nanopub 1.2.9

Python client for Nanopub

nanopub

The nanopub library provides a high-level, user-friendly python interface for searching, publishing and retracting nanopublications.

Nanopublications are a formalized and machine-readable way of communicating the smallest possible units of publishable information. See the documentation for more information.

Documentation

Checkout the user documentation

Setup

Install using pip:

pip install nanopub

To publish to the nanopub server you need to setup your profile. This allows the nanopub server to identify you. Run the following command in the terminal:

setup_nanopub_profile

This will ask you a few questions, then it will use that information to add and store RSA keys to sign your nanopublications with, (optionally) publish a nanopublication with your name and ORCID iD to declare that you are using using these RSA keys, and store your ORCID iD to automatically add as author to the provenance of any nanopublication you will publish using this library.

Quick Start

Publishing nanopublications

from nanopub import Publication, NanopubClient
from rdflib import Graph, URIRef, RDF, FOAF

# Create the client, that allows searching, fetching and publishing nanopubs
client = NanopubClient()

# Either quickly publish a statement to the server
client.claim('All cats are gray')

# Or: 1. construct a desired assertion (a graph of RDF triples)
my_assertion = Graph()
my_assertion.add( (URIRef('www.example.org/timbernerslee'), RDF.type, FOAF.Person) )

# 2. Make a Publication object with this assertion
publication = Publication.from_assertion(assertion_rdf=my_assertion)

# 3. Publish the Publication object. The URI at which it is published is returned.
publication_info = client.publish(publication)
print(publication_info)

Searching for nanopublications

from nanopub import NanopubClient

# Search for all nanopublications containing the text 'fair'
results = client.find_nanopubs_with_text('fair')
print(results)

Fetching nanopublications and inspecting them

# Fetch the nanopublication at the specified URI
publication = client.fetch('http://purl.org/np/RApJG4fwj0szOMBMiYGmYvd5MCtRle6VbwkMJUb1SxxDM')

# Print the RDF contents of the nanopublication
print(publication)

# Iterate through all triples in the assertion graph
for s, p, o in publication.assertion:
    print(s, p, o)

Dependencies

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