elab2ARC

I documented some of my protocols and data in the electronic lab notebook eLabFTW! Can I somehow convert this entries into a format that can be used in the ARC?

Yes, you can! We developed a browser-based tool bridging eLabFTW with ARCs. We will use pre-created entries as examples.

Authentification

Section titled Authentification

elab2ARC

1. Open the website elab2ARC and go to the Token tab
2. Select the eLabFTW instance: DataPLANT
3. Click Get a test API key to optain an eLabFTW API Key
4. Click Get a token to automatically generate a token for your DataHUB account.
5. Click Save.

You have now authenticated your account and can use the tool to convert your eLabFTW data directly into the ARC.

I have several eLabFTW entries, some belong to the study part, others to assays. How can I handle that?

The tool allows you to choose which part of the ARC you entries should belong to. We will first create an example for the study part.

Add an eLabFTW entry as study

Section titled Add an eLabFTW entry as study

elab2ARC

1. Go to the eLabFTW tab. Here you can see all demo eLabFTW entries along with their metadata.
2. Click the Preview button of entry 66: Arabidopsis growth protocol to view its content. Close the preview afterwards.
3. Select the entry 66: Arabidopsis growth protocol and click Confirm eLabFTW Selection.
4. In the ARC tab you can now see the ARC that we created earlier. Click Select study to define the target folder. This will update the Target Path shown at the bottom.
5. Click Start Conversion to begin the conversion. The converted data will be uploaded directly to the ARC.
6. In the Conversion Status window, you can monitor the progress. Once the process is finished, go to View ARC and the ARC is opened in the DataHUB.

Now a new study folder containing the content of the eLabFTW entry is now created in the ARC. The structure ARC including the converted data looks like this:

• Directorystudies

  • DirectoryAthalianaColdStress

    • README.md
    • isa.study.xlsx
    • Directoryprotocols

      • growth_protocol.md
    • resources
  • DirectoryArabidopsis_growth_protocol

    • README.md
    • isa.study.xlsx
    • Directoryprotocols

      • eLabFTW_protocol_66_Arabidopsis_growth_protocol.elab2arc.md
    • resources
• Directoryassays

  • DirectorySugarMeasurement

    • README.md
    • Directorydataset

      • sugar_result.csv
    • isa.assay.xlsx
    • Directoryprotocols

      • sugar_extraction_protocol.md
• isa.investigation.xlsx
• Directoryworkflows

  • …
• Directoryruns

  • …

Add an eLabFTW entry as assay

Section titled Add an eLabFTW entry as assay

elab2ARC

1. Go back to the eLabFTW tab.
2. Click the Preview button of entry 68: Sugar extraction & measurement to view its content. This entry also includes the attachment sugar.results.csv. Close the preview afterwards.
3. Select the entry 68: Sugar extraction & measurement and click Confirm eLabFTW Selection.
4. In the ARC tab, click Select assay to define the target folder.
5. Enable LLM Annotation Table to automatically extract metadata from the eLabFTW entry and fill it into the isa.assay sheet.
6. Click Start Conversion to begin the conversion. The converted data will be uploaded directly to the ARC.
7. In the Conversion Status window, you can observe the LLM Response Stream during the conversion process. Once it is finished, go to View ARC to directly check it in the DataHUB.

A new asssay folder containing the content of the eLabFTW entry is now creating in the ARC. Because the eLabFTW entry includes a file attachment, it is also added to the assay’s dataset folder. The metadata extracted by the LLM is added to the isa.assay sheet, which we later check in ARCitect.

• Directorystudies

  • DirectoryAthalianaColdStress

    • README.md
    • isa.study.xlsx
    • Directoryprotocols

      • growth_protocol.md
    • resources
  • DirectoryArabidopsis_growth_protocol

    • README.md
    • isa.study.xlsx
    • Directoryprotocols

      • eLabFTW_protocol_66_Arabidopsis_growth_protocol.elab2arc.md
    • resources
• Directoryassays

  • DirectorySugarMeasurement

    • README.md
    • Directorydataset

      • sugar_result.csv
    • isa.assay.xlsx
    • Directoryprotocols

      • sugar_extraction_protocol.md
  • DirectorySugar_extraction___measurement

    • README.md
    • Directorydataset

      • sugar_result_166.elab2arc.csv
    • isa.assay.xlsx
    • Directoryprotocols

      • eLabFTW_protocol_68_Sugar_extraction_measurement.elab2arc.md
• isa.investigation.xlsx
• Directoryworkflows

  • …
• Directoryruns

  • …

Thats great! I can easily convert my eLabFTW entries into the ARC and have all the data and metadata together. This will save me a lot of time in the future!

To get a better understanding of the conversion process, take a look at the image below. The tool uses the eLabFTW title as the name of the created study or assay folder in the ARC. The main text of the eLabFTW entry is converted into a Markdown file and added to the protocols folder. All attachements of the eLabFTW entry are added to the dataset folder. Low-level administrative metadata (e.g. creation date, author, etc.) are added to the isa.study or isa.assay sheet. If you enable the LLM Annotation Table, the tool will also extract experimental metadata from the main text of the eLabFTW entry and add it to the corresponding isa.study or isa.assay sheet.