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Report from the InChI Technical Sessions in Cambridge, UK

Technical sessions were held in-person and virtually from June 17 to 19 for several of the extension projects for the InChI Standard. Topics covered included organometallics, extended stereochemistry and tautomers.

Notably, the group agreed to maintain metal connectivity in further InChI developments which will solve many problems in the description of molecular inorganic compounds – arguably the most important conclusion of the meeting. If you are interested in the InChI Outreach to receive the latest news and information about the InChI code, please click here.

First Chemistry Paper Using RADAR4Chem

In the research article in the Journal of Computational Chemistry entitled “Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III)” Herres-Pawlis & Leonhardt et al. describe copper model complexes for the entatic state theoretically.

They use the semi-empirical tight-binding method GFN2-xTB, the density functional TPSSh and the double-hybrid functional B2PLYP and evaluate the methods on five different complex pairs (Cu(I) and Cu(II) complexes), and compare how well calculated energies can predict the redox potentials. They find that B2PLYP and TPSSh yield better accordance with the experimental structures but that GFN2-xTB performs surprisingly well in the geometry optimisation at a fraction of the computational cost. TPSSh offers a good compromise between computational cost and accuracy of the redox potential for real-life complexes.

The DFT coordinates have been deposited at the RADAR4Chem repository (dataset). RADAR4Chem accepts every kind of chemical data annotated with their metadata.

Guidelines for Sharing in Chemotion – Published in Chemistry-Methods

Sharing of data with the scientific community plays an important role in conducting FAIR and sustainable research. As an example, reporting experimental results (also negative ones) in a systematic, machine-readable way will enable automated data curation and machine learning processes in the near future.

On the smallest scale, experimental data are shared within laboratories, working groups, or institutions. The electronic laboratory notebook Chemotion provides a sharing feature which allows to share data easily with others on various hierarchy levels and furthermore offers the possibility to generate joint databases for almost every desirable need.

In this publication in Chemistry-Methods, we explain the sharing feature of Chemotion and propose a sharing policy as a best practice model to have a consistent and easily applicable guideline for all scientists in a laboratory, working group, or institution. These guidelines may serve as a foundation and recommendation for other scientists who like to use the ELN Chemotion and its sharing feature.

Read more: F. Fink, H. M. Hüppe, N. Jung, A. Hoffmann, S. Herres-Pawlis,Sharing is Caring: Guidelines for Sharing in the Electronic Laboratory Notebook (ELN) Chemotion as applied by a Synthesis-oriented Working Group, Chem. Methods 2022, doi: 10.1002/cmtd.202200026.

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.

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.

Analytica Conference 2022 in Munich

From June 21 to 24, the world’s leading trade fair for laboratory technology, analysis, and biotechnology, the Analytica, took place in Munich. At the accompanying Analytica conference researchers, scientists, users, and manufacturers from around the world gave talks to promote the interconnection of science and industry. The programme distributed over three days and several sessions focussed as usual on various interdisciplinary and future-oriented topics, e.g. analytics, diagnostics, measurements or biotechnology.

As one of this year’s highlights, the German Society for Biochemistry and Molecular Biology (GBM), the German Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL), and the German Chemical Society (GDCh) dedicated a whole conference day to the topic of Research Data Management (RDM). On June 23 three consecutive sessions chaired by the respective societies featured different aspects of RDM. Within GDCh’s final session “Research Data Management III” Fabian Fink from the Herres-Pawlis group at RWTH Aachen University presented NFDI4Chem and the software Chemotion with its electronic laboratory notebook (ELN) and repository. The presentation slides are published on Zenodo, where they are freely accessible and downloadable. The presentation preceded a talk about the BAM Data Store by Dr. Rukeia El-Atman, a short introduction on The Carpentries by chair Dr. Claudia Beleites, and a panel discussion on the necessity and challenges of RDM. This fruitful discussion between the speakers, the chair, and the audience was a successful conclusion to the particular session and the Analytica conference in general.

Repositories in Profile – STRENDA DB

For chemists, it is crucial to know the advantages of different data repositories in order to find the best fit for their research data requirements. Here, we provide a brief overview of STRENDA DB as part of our series “repositories in profile”.

STRENDA DB – Standards for Reporting Enzymology Data

Figure 1: Screenshot STRENDA DB.

Basic information

❏      Creation date: 2016

❏      Country: DE

❏      Domain: Life Science, Chemistry, Biological and food chemistry, Molecular Chemistry

❏      Usage: Open Access (data view), registration required (data contribution)

❏      Target group: Biochemists, systems biologists, biocatalysts

❏      Number of datasets: 150

❏      Recommended by journals/societies: STRENDA Guidelines by over 55 international biochemistry journals recommended

❏      Listed in: re3data: r3d100012329, FAIRsharing: FAIRsharing.ekj9zx, Wikidata: Q58034053

Functionalities and technical information

❏      Content: Functional enzymology data (kinetic and experimental data)

❏      Content origin: From manuscripts, publications

❏      Searchable content: Enzyme kinetic data along with experimental conditions

❏      Accepted data types: Currently none, EnzymeML (in development)

❏      Used standards/ontologies: DataCite, InChI, EnzymeML (in development)

❏      Curation: Via automated data checking based on STRENDA Guidelines, fact sheet 

         (PDF) with submittable input data

❏      Access rights/license information/embargo: Creative Commons Attribution 4.0 International (CC BY 4.0), Term of Use, no embargo

❏      AAI solution: Internal user administration (user, administrator)

❏      Persistent Identifier system: DOI (Digital Object Identifier), PMID (PubMed Identifier)

❏      Authority identifier system: ORCID (Open Researcher and Contributor iD)

❏      Used Software: Oracle database, multilayer architecture

❏      Interfaces: HTML interface (GUI) 

❏      Further functionalities/tools: Automated plausibility and quality check/peer review

TA-PM Retreat in Berlin

On May 23 and 24 , the FIZ Karlsruhe’s department for mathematics in Berlin hosted the first in person meeting of the NFDI4Chem TA-PMs (task area project managers). The meeting’s agenda featured a general training on OpenProject as well as discussions on various administrative topics.

For those unfamiliar with the operative structure of NFDI4Chem, the leads of all six task areas have appointed one or two task area project managers (TA-PMs) each. They meet on a regular basis, usually every two weeks via Zoom, to complete various administrative tasks, monitor the project’s progress, share success stories and discuss problems being met.

On May 23 and 24, all seven of them (see list and picture below), met in person at the department for mathematics of the FIZ Karlsruhe in Berlin. The busy agenda started with a 1.5 hour training on OpenProject and continued with topics such as format and documentation of deliverables, the upcoming midterm report and general processes in the consortium such as onboarding or management of the project’s file sharing system.

24 hours later, the TA-PMs left the meeting at the German capital with new tasks in their pockets, personal connections forged and a bottle of authentic Hessian “Ebbelwoi”, kindly provided by John Jolliffe.

TAName (partner)
TA1Christian Popp (FSU)
TA2Adam Basha (KIT)
TA3Christian Bonatto Minella (FIZ)
TA4David Rauh (IPB)
TA5John Jolliffe (JGU)
TA5Jochen Ortmeyer (RWTH)
TA6Katharina Hanske (TIB)

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.

Work in Sections/Contribution to the Base4NFDI Proposal

The sections are bodies of the NFDI e.V. in which members of all NFDI consortia work together on various cross-cutting topics of common interest. This spring the sections elected their spokespersons. We congratulate all newly elected spokespersons, particularly of course the members of our own consortium:

Section (Meta)data, Terminologies, Provenance (Metadata)
Spokespersons: Dr. Oliver Koepler (TIB), Jun. Prof. Dr. Brigitte Mathiak (University of Cologne)

Section Education and Training (EduTrain)
Spokespersons: Prof. Dr. Peter Pelz (University of Darmstadt), Prof. Dr. Sonja Herres-Pawlis (RWTH Aachen University)

Section Common Infrastructures (CI)
Spokespersons: Dr. Michael Diepenbroek (Gesellschaft für Biologische Daten e.V. (GFBio e.V.), Prof. Dr. Sonja Schimmler (Fraunhofer FOKUS)

Section Ethical, Legal & Social Aspects
Spokespersons: Prof. Franziska Boehm (FIZ Karlsruhe), Ulrich Sax (Georg-August-Universität Göttingen)

More information about the sections, their agenda and working groups will be published on the NFDI website soon. If you are interested in joining one of the working groups in the sections please get in touch with the responsible spokespersons.

All sections have contributed to the proposal for “Basic Services for the NFDI” Base4NFDI which was submitted as a joint proposal of all 19 NFDI consortia on April 29. Base4NFDI will develop basic services for the NFDI and is the final outcome of the cross-cutting topics discussion across the consortia since the beginning of NFDI in 2019. As a result, more than a dozen topics emerged where NFDI-wide services seem plausible and/or desirable to enable interoperability, achieve synergies and economies of scale and/or cost-efficient development and operation. [ref: https://www.dfg.de/download/pdf/foerderung/programme/nfdi/absichtserklaerungen_2022/2022_base4_nfdi.pdf]

Consortium Meeting 2.5 – Connecting the Dots

On April 28, 2022, members of the NFDI4Chem consortium came together virtually in the morning to reflect on the progress of the project so far. Presentations set around three cross-cutting topics and a session dedicated to additional highlights also allowed for casting an eye into the future of the initiative. Roughly 60 participants from across the consortium were joined by ten members of the initiative’s four advisory boards.

Activities within NFDI4Chem are steadily increasing, resulting in an ever growing output of the consortium. Oliver Koepler, co-speaker of NFDI4Chem, highlighted this nicely in his welcoming remark to the Consoritum Meeting 2.5 on April 28, 2022. His short presentation featured an impressive slide headed “NFDI4Chem in numbers” (see figure 1). A staggering 100.000 messages exchanged on rocketchat and over 100 meetings, workshops, talks etc having taken place since the start of the project, bear witness to the truly communicative nature of the initiative.

Figure 1: NFDI4Chem in numbers.

To better illustrate the interconnectedness of the six task areas in NFDI4Chem, cross-cutting topics formed the backbone to the meeting agenda with contributions from across the consortium. Three sessions titled Metadata4chem, NMR4Chem and BestPractice4Chem featured presentations on the respective areas.

Steffen Neumann from the IPB led the first session. Together with Johannes Hunold, Bhavin Katabathuni and Philip Strömert he followed the flow of metadata in the research data life cycle and discussed models, storage and transport solutions for metadata in chemical research.

To present the work that has gone into FAIRifying data originating from NMR analysis, Johannes Liermann enlisted the help of Steffen Neumann, Nicole Jung, Michael Klix, Philip Strömert and Chandu Nainala. They gave an overview of how NMR data find their way from the lab to repositories and journals.

In the third session on best practices in NFDI4Chem, Nicole Jung with the help of Johannes Liermann and John Jolliffe recapitulated the advantages of ELNs, showcased the NFDI4Chem award and called for a cultural change in how errors are dealt with in academic research.

In the final session on recent highlights, Ulrich Schatzschneider presented TUCAN, a molecular identifier and descriptor that facilitates handling of metal complexes in ELNs.
Next, Kerstin Soltau introduced RADAR4Chem a new, generic repository for chemistry data, which the FIZ, partner in NFDI4Chem, recently launched.

The meeting closed with a lively discussion with questions from consortium members as well as from the advisory board.