Author: Florian Schön

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. In this and upcoming newsletters, we provide a brief overview of individual data repositories in chemistry.

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The Chemotion repository

To support research data management, Chemotion not only offers a freely available electronic laboratory notebook but also a repository for molecules, reactions and research data. The seamless connection between both tools saves a lot of time. The Chemotion repository provides solutions for current challenges to store research data in a convenient manner, allowing the conservation of domain-specific information in a machine-readable format. A main advantage of the repository Chemotion is its comprehensive functionality, offering options to collect, prepare and reuse data with discipline-specific methods and data processing tools. For selected analytical data, automated procedures facilitate the curation of the data. Chemotion provides functions for convenient data publishing including automated Digital Object Identifier (DOI) generation and workflows for peer-reviewing of submissions including embargo settings. The research data infrastructure built on these developments provides a new community-driven repository as a comprehensive alternative to commercial databases.

Learn more about the Chemotion repository in a recent publication in Angew. Chem., or watch our Chemotion “Stammtisch” talk about the repository on YouTube.

Figure 1: Screenshot of the webpage of the Chemotion repository.

The Place for Discussions Around Chemotion and more

In January, our monthly “Stammtisch” on the electronic laboratory notebook (ELN) and repository Chemotion opened with a brief summary of the NFDI4Chem project by Prof. Christoph Steinbeck. Afterwards, Dr. Patrick Hodapp presented the main functions of the ELN Chemotion. In the subsequent gatherings in February and March, Dr. Nicole Jung gave an overview of the Chemotion repository and Dr. Johannes Liermann introduced ontologies, respectively. Recordings of their presentations are available on the NFDI4Chem YouTube channel. Importantly, however, these presentations serve as an introduction for the main, unrecorded part of the “Stammtisch”: an open and wide discussion, in which comments and suggestions for enhancements around Chemotion or RDM in the field of chemistry, in general, are most welcome. These will help NFDI4Chem to improve its services and to best serve the needs of the chemical community. The next “Stammtisch” is scheduled for April 30th. Sign up now and help us improve Chemotion!

Enjoy watching our last presentations on YouTube:

01/29/21: Overview of NFDI4Chem (Prof. Christoph Steinbeck); Introduction to the ELN of Chemotion (Dr. Patrick Hodapp)

02/26/21: Introduction to the repository of Chemotion (Dr. Nicole Jung)

03/26/21: Introduction to ontologies (Dr. Johannes Liermann)

Please be aware that the main part of the Stammtisch is the discussion which is not recorded!

Coming soon:

• Representations of inorganic structures with InChI, SMILES, …
• Overview of the Repository NMRshiftDB

Interested in using Chemotion? Subscribe to the Chemotion YouTube-Channel!

Overview of the Task Areas (TA):

• TA1 – Management: Christoph Steinbeck (Friedrich Schiller University Jena)
• TA2 – Smart Lab: Nicole Jung (Karlsruhe Institute for Technology)
• TA3 – Repository: Felix Bach (Karlsruhe Institute for Technology) & Matthias Razum (FIZ Karlsruhe – Leibniz Institute for Information Infrastructure)
• TA4 – Metadata, Data Standards and Publication Standards: Steffen Neumann (Leibniz Institute for Plant Biochemistry) & Christoph Steinbeck (Friedrich Schiller University Jena)
• TA5 – Community Involvement and Training: Sonja Herres-Pawlis (RWTH Aachen University) & Johannes Liermann (Johannes Gutenberg University Mainz)
• TA6 – Synergies: Oliver Koepler (Leibniz Information Center for Science and Technology TIB Hannover)
  

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Christoph Steinbeck studied chemistry at the University of Bonn, where he received his diploma and doctoral degree at the Institute of Organic Chemistry. His doctoral thesis focused on computer-assisted structure elucidation of organic compounds. Realizing that his research was hampered by the lack of open spectroscopic data, he diverted into creating databases in chemistry and biology and becoming an evangelist of open data, open-source and open science.

It further led him to become head of cheminformatics and metabolism at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. During this time, his group developed production-quality, open chemistry databases for the biosciences, such as ChEBI, the dictionary and ontology of Chemical Entities of Biological Interest, and the MetaboLights database, a repository and reference database for Metabolomics. Steinbeck gained experience in managing large infrastructure projects through leading the European e-infrastructure projects COSMOS (Coordination of Standards in Metabolomics) and PhenoMeNal (large scale computing with human metabolic phenotyping data). Today, Christoph Steinbeck is Professor for Analytical Chemistry, Cheminformatics, and Chemometrics at the Friedrich Schiller University in Jena, Germany

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Oliver Koepler studied chemistry at the University of Kiel. After his diploma, he enrolled at TU Braunschweig where he received his PhD in the field of natural product synthesis in organic chemistry. He discovered his passion for chemistry software development during the final phase of his studies by working on the chemistry software Chemograph Plus and the later development of the web database Designer Drugs Online derived from the databank Mass Spectra of Designer Drugs.

Inspired by the thrilling opportunities of digitization in chemistry, Oliver Koepler joined the TIB, where he started developing digital libraries, e-infrastructures, and research data management services for chemistry. His work included text-mining and chemical entity recognition for document discovery, metadata standards, knowledge management systems, and interactive, graphical retrieval processes for research data. He introduced a user-centered design approach applying usability and UX methods for the development of the TIB discovery and delivery service. Since 2019 Oliver Koepler has been head of the Lab Linked Scientific Knowledge, part of the Digital Library and Data Science research group of Prof. Sören Auer at TIB,  focussing on knowledge engineering, ontologies, and developing services for research data management. Besides NFDI4Chem current projects include the development of a research data and knowledge management system for two CRCs INF-projects in engineering sciences.

Ontologies can help describe research objects, processes, and results in a way that not only humans but also machines can understand and work with. This paves the way for merging research data of various types and sources into a joint data space. In January, NFDI4Chem together with NFDI4Ing and NFDI4Cat hosted a joint webinar on ontologies in science and engineering. Nearly 200 participants attended to learn how ontologies can be used to formally describe the knowledge of a domain and to generate machine-interpretable research data. Presentations covered topics from knowledge engineering, ontology design to best practices in academic and industry projects. After a general introduction to knowledge engineering and ontologies for the three scientific domains of chemistry, catalysis, and engineering, a report on the development and application of ontologies from two CRCs (Collaborative Research Centres) in the engineering sciences, and the implementation of OntoCape into the work of the NFDI4Cat consortium followed. The session ended with exciting insights into ontology management, knowledge systems, and digitalization in R&D at BASF.

The final discussion with the participants illustrated a great interest in ontologies.

In case you missed the webinar, you can download the slides of the presentations on our website or watch a recording of the webinar on our Youtube channel. More events on this topic will follow. We will inform you in due time via our website, our newsletter, and Twitter.

Figure 1: Screenshot of the joint webinar on ontologies on 19th January 2021.

Overview of the First Project Phase

The article, published in German, appeared in the 2/2021 issue of the Bunsen-Magazin and gives an overview of NFDI4Chem’s main tasks in the first project phase. It summarizes the work on digitization and research data management of the five technical task areas of NFDI4Chem: 1) The smart-lab as a concept for digitization of the experimental work environment; 2) Repositories as a key infrastructure for the linkage of research data; 3) Development of (meta)data and minimal information standards for the enhancement of the interoperability of existing infrastructures; 4) Strategies for the involvement of the chemical community into the process of NFDI4Chem; 5) Joint development of cross-cutting topics in the national and international context. Interested? Read the full text of the open-access publication in the Bunsen-Magazin.

Teaching RDM at the RWTH Aachen University in an inorganic chemistry lab

Basic concepts of research data management (RDM) are becoming more and more important in the course of digitizing laboratories. Recently, the RWTH Aachen University taught RDM to 5th-semester students as part of an advanced inorganic chemistry course, introducing the topic to aspiring chemists before they start their bachelor thesis. To make general RDM concepts more accessible, short videos were produced, helping the students to familiarize themselves with RDM in chemistry. Furthermore, the acquired knowledge was applied to a practical experiment (the synthesis of ferrocene), using the electronic laboratory notebook Chemotion. We are currently evaluating a survey of the students to further improve our RDM videos, which are available on the NFDI4Chem YouTube channel.

Figure 1: Screenshot of one of the recorded teaching videos, explaining the types of research data in chemistry.

 

Start to save your research data in an up-to-date way!

The storage of research data according to the FAIR data principles (Findable, Accessible, Interoperable, Reusable) is crucial for upcoming machine learning approaches or big data analysis. Several working groups of NFDI4Chem and beyond, among them the group of Sonja Herres-Pawlis at RWTH Aachen University, Stefan Bräse and Frank Biedermann at Karlsruhe Institute of Technology (KIT), already save research data in the repository Chemotion. For every entry, a DOI is generated which is linked to the corresponding publication in a journal to guarantee findability. Furthermore, the repository Chemotion is linked to other databases (e.g. pubchem) to ensure best visibility and a user friendly search of research data.

Figure 1: Screenshot of a zinc guanidine complex, published in Angew. Chem. Int. Ed.^[1] and linked to the Chemotion repository.

As examples the following publications and their data can be accessed:

(1) A. Hermann, S. Hill, A. Metz, J. Heck, A. Hoffmann, L. Hartmann, S. Herres‐Pawlis: “Next Generation of Zinc Bisguanidine Polymerization Catalysts towards Highly Crystalline, Biodegradable Polyesters” Angew. Chem. Int. Ed. 2020, 59, 21778-21784. [DOI: 10.1002/anie.202008473]

(2) M. Paul, M. Teubner, B. Grimm-Lebsanft, C. Golchert, Y.  Meiners, L. Senft, K. Keisers, P. Liebhäuser, T. Rösener, F. Biebl, S. Buchenau, M. Naumova, V. Murzin, R. Krug, A. Hoffmann, J. Pietruszka, I. Ivanović-Burmazović, M. Rübhausen, S. Herres-Pawlis: “Exceptional Substrate Diversity in Oxygenation Reactions Catalyzed by a Bis(μ-oxo) Copper Complex”. Chem Eur. J. 2020, 26, 7556-7562. [DOI: 10.1002/chem.202000664]

(3)  C. Hu, L. Grimm, A. Prabodh, A. Baksi, A. Siennicka, P. A. Levkin, M. M. Kappes, F. Biedermann: “Covalent cucurbit[7]uril–dye conjugates for sensing in aqueous saline media and biofluids”. Chem. Sci., 2020, 11, 11142-11153. [DOI: https://doi.org/10.1039/d0sc03079a]

(4) S. Marschner,  R. Haldar,  O. Fuhr,  C. Wöll, S. Bräse: “Modular Synthesis of trans‐A2B2‐Porphyrins with Terminal Esters – Systematically Extending the Scope of Linear Linkers for Porphyrin‐Based MOFs”. Chem. Eur. J. 2020, accepted article, [DOI: https://doi.org/10.1002/chem.202003885]

(5) R. M. Bär, L. Langer, M. Nieger, S. Bräse: “Bicyclo[1.1.1]pentyl Sulfoximines: Synthesis and Functionalisations”. Adv. Synth. Catal. 2020, 362, 1356-1361. [DOI: https://doi.org/10.1002/adsc.201901453]

This national survey serves as a starting point for all upcoming efforts in research data management in chemistry.

Research data management is an important task to make research sustainable and comprehensible for other researchers. In our first community survey we asked chemists in Germany about their experience in data management, from the beginning of data production to the publication and reuse of research data. A detailed evaluation of the survey was published in the journal “Zeitschrift für anorganische und allgemeine Chemie” (open access). A short summary can be found hot off the press in the “Nachrichten aus der Chemie” (open access).

The most important results are:

1) Less than a fifth of chemists use electronic laboratory notebooks.

2) When researchers still record their data manually but save the data digitally, this is often due to missing tools;´.

3) Linking of research data with metadata, like methods or information about the sample, ensures the reproducibility of the results.

4) Chemists are open to share their research data with other scientists or to reuse research data from foreign researchers.

The NFDI4Chem consortium met in October to mark the official start of the project.

On October 14 and 15, the members of the NFDI4Chem consortium met virtually to kick off the national research data infrastructure for the German chemistry community (NFDI4Chem). Around 50 representatives of the consortium’s 27 partners gathered to present and discuss the workplan for the five years that lie ahead.

After its successful application in the first NFDI selection round, funding for the NFDI4Chem consortium started on 1 October 2020. Exactly two weeks into the project, on 14 and 15 October, the initiative assembled its members for a virtual Kick-Off. While a physical meeting had originally been scheduled to take place in the Rosensäle of the Friedrich-Schiller University (FSU), developments in the ongoing pandemic led the organisers to adapt an online format. The meeting, which was opened enthusiastically by the president of the FSU Jena, Prof. Walter Rosenthal, brought together around 50 members from across all 27 partners of the project.

Amongst the participants was also the director of the NFDI, York Sure-Vetter, who presented the collaborative and interdisciplinary context of the overarching NFDI initiative. The NFDI, which recently became an “eingetragener Verein” (e.V.), is also a mandated member of the European Open Science Cloud (EOSC).

Completing the introductions with a presentation on the mission of NFDI4Chem, namely building an open and FAIR infrastructure for research data management in chemistry, the consortium speakers Christoph Steinbeck and Oliver Koepler set the scene for the core part of the meeting, the presentation and discussion of the task areas. In short and succinct ignite talks the TA leaders gave overviews of the individual work plans: TA 2 Smart labs (Nicole Jung), TA 3 Repositories (Felix Bach & Matthias Razum), TA4 Standards (Steffen Neumann & Christoph Steinbeck), TA5 Community (Johannes Liermann & Sonja Herres-Pawlis) und TA6 Synergies (Oliver Koepler). With time as the limiting factor at the Kick-Off, all TA leads are now planning individual meetings with the task area members to discuss in depth the next steps to embark on realising the project.

The second day of the Kick-Off meeting dealt with administrative aspects of the project. The speaker Christoph Steinbeck and the project manager Christian Popp, gave an overview of the structural aspects, updates on the progress of the consortium agreement as well as financial matters concerning the distribution of funds and discussed with the consortium the tools and communication channels that they intend to use.

The success of NFDI4Chem will greatly depend on effective interaction with existing national and international efforts, as well as close collaboration within the NFDI. With this in mind, the last leg of the Kick-Off journey comprised of a presentation from Florian Schön (RWTH Aachen, TA5) on national initiatives and networking maps and a talk by Oliver Köpler about the cross-cutting topics that unify all NFDI consortia.

The NFDI4Chem Kick-Off meeting, which had also featured interactive coffee breaks and a social, albeit virtual evening gathering with beer and wine, closed with a final discussion round. The NFDI4Chem partners are now busy filling the approximately 40 positions that are funded by the project. While a handful of people have taken up their work already, recruiting the workforce that is necessary to realise the initiative’s ambitious plans, which you can find described in detail here (RIO article), will likely continue well into 2021.