Searching the nanopub server

The NanopubClient provides methods for searching the nanopub server. It provides an (uncomplete) mapping to the nanopub server grlc endpoint.

Text search

Search for all nanopublications containing some text using NanopubClient.find_nanopubs_with_text()

from nanopub import NanopubClient
client = NanopubClient()
results = client.find_nanopubs_with_text('fair')

Triple pattern search

Search for nanopublications whose assertions contain triples that match a specific pattern.

from nanopub import NanopubClient
client = NanopubClient()
# Search for nanopublications whose assertions contain triples that are ```rdf:Statement```s.
results = client.find_nanopubs_with_pattern(
                pred='http://www.w3.org/1999/02/22-rdf-syntax-ns#type',
                obj='http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement')

Search on introduced concept

Search for any nanopublications that introduce a concept of the given type, that contain text with the given search term.

from nanopub import NanopubClient
client = NanopubClient()
# Search for nanopublications that introduce a concept that is a ```p-plan:Step```.
results = client.find_things('http://purl.org/net/p-plan#Step')

Interpreting search results

Each search method returns a generator of dicts depicting matching nanopublications.

Each dict has the following key-value pairs:

date: The date and time the nanopublication was created.
description: A description of the nanopublication that was parsed from the nanopublication RDF.
np: The URI of the matching nanopublication.

Example results (from NanopubClient.find_nanopubs_with_text('fair')):

>>> print(list(results))
[{'date': '2020-05-01T08:05:25.575Z',
  'description': 'The primary objective of the VODAN Implementation Network is '
                 'to showcase the creation and deployment of FAIR data related '
                 'to COVID-19',
  'np': 'http://purl.org/np/RAdDKjIGPt_2mE9oJtB3YQX6wGGdCC8ZWpkxEIoHsxOjE'},
 {'date': '2020-05-14T09:34:53.554Z',
  'description': 'FAIR IN community',
  'np': 'http://purl.org/np/RAPE0A-NrIZDeX3pvFJr0uHshocfXuUj8n_J3BkY0sMuU'}]

Returning retracted publications in search

By default nanopublications that have a valid retraction do not show up in search results. A valid retraction is a retraction that is signed with the same public key as the nanopublication that it retracts. You can toggle this behavior with the filter_retracted parameter, here is an example with NanopubClient.find_nanopubs_with_text:

from nanopub import NanopubClient
client = NanopubClient()
# Search for nanopublications containing the text fair, also returning retracted publications.
results = client.find_nanopubs_with_text('fair', filter_retracted=False)

Filtering search results for a particular publication key

You can filter search results to publications that are signed with a specific publication key (effectively filtering on publications from a single author). You use the pubkey argument for that. Here is an example with NanopubClient.find_nanopubs_with_text:

from nanopub import NanopubClient, profile
# Search for nanopublications containing the text 'test',
# filtering on publications signed with my publication key.
client = NanopubClient(use_test_server=True)
my_public_key = profile.get_public_key()
results = client.find_nanopubs_with_text('test', pubkey=my_public_key)