Add an evidence to an existing association

This tutorial will show you how to use the Nanobench to:

• Publish a biomedical association as a Nanopublication
• Add an evidence to a biomedical association published as a Nanopub

The biomedical associations and evidences uses the BioLink model.

Duration: 10min 🕐

Start the Nanobench 🛋️

You need to have Java installed (version 1.7 or higher), which you can download here.

From the latest release

1. Download the nanobench.jar from the latest release on GitHub
2. Run the jar:

java -jar nanobench.jar -httpPort 37373 -resetExtract

Access at http://localhost:37373

Or from the source code

You will need to have maven installed to start the application from the source code.

1. Clone the repository

git clone https://github.com/vemonet/nanobench.git
cd nanobench

2. Start the Nanobench at http://localhost:37373

mvn clean tomcat7:run

N.B.: a precompiled jar will be provided later.

Create an association 🔗

This step is optional if the association has already been published.

1. Go to http://localhost:37373/publish

2. Click on the template Defining a biomedical association.

3. Fill the association informations in the template, using autocomplete for:

   • subject and object with the Translator Name Resolver API.
   • relation with the BioLink model through BioPortal search API (only classes available, properties no properly parsed by BioPortal).

Search for the association 🔎

Use the Nanobench Search page at http://localhost:37373/search to search for an association, e.g. paracetamol

Add an evidence 📝

Click on add evidence at the right of the Nanopub URL

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Add the evidences information in the prefilled Nanopub template, using autocomplete for ECO codes.