Electronic Lab Notebooks (ELNs)
Introduction
Information technology continuously develops at a fast pace. For example, the smartphones we all carry on a daily basis in our pockets are much faster than a supercomputer from the 80s which you could barely fit in an average bedroom. Unfortunately, this accelerated advancement of information technology has not yet fully reached our chemical laboratories. The paper laboratory notebook is just as popular and widespread as it was 100 years ago, with the very essence of how chemical research data is documented - literally with pen and paper - having only made little progress over the last century.
Transferring the advancement of the information technology into the lab (smartlab) does not necessarily mean tablets & touch screens in every corner of your laboratory. The term Smartlab is more about the interconnectivity of the entire workflow and handling research data according to the FAIR principles. ELNs help to assign rich metadata to experiments and make the collected data traceable as well as reusable. With the possibility to transfer data from measurement devices directly into the ELN, the ELN is the central storage with all data in one place. From the ELN, data can be easily published into repositories and transferred to suitable long-term archiving.
One of the most important things, that distinguishes an ELN from a white blank paper is the possibility to document metadata in a structured and ideally in a human as well as machine-readable way. See the following overview for more information on the differences between blank sheets, ELNs and laboratory information management systems (LIMS).
Advantages of an ELN
ELNs help to link experimental descriptions directly to the collected data so that all information can be found in one place. Furthermore, data loss is avoided by secure data storage and backups. Storing all the data in one central place helps also with knowledge management because the data is easily findable and accessible, even for new members in a research project. The biggest advantage of an ELN is that metadata is stored in a structured and standardised way. This also helps with publishing research results and transferring research data to a repository.
The right ELN
To date, there is not one ELN, that fits the requirements for all chemical disciplines. Furthermore, only a few ELNs meet the basic requirements for chemical sciences. This is most likely due to the challenges arising from drawing and processing chemical structures, a crucial and central step in being able to correlate research data to the corresponding chemical reaction or structure. The organisation of work with ELNs that support chemistry-specific functions can offer several benefits, such as the availability of chemical structure identifiers and standardised formats as well as the integration of manifold tools and workflows that facilitate scientific work. The direct integration of tools enables a direct support of the scientist without the need to search for additional services and software, thus bringing new developments and information directly to the scientists’ awareness. Some Open Source examples for systems in chemistry that offer the necessary support for chemical structures include Indigo-ELN, LabTrove, OpenEnventory, and Chemotion ELN.
Therefore, choosing the right ELN is crucial for a successful implementation of an ELN in a laboratory. Three steps should be taken to establish an ELN: 1) Needs assessment, 2) Testing and 3) Introducing the chosen ELN.
- Analysing current situation (budget, IT resources, software environment)
- Definition of important features
- ELN concept (generic, discipline-specific)
- Drawing on experiences of other research Institutions
- Demo versions or free trial access for individual users
- Testing no more than 2-3 ELNs
- In-depth testing using real-life use cases from the lab
- Run training courses, training material
- Designate contact persons from the test team
- Continuous mentoring
Criteria for selecting an ELN
| Category | Explanation |
|---|---|
| License model | Commercial ELNs mostly use proprietary file formats, the source code is closed source and a license fee is charged. Open source ELNs are free of charge, use open standard formats, source code is openly accessible and further developed by an active developer community. Implementation and maintenance require the appropriate human resources. |
| Providing model | Software can be provided either in a cloud (SaaS - Software as a Service) or server-based for local installation at the customer's site (on-premises). |
| File storage | Data storage in the cloud of the ELN provider (or their service provider, e.g. in the EU) or the possibility of storage on own local servers/in the own cloud are offered. |
| Concept | Concept refers to the subject-specific orientation. Generic tools can be used in all subjects, but usually do not provide specific features, such as structure editors for chemistry. |
| Standard interface | Standard interfaces enable data exchange with external programs, e.g. ChemDraw, Marvin JS, ChemDoodle, MS Office, Libre Office, ImageJ, Slack |
| Pragramming interfaces | An API is needed for integration into an existing IT environment, e.g. own storage solutions. |
| File import/export | Export/import of both human- and machine-readable formats should be possible (e.g. pdf, zip, csv, json, xml), ideally also larger units, such as the ELN. |
| Metadata | Providing metadata is a crucial factor in ensuring findability and understanding of data. Metadata should be recorded in a structured, machine- and human-readable format. |
| Collaboration | Collaboration simplifies the exchange of data and results. It should be possible to define roles, e.g. who has access and to what extend (role management). |
| Sharing/Publication | ELNs allow direct exchange of data with portals for publishing/sharing research data. |
| Search | The search function allows data to be retrieved and filtered. |
| Templates | Templates are used for time saving and standardization. One advantage is the option to create templates according to one’s own needs. |
| Workflows | Documenting processes significantly increases efficiency, traceability and contributes to transparency and transporting of know-how. |
| Security of evidence | Evidence security means the traceable documentation in compliance with legal regulations, e.g. providing the entries with a time stamp, electronic signature, versioning. |
| Rule compliance | The tool must enable compliance with regulatory requirements, e.g. GLP, GCP. |
Table Attribution: ZB MED PUBLISSO ELN-Filter, 2921-06 english.
Electronic Lab Notebooks (ELNs) in NFDI4Chem
NFDI4Chem will support those ELNs that are relevant for documentation of chemical research activities. This support will include hosting one ELN instance for each of the relevant ELNs at KIT for teaching and training purposes. This service will be established in 2022 to allow all scientists to compare ELNs and their functionalities. Comparing and testing different ELNs is a prerequisite for making the right choice. Furthermore, NFDI4Chem organises various seminars with the goal of giving a first impression of different ELNs. These seminars are a good opportunity for ELN providers to demonstrate their ELN's usefulness and possible applications. For past and forthcoming seminars, please see the Stammtisch event page.
Chemotion ELN
Chemotion is the ELN reference instance in NFDI4Chem. The Chemotion ELN is developed by several software developers at different NFDI4Chem sites. The ELN development started at the Karlsruhe institute of Technology (KIT) in Karlsruhe as part of a DFG-funded project. The extension of the software was and is further supported by the State Ministry of Baden-Wuerttemberg for Sciences, Research and Arts, the Karlsruhe Institute of Technology, and the German Research Foundation (DFG).
The Chemotion ELN was designed for chemists and adapted to the special requirements of chemical laboratory work and documentation. It therefore serves as a digitalization instrument for work in chemistry, developed to overcome the current limitations of the existing systems. To reach this goal, the development, improvement, and extension of the ELN is a community effort. The ELN is also used in other disciplines beyond chemistry as it offers a broad generic functionality to meet the needs of scientists working in interdisciplinary environments. These generic functions are still being extended and adapted.
Chemotion ELN offers a specific function that facilitates the publication of research data: it supports the transfer of data from a user's ELN account to a research data repository. This function reduces the scientists' effort in allowing access to research data, which is required by many funding agencies and helpful for the publication of scientific text publications. Currently, the ELN supports the transfer of data to the Chemotion repository. The NFDI4Chem team is working on establishing connections to further repositories, in particular, the repositories supported and recommended by NFDI4Chem.
A short introduction to the Chemotion ELN as well as the connection to the Chemotion repository is demonstrated in this video:
Documentation, information, and contact
Chemotion ELN and its functions were described in various publications (see below). For users, developers, and admins, a documentation is available via the project's website. Chemotion ELN is an Open Source development; the source code is available on GitHub.
Sources and further information
- Chemotion ELN: an Open Source electronic lab notebook for chemists in academia
- Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications
- CHEMSCANNER: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
- Chemotion ELN documentation
- Chemotion ELN on Github