Setting publication info and provenance

Here we show how you can control the publication info and provenance parts of the nanopublication.

Specifying where the nanopublication is derived from

You can specify that the nanopub’s assertion is derived from another URI (such as an existing nanopublication):

from rdflib import URIRef, Graph, BNode, RDF, FOAF
from nanopub import Nanopub

my_assertion = Graph()
my_assertion.add((BNode('timbernserslee'), RDF.type, FOAF.Person))

np = Nanopub(
    assertion=my_assertion,
    conf=NanopubConf(
        add_prov_generated_time=True,
        add_pubinfo_generated_time=True,
        attribute_publication_to_profile=True,
        derived_from=URIRef('http://www.example.org/another-nanopublication'),
    )
)

Note that derived_from may also be passed a list of URIs.

The provenance part of the publication will denote:

@prefix sub: <http://purl.org/nanopub/temp/mynanopub#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

:provenance {
    sub:assertion prov:wasDerivedFrom <http://www.example.org/another-nanopublication> .
}

Attributing the assertion to someone

You can attribute the assertion to someone by specifying the assertion_attributed_to argument:

from rdflib import URIRef, Graph, BNode, RDF, FOAF
from nanopub import Nanopub

my_assertion = Graph()
my_assertion.add((BNode('timbernserslee'), RDF.type, FOAF.Person))

np = Nanopub(
    assertion=my_assertion,
    conf=NanopubConf(
        add_prov_generated_time=True,
        add_pubinfo_generated_time=True,
        attribute_publication_to_profile=True,
        assertion_attributed_to=URIRef('https://orcid.org/0000-0000-0000-0000'),
    )
)

The provenance part of the publication will denote:

@prefix : <http://purl.org/nanopub/temp/mynanopub#> .
@prefix prov: <http://www.w3.org/ns/prov#> .

:provenance {
    :assertion prov:wasAttributedTo <https://orcid.org/0000-0000-0000-0000> .
}

Note: Often the assertion should be attributed to yourself.

Instead of passing your ORCID iD to assertion_attributed_to, you can easily tell nanopub to attribute the assertion to the ORCID iD in your profile by setting attribute_assertion_to_profile=True.

Specifying custom provenance triples

You can add your own triples to the provenance graph of the nanopublication by passing them in an rdflib.Graph object to the provenance_rdf argument:

import rdflib
from nanopub import namespaces, Nanopub

my_assertion = rdflib.Graph()
my_assertion.add((rdflib.term.BNode('timbernserslee'), rdflib.RDF.type, rdflib.FOAF.Person))

provenance_rdf = rdflib.Graph()
provenance_rdf = provenance_rdf.add((
    BNode('timbernserslee'),
    namespaces.PROV.actedOnBehalfOf,
    BNode('markzuckerberg')
))

np = Nanopub(
    assertion=my_assertion,
    provenance_rdf=provenance_rdf,
    conf=NanopubConf(
        add_prov_generated_time=True,
        add_pubinfo_generated_time=True,
        attribute_publication_to_profile=True,
    )
)

Specifying custom publication info triples

You can add your own triples to the publication info graph of the nanopublication by passing them in an rdflib.Graph object to the pubinfo_rdf argument:

from rdflib import Graph, BNode, RDF, FOAF
from nanopub import namespaces, Nanopub

my_assertion = Graph()
my_assertion.add((BNode('timbernserslee'), RDF.type, FOAF.Person))

pubinfo_rdf = rdflib.Graph()
pubinfo_rdf = pubinfo_rdf.add((
    BNode('activity'),
    RDF.type,
    namespaces.PROV.Activity
))

np = Nanopub(
    assertion=my_assertion,
    pubinfo=pubinfo_rdf,
    conf=NanopubConf(
        add_prov_generated_time=True,
        add_pubinfo_generated_time=True,
        attribute_publication_to_profile=True,
    )
)