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Searching the nanopub server

The NanopubClient provides methods for searching the nanopub server. It provides an (incomplete) 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')

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'}]

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.public_key
results = client.find_nanopubs_with_text('test', pubkey=my_public_key)