Setup instructions

Install nanopub library

Install using pip:

pip install nanopub

Nanopub-java dependency

The nanopub library currently uses the nanopub-java tool for signing and publishing new nanopublications. This is automatically installed by the library.

Java

If you want to publish nanopublications you need to have the java runtime environment installed, this might already be installed on your system. You can check this for unix:

java --version

Or follow these instructions for windows

Installing java

If java is not installed follow these instructions

Setup for users new to python

We recommend using anaconda to install python and manage python dependencies

Setup your profile

To publish to the nanopub server you need to setup your profile (note that you can use fetch and search functionality without a profile). This allows the nanopub server to identify you.

Run the following interactive command:

setup_nanopub_profile

This will setup the following:

Stored profile

A local version of the profile will be stored in the nanopub user config dir (by default HOMEDIR/.nanopub/profile.yml)

RSA keys

It will add and store RSA keys to sign your nanopublications. By default they are stored under HOMEDIR/.nanopub/id_rsa and HOMEDIR/.nanopub/id_rsa.pub.

ORCID iD

This includes your ORCID iD (i.e. https://orcid.org/0000-0000-0000-0000). If you don’t have an ORCID iD yet, you need to register. We use the ORCID iD to automatically add as author to the provenance of any nanopublication you will publish using this library.

Introductory nanopublication

We encourage you to make use of setup_nanopub_profile’s option to publish your profile to the nanopub servers. This links your ORCID iD to your RSA key, thereby making all your publications linkable to you. Here is an example introductory nanopublicaiton.

The link to this nanopublication is also stored in your profile.