To overcome this challenge, automation is becoming a transformative force. Recent advances in digital tools and software are streamlining the process and accelerating model development and validation. By automating tasks and harnessing computational power, researchers can explore a wider range of catalytic systems efficiently and with fewer errors.

This shift towards automation heralds a new era of catalysis research characterised by accelerated discovery and improved precision. The further development of automation promises to have a profound impact on catalysis research, opening up unprecedented opportunities for innovation and progress.

A KIT team led by our partner Prof. Dr. Olaf Deutschmann, consisting of Rinu Chacko, Dr. Hendrik Gossler and Dr. Sofia Angeli, has published an exciting new paper in ChemCadChem on this topic. The title is “Interconnected Digital Solutions to Accelerate Modeling of the Reaction Kinetics in Catalysis”. You can find the full paper here.

The Werner Siemens Foundation (WSS) has announced a long-term “project of the century” in which a research centre for the development of catalytically driven production processes for a multidimensional circular economy in the chemical industry is to be established. A total of 123 ideas were submitted for the project by researchers from Germany, Austria and Switzerland.

The “catalaix: Catalysis for a circular economy” project was selected for a grant of 100 million Swiss francs over ten years. It aims to enable the efficient recycling of plastic mixtures and the reuse of molecular building blocks in a versatile, flexible circular economy.

The centre, will be led by Professors Regina Palkovits and Jürgen Klankermayer from RWTH Aachen University, will focus on the development of new catalysis processes for the targeted degradation and reuse of products at the end of their life cycle. This initiative is intended to make a significant contribution to the sustainable transformation of the chemical industry and was launched as the Werner Siemens Foundation’s largest project to date.

We are proud to call Regina Palkovits part of our NFDI4Cat team and wish her and Jürgen Klankermayer every success in this exciting and promising project.

If you are interested, please read on here.

© WSS

NFDI4Cat and Chemistry Europe are proud to announce Dr. Mark Doerr as the winner of the Digital Chemist Award 2023. Jointly presented by NFDI4Cat and Chemistry Europe, this award underlines the importance of the FAIR principles – Findability, Accessibility, Interoperability, and Reusability – in scientific research.

 

Dr. Mark Dörr: The Winner’s Profile

A biochemist and programmer by profession, Dr. Doerr works at the University of Greifswald’s Department of Biotechnology & Enzyme Catalysis, in the group of Prof. Dr. Uwe T. Bornscheuer. His focus is on deep, mechanistic understanding of biocatalysts, which can also be tailored for industrial applications. The award, presented during the Annual Digital Catalysis-Related Sciences Conference 2023 (ADCR 2023) in Frankfurt am Main, Germany, celebrates his innovative work on LARAsuite.

 

“Special thanks to my wife and family for their unwavering support and to Stefan Born, Stefan Maak, Prof. Dr. Uwe T. Bornscheuer, the KIWI-bioblab and the NFDI4Cat TA1-3 teams for their invaluable support, as well as to the brilliant developers behind the tools that form the backbone of LARAsuite, your contributions have been instrumental in my journey.”  – Dr. Mark Doerr

 

LARAsuite: A Revolutionary Tool in Digital Chemistry

Dr. Doerr’s award-winning innovation, LARAsuite, is a comprehensive assembly of applications, databases, open communication protocols and tools aimed at enhancing and simplifying scientific research. It’s not just another Electronic Lab Notebook (ELN); it’s a next-generation, modular platform designed to cover all aspects of laboratory work, dramatically reducing the burden of manual documentation. LARAsuite excels in automated handling of large datasets, with a focus on Design-of-Experiments, AI, and machine learning applications. LARAsuite stands out as a comprehensive publicly accessible toolkit for the scientific community, aiming at scientists who can focus on their creative and explorative work, not on documentation.

 

Key Features of LARAsuite

1. Modularity and Versatility: It encompasses a range of modules that represent various aspects of scientific work. It seamlessly merges the modularity of the open-source software Django with the concepts of the linked data/semantic web realm. As a result, data from LARASuite automatically build knowledge graphs, a feature not commonly found in other ELNs.
2. Uniform Framework: LARAsuite aims to encapsulate all laboratory work steps within a standardised framework, using open communication protocols and data formats like SiLA2, JSON-LD (SciDat) and AnIML.
3. Integration with Robotic Platforms: Its ability to integrate with robotic platforms for high-throughput catalyst development is a testament to its advanced capabilities in managing control and data in complex, modern automated laboratory environments.
4. Education and Outreach: Dr. Doerr extends his expertise through his YouTube channel, educating users on the effective utilisation of LARAsuite.

 

About the Digital Chemist Award

The NFDI4Cat – Digital Chemist Award is not just an accolade; it’s a mission to empower scientists in chemistry, catalysis, and materials science. It underscores the importance of understanding and implementing the FAIR principles – Findability, Accessibility, Interoperability, and Reusability – in research. This initiative by NFDI4Cat and Chemistry Europe rewards scientists who have pioneered these principles with a cash prize, awarded by hte GmbH and BASF SE, and promoting their groundbreaking work.

The announcement of Dr. Doerr’s accomplishment was a highlight of the ADCR 2023, held at DECHEMA House in Frankfurt am Main. Here, the scientific community celebrated the intersection of digital innovation and catalysis research.

The presentation ceremony saw Dr. Katrin Friese from BASF SE and Prof. Stephan Schunk from hte GmbH joining hands with representatives from Chemistry Europe – Dr. Charlotte Gers-Panther and Dr. Sandra Gonzales Gallardo, along with NFDI4Cat’s spokesperson Andreas Förster, in honouring Dr. Doerr’s groundbreaking work.

 

Next Steps

Chemistry Europe has invited Dr. Doerr to write a “Perspective” article for ChemCatChem, presenting his innovative tool. Additionally, Dr. Doerr will be featured in a virtual symposium for Chemistry Europe, further raising awareness of the importance of the FAIR principles, Research Data Management (RDM), and data sharing in the field. The date will be announced soon….

 

Dr. Mark Doerr’s achievement in developing LARAsuite is a significant milestone in the realm of digital chemistry. It is intended to inspire the community to contribute and extend this framework for a next generation of science. His work exemplifies the essence of the Digital Chemist Award, advancing the application of the FAIR principles in a practical, innovative, and accessible manner. His contribution is not just a tool for today’s scientists but a foundation for the future of digital catalysis and catalysis-related sciences.

In the world of scientific research, data is the lifeblood that fuels innovation and discovery. However, different disciplines often face unique challenges when it comes to managing and utilizing this valuable resource. On September 29, the inaugural workshop, hosted by the Physical Sciences in NFDI colloquium and facilitated by NFDI4Chem, NFDI4Cat, DAPHNE4NFDI, and FAIRmat, took a significant step toward addressing these challenges. The event sought to foster cross-disciplinary understanding by illuminating shared perspectives and objectives.

 

Webinar Highlights:

• Exploring FAIR Data Principles: The webinar was an engaging journey into the world of FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Our expert speakers illustrated the tools with which these principles can be applied to benefit researchers across diverse NFDI consortia.
• The Advantages of FAIR Data Principles: Our speakers emphasized the critical importance of adhering to FAIR data principles. These principles enhance data management, foster collaboration, and accelerate scientific breakthroughs, offering valuable insights into the future of research.
• Challenges and Solutions: Attendees actively participated in thought-provoking discussions about the challenges encountered in achieving FAIR data principles. Together, we explored innovative solutions that have the potential to reshape the landscape of research data management.

Incredible Participation: Over 50 participants from around the globe enriched our discussions with their invaluable contributions during the Q&A sessions. The event was truly a gathering of bright minds!

Webinar Resources: The presentation slides are accessible at Unlocking the Potential of Data – FAIR Data Principles in NFDI (zenodo.org), allowing interested audience to delve deeper into the content.

A recording of the talk is uploaded on our Youtube channel:

 

International Collaboration: Prof. Jennifer Strunk’s Insights from the Collaboration with Hokkaido University

We are delighted to share the invaluable experiences of Prof. Jennifer Strunk during her collaboration with Prof. Keisuke Takahashi in Japan. Through her partnership with the esteemed Hokkaido University, Prof. Strunk has made a significant contribution to advancing the goals of NFDI4Cat on an international scale. Join us as we explore the enriching outcomes of this fruitful cooperation!

In December 2022, Prof. Jennifer Strunk and Dr. Abdo Hezam Mohsen traveled to Sapporo for one week to interlink the activities in NFDI4Cat with Prof. Keisuke Takahashi, who is one of the leading international experts in the field of “Data Science in Catalysis”.

The aim of the visit was to compare the ontologies and databases developed and to be further developed in NFDI4Cat with the ongoing databases of the Takahashi group, using the example of “halide perovskites” in photocatalytic applications. However, the latter are not thematically broad, as is the goal in NFDI4Cat, but relate very closely to the research topic of heterogeneously catalysed methane activation. The approach in NFDI4Cat can consequently be described as “top down”, whereas here a more “bottom up” approach was followed.

In Japan, the collaboration followed a specific division of labor: Jennifer Strunk worked on ontology development with Dr. Lauren Takahashi, focusing on their expertise. Meanwhile, Abdo Mohsen teamed up with Keisuke Takahashi to handle database work, including data extraction and integration into machine learning. The topic of photocatalysis brought by the German team was novel and introduced fresh perspectives to our Japanese partners.

During the collaboration, a profound understanding of each other’s perspectives was achieved, and the ontology development was effectively visualized. Abdo Mohsen learned the structure of the database, the automated extraction of the data, and he applied it to an Excel spreadsheet he brought with him based on literature data on the photocatalytic activity of halide perovskites. The machine learning itself failed, but this led to the crucial realization that the data reported nowadays in scientific publications are insufficient. There is a lack of negative results, and insufficient detail in the reporting of experimental parameters. Both are important findings to improve the new databases in NFDI4Cat. A publication of the results in a short article (e.g., as a perspective article) is planned.

“The machine learning itself failed, but this led to the crucial realization that the data reported nowadays in scientific publications are insufficient. There is a lack of negative results, and insufficient detail in the reporting of experimental parameters. Both are important findings to improve the new databases in NFDI4Cat.”

– Frau Prof. Jennifer Strunk

Opportunities for specific international exchange are an asset for NFDI4Cat, and the currently advanced development of activities in this area is very positively evaluated. The stay in Japan would not have been possible without the support of NFDI4Cat. Although we developed the suspicion that machine evaluation of literature databases might fail because of the quality of the data itself already before our stay, we were now able to verify it in this collaboration. This laid the foundation to do better in NFDI4Cat. The mutual understanding of scientists in the fields of thermal catalysis (Japan) and photocatalysis (Germany) also helped because the Japanese databases did not include photon-driven processes. The broadening of the knowledge base thus achieved on both sides also advances the field of “data science” as such.