Changes in our Advisory Boards

This year we also had two changes in the composition of our advisory boards.

In October Prof. Ulrike Holzgrabe, Institute of Pharmacy & Food Chemistry, University of Würzburg and representative of the German Pharmaceutical Society (DPhG), has retired from our National community advisory board. We thank Prof. Holzgrabe very much for her time and support for NFDI4Chem.

Prof. Stefan Laufer

As her successor we welcome Prof. Stefan Laufer, Pharmaceutical Institute, Eberhard Karls University Tübingen as new member of the National community advisory board, representing DPhG and the pharmaceutical community. Prof. Laufer obtained his PhD in pharmaceutical chemistry at the University of Regensburg in 1989. He was appointed to Chairman for Pharmaceutical Chemistry and Head of Medicinal Chemistry at the University of Tübingen in 1999. He is member of the DPhG (President 2016-2019, Vice President 2012-2015) and author of more than 500 publications.

Dr. Josef Eiblmaier

The second change was in the Industry advisory board. We warmly welcome Dr. Josef Eiblmaier from OSTHUS. Dr. Eiblmaier obtained his PhD in chemistry at the TU Munich in 1998. He has worked at InfoChem GmbH as developer, project manager and was part of the InfoChem management team. Since 2021 he has been working as a management consultant at OSTHUS in Aachen. The addition of Dr. Eiblmaier strengthens the expertise in data standards and data management in R&D in the chemical industry.

New Participants NFDI4Chem

We are very pleased to welcome Prof. Jürgen Pleiss, Institute of Biochemistry and Technical Biochemistry at the University Stuttgart as new participant in the NFDI4Chem consortium.

Prof. Pleiss is a member of the committee “Research Data & Software Management” of the Cluster of Excellence “Data-integrated simulation science” (EXC 2075), PI of the INF project within CRC 1333 “Molecular heterogeneous catalysis in confined geometries”, and developed the standardised data exchange format EnzymeML, which is the basis of an RDM infrastructure in enzymology and biocatalysis. Prof. Pleiss and his team will contribute namely to task areas 2, 4 and 5. This includes contributions to design of chemotion ELN for the subdiscipline of Biochemistry with EnzymeML platform for RDM of enzymatic data in TA2. In addition, Prof. Pleiss and his team will link NFDI4Chem to the enzymology community.

In TA4, EnzymeML will serve as a showcase to demonstrate the benefits of good scientific data management practice, with concepts that are transferable to describing non-enzymatic reactions. Finally, the training courses in research data management, which Prof. Pleiss and his team have put together, will enhance the existing and continuously growing training portfolio of NFDI4Chem under TA5.

Call for participation: Vibrational Spectroscopy Ontology Working Group

Until now the focus of NFDI4Chem and Ontologies4Chem was mainly contributing to existing ontologies, improving the quality and extending their scope. Our latest activities included the Ontologies4Chem Workshop.
Together with domain experts from chemistry we recently have identified the need for an ontology to describe Vibrational Spectroscopy and related devices, methods and data.
The Vibrational Spectroscopy Ontology (VIBSO) is our first joint project conducted by domain experts from Analytical Chemistry and ontology experts.

VIBSO is a community effort. We plan open, regular meetings of the development team to work on and discuss about VIBSO. These meetings will be open to anyone interested.

You are working in the field of Vibrational Spectroscopy and are interested in enhancing the way you handle your data?

Join our first public call on VIBSO 13th December 2022, 2 pm CET.

Agenda: Vibrational Spectroscopy Ontology (VIBSO) development call | Rolling Agenda

Further reading: VIBSO documentation

Workshop: Ontologies4Chem

The first Ontologies4Chem Workshop organised by NFDI4Chem took place on September 7th – 8th 2022. Over 50 international participants accepted the invitation to the online event. The overarching aim of the workshop was to bring together experts from various ontology projects with domain/ontology experts, software developers and service providers from NFDI4Chem and other NFDI consortia related to chemistry.

Focus on reports and discussion

A brief introduction of NFDI4Chem and our previous work on identifying ontologies relevant to the NFDI4Chem context was the first item. After that, The focus of the first day of the workshop was on reports and discussion of the current state and future plans of most of the relevant chemistry ontologies (CHEMINF, Chebi, ChIRO, EDAM, CHEMROF, OBI, SIO, CHMO, RXNO, MOP) presented by their curators. The IUPAC Gold Book as definition source complemented the presentation of the ontologies. As an additional perspective, NFDI4Cat and NFDI4Health presented their plans and application of ontologies.

The first day closed with an update on tools like ROBOT, NFDI4Chem Terminology Service and ODK, used for developing and working with ontologies. The second day of the workshop was focused on exchanging experiences and discussing best practices in ontology development and curation as well as on data annotation using ontologies. It began with previous work done in NFDI4Chem towards Raman & NMR spectroscopy and future developments for the Terminology Service. Ontology development workflows in NFDI4Cat followed, extending towards chemistry, the IUPAC FairSpec project, the application of ontologies in Pubchem and ClassyFire framework. The day ended with two parallel breakout sessions for deeper discussions and hands-on demonstrations on data annotations and ontology curation.

The next steps

The most important outcome of the workshop was a wide agreement on working closer together with the involved communities. The aim is to improve the quality of existing chemical ontologies and involve more experts in the field. A mailing list and a dedicated chemistry channel in the OBO Slack were launched to stay in touch and plan the next steps.

There will be a second Ontologies4Chem Workshop in 2023! 

Further links:
Slides of the presentations are available from the workshop agenda and joint notes.
Recordings of the presentations are available on NFDI4Chem YouTube channel

Ontologies4Chem: The Landscape of Ontologies in Chemistry Published

Why are ontologies an essential building block not only for NFDI4Chem, but all NFDI?

FAIR data is all about human AND machine-readable data. Ontologies are used to semantically describe data, information and knowledge in a domain. Terms, relationships, and logic described in an ontology enable us to semantically annotate and link data to create knowledge graphs. Quite a few chemical ontologies already exist to describe molecules, reactions, the role of molecules in reactions and analytical procedures. These semantic descriptions take data to the next level, making them machine-understandable.

Grafic of different descriptors in chemistry

To address the application of ontologies in research data management we recently published an overview of ontologies in chemistry suitable to represent concepts of research and research data in Pure and Applied Chemistry. The reviewed ontologies were evaluated against several criteria derived from the FAIR data principles and their possible application in the digitisation of RDM workflows. To summarise our criteria shortly; to be included an ontology had to be made by domain experts, published and maintained in a FAIR way, being actively and openly maintained as well as being used in established applications.

Read more: P. Strömert, J. Hunold, A. Castro, S. Neumann, O. Koepler, Ontologies4Chem: the landscape of ontologies in chemistry, Pure Appl. Chem. 2022, doi: 10.1515/pac-2021-2007.

Ontologies4Chem Workshop

September 7 & 8, 2022, 14.00 – 18.00 CEST, Online

Ontologies are a cornerstone of FAIR machine-readable data. They provide terms, relations and logic to semantically annotate and link research data building knowledge graphs. Integrating ontologies into electronic lab notebooks, data repositories and software tools enables users to create rich annotated data from the very beginning. In the past, several ontologies with relation to the chemistry domain have been developed. In Task Area 6 Synergies we evaluate the application of these ontologies for research data management, identify gaps and initiate the development of missing ontologies.

To our first Ontologies4Chem Workshop we invite ontology curators, ontology engineers, software and data repository developers and domain experts currently applying ontologies or with an interest to do so in the future.

Aims of the workshop are:

  • Deepen and/or establish collaboration between ontology curators and NFDI4Chem + other NFDI consortia related to chemistry
  • Develop joint strategies: ontologies for research data management and beyond
  • Application of ontologies in research data annotations
  • Inspire service developers and data repository developers to use ontologies
  • Inspire chemists to use ontologies
  • Work concretely on ontologies

The first day will offer flash talks about current and future developments on ontologies and ontology tools. The second day will be all about best practice and two hands-on sessions on ontology curation and data annotation using ontologies.

Registration is open now.

Event Throwback: Minimum Information Standards, NFDI4Chem Takes the International Stage – Part I

Efforts for the development of minimum information standards for research data in chemistry have to be addressed in an international context. Thus, Dr. Johannes Hunold (TIB) presented NFDI4Chem’s vision for terminologies and semantic annotation of research data in the “Gold Book project session” dedicated to the IUPAC Compendium of Chemical Terminology (informally known as “Gold Book”) at the 51st IUPAC General Assembly, from August 9-15. In his talk Dr. Hunold outlined the impact and interdependence of the current development of chemistry terminologies and a terminology service by NFDI4Chem on the latest activities around the Gold Book. Participants of the session thoroughly discussed the results of the “Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website” project and the next steps toward further semantification of the Gold Book and its role in the context of ontology development (see project “Development of an IUPAC Recommended Term Management System for Expansion of the Coverage of the IUPAC Compendium on Chemical Terminology“). The participants agreed that the Gold Book should continue to serve as a “source of truth” and uniform standard for the definition of relevant terms in the field of chemistry to be reused in chemistry ontologies whenever possible.

It was agreed that terminologies in particular play an important role in the implementation of the FAIR data principles and a sustainable RDM. The editing and semantic annotation of research data will be an elementary part of the everyday research process in the future. This will lay the foundation for machine-readable data and the application of methods such as machine learning.

Long-term, well-funded and community-driven infrastructure projects such as NFDI4Chem are important key players to support IUPACs mission in the implementation process of chemical standards in the digital domain.

With Prof. Dr. Christoph Steinbeck joining the CPCDS committee (Committee on Publications and Cheminformatics Data Standards) in January 2022, the NFDI4Chem consortium will be able to contribute even more directly to the standardisation of research data management in the field of chemistry.

NFDI4Chem Terminology Service Launched

NFDI4Chem proudly announces the launch of its Terminology Service for the Chemistry community. 

What is it good for, you ask?

As you probably know, the FAIR data principles play a key role in the development of the NFDI. Specifically, one  of the principles calls  for rich metadata describing data by using a formal, accessible, shared, and broadly applicable language for knowledge representation. The ambiguity of natural language words and phrases used to annotate data with their meaning has been a major obstacle so far. Here we can achieve a significant improvement through the application of domain-specific terminologies which allows us to unambiguously annotate data semantically. Standardised vocabularies mapped across the various disciplines enable real data interoperability, discovery and exploitation beyond our own domain.

Our Terminology Service provides such chemistry specific terminologies or ontologies. This enables researchers, software tools and services of NFDI4Chem to create machine- and human-readable descriptions of research data.

The first release of the Terminology Service facilitates exploration and browsing of existing ontologies in chemistry. You can search for terms and their usage in the different ontologies. Additionally, you can view ontology statistics and associated descriptive metadata or download ontology files. Various visualisation options are available to explore an ontology and the relations of terms. The curation function supports the suggestion of new ontologies or the recommendation of missing terms to the curator.

The Terminology Services further provides an extensive API to be used by other services and software tools. One example is the integration of terminologies when using the chemotion ELN to annotate experimental descriptions with terms of name reactions in organic chemistry from the RXNO ontology. RXNO provides a controlled vocabulary to unambiguously describe applied reactions. The encoded semantics, logic and taxonomy of reaction classes enable semantic queries on annotated data in the future. In the same way data repositories can use the Terminology Service to support the semantic annotation of research data during the upload process.

In the future this approach will enable interoperability of heterogeneous databases and cross-database semantic search. This will allow to overcome the limitation of keyword based searches moving to a search using the meaning of a keyword instead. 

The first release of the Terminology Service provides 18 ontologies identified to be useful for NFDI4Chem. It will be further developed in the future to include more ontologies, extended features, and linking tools for ontology curation and design.

If you have suggestions for terminologies / ontologies to be added or are interested in joining NFDI4Chem ontology activities, please contact

The Terminology Service is developed and maintained by TIB – Leibniz Information Centre for Science and Technology. As one of the infrastructure partners within NFID4Chem TIB leads the activities of Task Area 6 – Synergies.

NFDI4Chem statement on Cross-Cutting Topics

The NFDI offers the opportunity to establish a science-driven, open, and high-quality national research data infrastructure. In August 2019, members of 11 consortia met to discuss common challenges posed by envisioned interoperability and data sharing across disciplines. As an important structural element for sustainable functionality of the NFDI, Cross-Cutting  Topics and their joint elaboration have been identified. As a first result 21 consortia agreed on a common list of cross-cutting topics, published in the Berlin declaration.

Since then, a number of initiatives have developed which address central issues of infrastructure development and in this way aim to support the discipline-oriented consortia in setting up the NFDI.

In February 2020, members of 14 consortia and 7 cross-cutting initiatives therefore met to discuss opportunities and challenges for a joint development of a national research data infrastructure.

NFDI4Chem welcomes and supports collaborative development of the Cross-Cutting Topics. We have therefore decided in agreement with the DFG to publish the chapter „The Consortium within the NFDI“ on the Cross-Cutting Topics describing our ideas and approach from the NFDI4Chem proposal as a contribution to an open and joint discussion of Cross-Cutting Topics. We hope that other consortia will follow suit and that we can jointly push forward the development of this important structural element of the NFDI.

You can download the PDF from our Downloads page.