Author: Oliver Koepler

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.

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 Bioschemas.org 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 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. 

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 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.

Find out more at https://terminology.nfdi4chem.de 

If you have suggestions for terminologies / ontologies to be added or are interested in joining NFDI4Chem ontology activities, please contact helpdesk@nfdi4chem.de

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.