Literature Biocuration Practices and Guidelines

Elixir - BioHackaton 2023 - Project 26

Preprint

BioHackEU23 report: Project 26: Literature Biocuration Practices and Guidelines

Browser extension

Installation

ELIXIR 2023 BioHackathon version

⚠️ Authentification was not implemented during the hackathon, so the installation procedure is cumbersome.

Go to the next section if you just want to give it try: you won't be able to publish the NanoPub, but all the steps before work.

Installation steps:

• Install Tampermonkey browser extension.
• Open TamperMonkey window
• Choose "Create a new script..."
• Copy and paste the content of annotations_to_nanopub.js.

Then to create a NanoPub you have to be logged in, which was not implemented during the hackathon:

• Login on https://api.collaboratory.semanticscience.org/docs
• Get the authentification header from https://api.collaboratory.semanticscience.org with OpenIdConnect (OAuth2, implicit)
• Try out the /generate-keys (only once).
• Make a call to /current-user
• Copy the Authorization header value to AUTH_TOKEN variable in the script.

The token is going to expire in about 30 minutes, so you have to repeat the above procedure except the call to /generate-keys.

Once ORCID login will be supported

• Install Tampermonkey browser extension.
• Follow this link https://raw.githubusercontent.com/MetabolicAtlas/biohackathon23/main/browser_extension/annotations_to_nanopub.js
• Tampermonkey will show a popup to install the script
• Click on the "Install" button

Dedicated browser extension

Of course, in the future, it makes sense to create a standalone browser extension so all the steps above will much simpler.

Usage

On:

• https://europepmc.org/article/
• https://www.ncbi.nlm.nih.gov/pubmed/
• https://www.nature.com/articles/
• https://www.science.org/doi/

When you select some text, a button appears:

When clicked, a cart appears at the bottom right of the screen:

You can make multiple selection:

You can add quotes from multiple documents (the extension keeps your cart across the pages):

Enter the assertion, and when ready, you can click on "Create NanoPub", the browser is going to open a new tab automatically.

Example of NanoPublication: https://np.petapico.org/RARpP8Q4RqW3uLUb2pT2C-zlwSofhvwfsXveK5-ccLq4k

The schema follows the Web Annotation Data Model.