Data Export

Export to File

Export Lab Notebooks

All levels of the Lab Notebook and Inventory can be exported, using the 2 export options in the More.. drop down, as shown below. It is possible to export metadata only, or metadata and data (up to 10 GBs).

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In this way, users can export their complete lab notebook with all data contained in it. Everything is exported to a zip file, which maintains the same structure used in openBIS. Each folder contains several file formats (.txt, .html, .json, .docx) with the metadata of the corresponding Project, Experiment, Object and Datasets (see below).

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A link to download the zip file is sent via email to the user. Email notification needs to be configured by a system admin during or after installation, as explained in Configure Data Store Server .

In a similar way, it is possible to export Projects, Experiments, Objects, Datasets.

Export Builder

It is also possible to export the content of openBIS using the Export to ZIP under Exports in the Utilities main menu.  Here users can select items from different Spaces and export them by clicking the Export Selected button.

Also in this case, a link to download the data is sent to the user via email, as described above.

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Updated on April 25, 2023

Export to Zenodo

Currently openBIS offers an integration with the Zenodo data repository (https://zenodo.org/).

This enables data direct data transfer from openBIS to Zenodo. First of all the connection to Zenodo needs to be configured by a system admin in the DSS service.properties (see How to configure the openBIS DSS) If this is configured, a lab manager, who has admin rights for the Settings, needs to enable it in the ELN, as explained in Enable Transfer to Data Repositories.

Create Zenodo Personal Access Token

In order to be able to export data to Zenodo, you need a valid Zenodo account. You also need to create a personal access token. This can be done from the Applications under Settings in Zenodo, as shown below:

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Save Zenodo Personal Access Token in openBIS

After creating the personal access token in Zenodo, this needs to be stored in openBIS, with the following procedure:

  1. Go to User Profile under Utilities in the main menu.

  2. Enable editing.

  3. Add the personal access token from Zenodo.

  4. Save.

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Export data to Zenodo

To export data to Zenodo:

  1. Go to Exports -> Export to Zenodo under Utilities in the main menu.

  2. Select the data you want to export from the menu.

  3. enter a Submission Title.

  4. Click Export Selected on top of the export form.

  5. The selected data are transferred as a zip file to Zenodo. You are now redirected to Zenodo, where you should fill in additional metadata information.

  6. Publish the entry in Zenodo.

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After you hit the Publish button in Zenodo, a new entry with the details of this submission will be created in the Publications folder in the Inventory. Please note that this may take a few minutes.

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Updated on April 25, 2023

Export to ETH Research Collection

The ETH Research Collection is a FAIR repository for publications and research data provided by ETH Zurich to its scientists.

Data can be uploaded to the ETH Research Collection only by members of ETH Zurich. This export feature is only available to ETHZ members.

To export data to the ETH Research Collection:

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  1. Go to Utilities -> Exports -> Export to Research Collection.

  2. Select what to export from the tree.

  3. Select the Submission Type from the available list: Data collection, Dataset, Image, Model, Sound, Video, Other Research Data.

  4. Select the Retention Period that will be used in the ETH Research Collection: 10 years, 15 years, indefinite. This is time for which the data will be preserved in the Research Collection.

  5. Click the Export Selected button on top of the page.

  6. The selected data are transferred as zip file to the ETH Research Collection. You will be redirected to the ETH Research Collection and will need to complete the submission process there.

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A new entry with the details of this submission will be created in the Publications folder in the Inventory after the submission process in complete. This may take a few minutes.

The size limit for one single export to the ETH Research Collection is 10GB.

Updated on April 25, 2023