How to use ELNs

This guide describes how to manually create entries and enter information via ELNs (electronic lab notebooks). NOMAD ELNs allow you to acquire consistently structured data from users to augment uploaded files.

Attention

This part of the documentation is still work in progress.

Create a basic ELN entry

Go to PUBLISH / Uploads. Here you can create an upload with the CREATE A NEW UPLOAD button. This will bring you to the upload page.

Click the CREATE ENTRY button. This will bring-up a dialog to choose an ELN schema. All ELNs (as any entry in NOMAD) needs to follow a schema. You can choose from uploaded custom schemas or NOMAD built-in schemas. You can choose the Basic ELN to create a simple ELN entry.

The name of your ELN entry, will be the filename for your ELN without the .archive.json ending that will be added automatically. You can always find and download your ELNs on the FILES tab.

The Basic ELN offers you simple fields for a name, tags, a date/time, and a rich text editor to enter your notes.

Add your own ELN schema

To make NOMAD ELNs more useful, you can define your own schema to create you own data fields, create more subsections, reference other entries, and much more.

You should have a look at our ELN example upload. Go to PUBLISH / Uploads and click the ADD EXAMPLE UPLOADS button. The Electronic Lab Notebook example, will contain a schema and entries that instantiate different parts of the schema. The *ELN example sample (sample.archive.json) demonstrates what you can do.

Follow the How-to write a schema and How-to define ELN guides to create you own customized of ELNs.

Integration of third-party ELNs

Attention

This part of the documentation is still work in progress.

NOMAD offers integration with third-party ELN providers, simplifying the process of connecting and interacting with external platforms. Three main external ELN solutions that are integrated into NOMAD are: elabFTW, Labfolder and chemotion. The process of data retrieval and data mapping onto NOMAD's schema varies for each of these third-party ELN provider as they inherently allow for certain ways of communicating with their database. Below you can find a How-to guide on importing your data from each of these external repositories.

elabFTW integration

elabFTW is part of the ELN Consortium and supports exporting experimental data in ELN file format. ELNFileFormat is a zipped file that contains metadata of your elabFTW project along with all other associated data of your experiments.

How to import elabFTW data into NOMAD:

Go to your elabFTW experiment and export your project as ELN Archive. Save the file to your filesystem under your preferred name and location (keep the .eln extension intact). To parse your ebalFTW data into NOMAD, go to the upload page of NOMAD and create a new upload. In the overview page, upload your exported file (either by drag-dropping it into the click or drop files box or by navigating to the path where you stored the file). This causes triggering NOMAD's parser to create as many new entries in this upload as there are experiments in your elabFTW project.

You can inspect the parsed data of each of your entries (experiments) by going to the DATA tab of each Entry page. Under Entry column, click on data section. Now a new lane titled ElabFTW Project Import should be visible. Under this section, (some of) the metadata of your project is listed. There two subsections: 1) experiment_data, and 2) experiment_files.

experiment_data section contains detailed information of the given elabFTW experiment, such as links to external resources and extra fields. experiment_files section is a list of subsections containing metadata and additional info of the files associated with the experiment.

Labfolder integration

Labfolder provides API endpoints to interact with your ELN data. NOMAD makes API calls to retrieve, parse and map the data from your Labfolder instance/database to a NOMAD's schema. To do so, the necessary information are listed in the table below:

project_url: The URL address to the Labfolder project. it should follow this pattern: 'https://your-labfolder-server/eln/notebook#?projectIds=your-project-id'. This is used to setup the server and initialize the NOMAD schema.

labfolder_email: The email (user credential) to authenticate and login the user. Important Note: this information is discarded once the authentication process is finished.

password: The password (user credential) to authenticate and login the user. Important Note: this information is discarded once the authentication process is finished.

How to import Labfolder data into NOMAD:

To get your data transferred to NOMAD, first go to NOMAD's upload page and create a new upload. Then click on CREATE ENTRY button. Select a name for your Entry and pick Labfolder Project Import from the Built-in schema dropdown menu. Then click on CREATE. This creates an Entry where you can insert your user information. Fill the Project url, Labfolder email and password fields. Once completed, click on the save icon in the top-right corner of the screen. This triggers NOMAD's parser to populate the schema of current ELN. Now the metadata and all files of your Labfolder project should be populated in this Entry.

The elements section lists all the data and files in your projects. There are 6 main data types returned by Labfolder's API: DATA, FILE, IMAGE, TABLE, TEXT and WELLPLATE. DATA element is a special Labfolder element where the data is structured in JSON format. Every data element in NOMAD has a special Quantity called labfolder_data which is a flattened and aggregated version of the data content. IMAGE element contains information of any image stored in your Labfolder project. TEXT element contains data of any text field in your Labfodler project.

Chemotion integration

NOMAD supports importing your data from Chemotion repository via chemotion parser. The parser maps your data that is structured under chemotion schema, into a predefined NOMAD schema. From your Chemotion repo, you can export your entire data as a zip file which then is used to populate NOMAD schema.

How to import Chemotion data into NOMAD:

Go to your Chemotion repository and export your project. Save the file to your filesystem under your preferred name and location (your_file_name.zip). To get your data parsed into NOMAD, go to the upload page of NOMAD and create a new upload. In the overview page, upload your exported file (either by drag-dropping it into the click or drop files box or by navigating to the path where you stored the file). This causes triggering NOMAD's parser to create one new Entry in this upload.

You can inspect the parsed data of each of this new Entry by navigating to the DATA tab of the current Entry page. Under Entry column, click on data section. Now a new lane titled Chemotion Project Import should be visible. Under this section, (some of) the metadata of your project is listed. Also, there are various (sub)sections which are either filled depending on whether your datafile contains information on them.

If a section contains an image (or attachment) it is appended to the same section under file Quantity.

Openbis integration

Openbis provides API endpoints to interact with your ELN data. NOMAD makes API calls to retrieve, parse, and map the data from your Openbis instance/database to NOMAD's schema. The necessary information is listed in the table below:

• project_url: The URL address to the Openbis project. It should follow this pattern: https://openbis.example.com. This is used to set up the server and initialize the NOMAD schema.
• username: The username (user credential) to authenticate and log in the user. Important Note: this information is discarded once the authentication process is finished.
• password: The password (user credential) to authenticate and log in the user. Important Note: this information is discarded once the authentication process is finished.

How to Import Openbis Data into NOMAD

To get your data transferred to NOMAD, follow these steps:

1. Go to NOMAD's upload page and create a new upload.
2. Click on the CREATE ENTRY button.
3. Select a name for your entry and pick Openbis Project Import from the Built-in schema dropdown menu.
4. Click on CREATE. This creates an entry where you can insert your user information.
5. Fill in the project url, username, and password fields.
6. Once completed, click on the save icon in the top-right corner of the screen. This triggers NOMAD's parser to populate the schema of the current ELN. Now, the metadata and all files of your Openbis project should be populated in this entry.

The normalizer will search for all entries in your Openbis project and attempt to import them one by one.

Under Development

The integration of third-party ELNs suite is planned to be moved to a new plug-in mechanism to allow for a smoother interface for interacting with other ELN providers.