nanopub-java: A Java Library for Nanopublications

nanopub-java:
A Java Library for Nanopublications
Tobias Kuhn
http://www.tkuhn.org
@txkuhn
VU University Amsterdam
5th Workshop on Linked Science (LISC) 2015
at ISWC 2015, Bethlehem, Pennsylvania, USA
12 October 2015

The nanopub-java Library
https://github.com/Nanopublication/nanopub-java
This library can be useful in a number of scenarios:
• To represent and share chunks of data in RDF in a
provenance-aware manner (as nanopublications)
• To make RDF content verifiable and immutable (with trusty
URIs)
• To define large or small datasets of RDF content where the
data entries can be individually addressed and recombined in
new datasets (with nanopublication indexes)
• To quickly publish RDF snippets in a verifiable and permanent
manner (relying on an existing server network)
• To retrieve existing nanopublications from the network
(5 millions and counting)
• To digitally sign RDF snippets (experimental)
Tobias Kuhn, VU University Amsterdam nanopub-java: A Java Library for Nanopublications 2 / 19

Nanopublications: Linked Data Containers for
Provenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org / @nanopub org

Nanopublication Example
sub:assertion {
sub:_3 a rdf:Statement ; rdf:subject schem:Adenosine%20triphosphate ;
rdf:predicate belv:decreases ; rdf:object sub:_1 ;
occursIn: obo:UBERON_0001134 , species:9606 .
sub:_1 a go:0003824 ; hasAgent: sub:_2 .
sub:_2 a Protein: ; geneProductOf: hgnc:12517 .
}
sub:provenance {
sub:assertion prov:hadPrimarySource pubmed:9703368 ;
prov:wasDerivedFrom beldoc: , sub:_4 .
beldoc: dce:description "Approximately 61,000 statements." ;
dce:rights "Copyright (c) 2011-2012, Selventa. All rights reserved." ;
dce:title "BEL Framework Large Corpus Document" ;
pav:authoredBy sub:_5 ; pav:version "20131211" .
sub:_4 prov:value "UCP1 contains six potential transmembrane a-helices (72) and
prov:wasQuotedFrom pubmed:9703368 .
sub:_5 rdfs:label "Selventa" .
}
sub:pubinfo {
this: dct:created "2014-07-03T14:34:13.226+02:00"^^xsd:dateTime ;
pav:createdBy orcid:0000-0001-6818-334X , orcid:0000-0002-1267-0234 .
}

Nanopublication Schema
np:Nanopublication rdf:type owl:Class.
np:Assertion rdfs:subClassOf rdfg:Graph.
np:Provenance rdfs:subClassOf rdfg:Graph.
np:PublicationInfo rdfs:subClassOf rdfg:Graph.
np:hasAssertion a owl:FunctionalProperty.
np:hasAssertion rdfs:domain np:Nanopublication.
np:hasAssertion rdfs:range np:Assertion.
np:hasProvenance a owl:FunctionalProperty.
np:hasProvenance rdfs:domain np:Nanopublication.
np:hasProvenance rdfs:range np:Provenance.
np:hasPublicationInfo a owl:FunctionalProperty.
np:hasPublicationInfo rdfs:domain np:Nanopublication.
np:hasPublicationInfo rdfs:range np:PublicationInfo.

Nanopublication Guidelines
We need libraries to enforce and check this!
http://nanopub.org/guidelines/working_draft/

check / CheckNanopub
Reads a nanopublication or several of them and checks whether any
of the well-formedness criteria are violated:
$ np check nanopubfile.trig
Summary: 3 valid (not trusty);

Trusty URIs: Cryptographic Hash Values for
Nanopublication Identifiers
Nanopublications with Trusty URIs are ...
Verifiable
+
Immutable
+
Permanent
.trighttp://example.org/r1. RA 5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70
http://trustyuri.net/
Kuhn, Dumontier. Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data. ESWC 2014.

mktrusty / MakeTrustyNanopub
Takes a non-trusty nanopublication and transforms it into one with
a newly created trusty URI:
$ np mktrusty nanopubfile.trig
or:
$ np mktrusty -v nanopubfile.trig
Nanopub URI: http://example.org/np1#RAHGB0WzgQijR88g rIwtP
Nanopub URI: http://example.org/np2#RA4xTdhe2gPctqvAwdgTU4
Nanopub URI: http://example.org/np3#RAEjvXP0xTkeIa2mKmYT66
This generates a ﬁle trusty.nanopubfile.trig:
$ np check trusty.nanopubfile.trig
Summary: 3 trusty (unsigned);

Decentralized and Reliable Publishing with a
Nanopublication Server Network
Nanopublications
with Trusty URIs
Publication
Retrieval
Propagation /
Archiving
http://npmonitor.inn.ac

publish / PublishNanopub
Uploads trusty nanopublications to the server network, and they
are then distributed among the servers of the network:
$ np publish trusty.nanopubfile.trig
3 nanopubs published at http://np.inn.ac/
In this way, a nanopublication is made permanent and its publication
cannot be undone.

status / NanopubStatus
Checks whether and how often a given nanopublication (identiﬁed by
its trusty URI) is found on the server network:
$ np status -a http://example.org/np1#RAHGB0WzgQijR88g rIw
URL: http://np.inn.ac/RAHGB0WzgQijR88g rIwtPCmzYgyO4wRMT7M
URL: http://ristretto.med.yale.edu:8080/nanopub-server/RAH
URL: http://nanopub-server.ops.labs.vu.nl/RAHGB0WzgQijR88g
URL: http://nanopubs.stanford.edu/nanopub-server/RAHGB0Wzg
URL: http://nanopubs.semanticscience.org/RAHGB0WzgQijR88g
Found on 5 nanopub servers.

get / GetNanopub
Retrieves given nanopublications from the server network, and
veriﬁes them according to their trusty URIs (only veriﬁed
nanopublications are returned):
$ np get http://www.tkuhn.ch/bel2nanopub/RAhV9IpiUEjbentzG
or:
$ np get RAhV9IpiUEjbentzGivp1Lbx0BVegp5sgE3BwS0S2RAYM

Deﬁning Datasets with Nanopublication Indexes
(which are themselves Nanopublications)
appends
has sub-index
has
element
(a) (b)
(c) (f)
(d) (e)

mkindex / MakeIndex
Takes a list of nanopublications and creates an index that refers to
them (which itself consists of one or more nanopublications):
$ np mkindex trusty.nanopubfile.trig
Index URI: http://np.inn.ac/RAFa x4h0ng NXtof35Ie9pQVsAY69
This creates a new ﬁle index.nanopubfile.trig containing the
index nanopublication(s).

Publishing / Retrieving Indexes
As indexes are also nanopublications, we can publish them in the
same way:
$ np publish index.nanopubfile.trig
1 nanopub published at http://np.inn.ac/
Retrieving the content of a nanopublication index (and not just the
top-most index nanopublication) with argument -c:
$ np get -c http://np.inn.ac/RAFa x4h0ng NXtof35Ie9pQVsAY6

Web Interface: http://nanopub.inn.ac

sign / SignNanopub (experimental)
Takes a nanopublication and digitally signs it with a given private
key.
Create a key pair:
$ np mkkeys
Digitally sign nanopublications (and make them trusty):
$ np sign nanopubfile.trig
This creates a ﬁle signed.nanopubfile.trig, which we can now
check:
$ np check signed.nanopubfile.trig
Summary: 3 signed and trusty;

Thank you for your attention!
Questions?
Further information:
• Paper for this talk: http://arxiv.org/abs/1508.04977
• Nanopublications: http://nanopub.org
• Trusty URIs: http://trustyuri.net
Come to my presentation at the main conference: Thursday, 15
October, 11:00 in the Scientiﬁc Data track: Publishing without
Publishers: a Decentralized Approach to Dissemination, Retrieval,
and Archiving of Data

nanopub-java: A Java Library for Nanopublications

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