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2.3 Example: Chemotion

The content in this section is adapted from RDM@KIT.

Chemotion offers a free-to-use infrastructure and open source software for the management of research data, especially for chemists and related sciences.

Chemotion includes a suite consisting of an electronic laboratory notebook (Chemotion ELN), a web repository and helpful tools. The goal is to simplify routine work with molecular data, thus increasing the amount of open data and improving the quality of the information obtained and published.

The software is increasingly being extended to related fields and further developed into a generic ELN (“LabIMotion”). You can find more information about Chemotion on the website, as well as via NFDI4Chem, which regularly holds events such as Q&As and hands-on workshops, and via the Chemotion ELN YouTube channel.

Syllabus Elements

Learning Objectives

At the end of the section the learners can ...

  • Recognizes basic elements in the program Chemotion
  • Define use cases for Chemotion
  • Determine whether Chemotion is suitable for them
  • Knows where to get further information on Chemotion

Target Audience

  • attendees of this course

Duration

  • 15 minutes

Prerequisites

Learning Tools

Example: Chemotion

Go to Chemotion ELN

What is Chemotion?

Chemotion ELN

The information in this section is adapted from Fink et al. (2023): Chemotion ELN Instruction Videos licenced under CC BY 4.0.

This video is used from Chemotion ELN published as Fink et al. (2023): Chemotion ELN Instruction Videos licenced under CC BY 4.0.

First instructional video on Chemotion can be found on Youtube:

Hands-on Chemotion ELN

  • Go to the Demo version of Chemotion ELN
  • Click on Sign up to create an account for the Demo version
  • Create a collection with your favorite name (e.g. 'My Lab Notebook')

Chemotion - How to create a collection

  • Add a sample by using the molecule structure editor Ketcher
    • Click on your new collection and then on the blue arrow near the + and Create sample
    • Then click in the Editor field
    • Scetch your desired chemical structure
    • Do not forget to save your sample! Therefore click on the blue Save-Button, and then on the yellow Save sample-Button

  • Add additonal information on your molecule
    • Click on your molecule and on CaL-1
    • Then add additional information like Amount, Density, Molarity, Concentration, Solvents Boiling point and so on.
    • Note: Adding the Density or the Molarity is essential. Automatic calculation of the mass (by volume)
    • Further down you can find the automatically generated SMILES and InChI codes
    • In the Analysis-Section you can add Analysis like NMR data
    • You can also add Literature by the DOI in the Literature-Section
    • For more information click here.

You can also add reactions and analysis and much more. When you want to publish your data you can do this directly in the Chemotion Repository.

Summary

  • Chemotion is an Electronic Lab Notebook and Repository for Chemistry Data.
  • It is an Open Source Software, developped at KIT.
  • It is being extended to related fields and further developed into a generic ELN (“LabIMotion”).

References

Further information

Suggested reading

  • Tremouilhac et al. (2017): Chemotion ELN: an Open Source electronic lab notebook for chemists in academia. In: Journal of cheminformatics 9 (1), p. 54. DOI: https://doi.org/10.1186/s13321-017-0240-0.
  • Kotov et al. (2018): Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications. In: Journal of cheminformatics 10 (1), p. 38. DOI: https://doi.org/10.1186/s13321-018-0292-9.