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<!DOCTYPE html>
<html lang="en">
<head>
<!-- trigger regeneration by this edit-->
<title>Nanopublication Guidelines</title>
<meta http-equiv='Content-Type' content='text/html;charset=utf-8'/>
<!--
=== NOTA BENE ===
For the three scripts below, if your spec resides on dev.w3 you can check them
out in the same tree and use relative links so that they'll work offline,
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<script class='remove'>
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// if your specification has a subtitle that goes below the main
// formal title, define it here
// subtitle : "an excellent document",
// if you wish the publication date to be other than today, set this
// publishDate: "2012-04-07",
// if the specification's copyright date is a range of years, specify
// the start date here:
// copyrightStart: "2009"
// if there is a previously published draft, uncomment this and set its YYYY-MM-DD date
// and its maturity status
// previousPublishDate: "1977-03-15",
// previousMaturity: "WD",
// if there a publicly available Editor's Draft, this is the link
edDraftURI: "http://nanopub.org/guidelines/working_draft",
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"css/common.css"],
// editors, add as many as you like
// only "name" is required
editors: [
{
name: "Paul Groth",
url: "http://www.few.vu.nl/~pgroth/",
company: "VU University Amsterdam",
companyURL: "http://www.vu.nl"
},
{name: "Erik Schultes", url: "", company: "LUMC", companyURL: "http://www.lumc.nl"},
{name: "Mark Thompson", url: "", company: "LUMC", companyURL: "http://www.lumc.nl"},
{name: "Zuotian Tatum", url: "", company: "LUMC", companyURL: "http://www.lumc.nl"},
{
name: "Michel Dumontier",
url: "http://dumontierlab.com",
company: "Stanford University",
companyURL: "http://stanford.edu"
},
{
name: "Tobias Kuhn",
url: "http://www.tkuhn.org/",
company: "VU University Amsterdam",
companyURL: "http://vu.nl/"
},
{
name: "Christine Chichester",
url: "",
company: "Swiss Institute of Bioinformatics (SIB)",
companyURL: "http://www.isb-sib.ch/"
},
],
authors: [
{
name: "Alasdair J G Gray", url: "http://www.alasdairjggray.co.uk/",
company: "Heriot-Watt University", companyURL: "http://www.hw.ac.uk/"
},
{name: "Kees Burger", url: "", company: "NBIC", companyURL: "http://www.nbic.nl"},
{name: "Spyros Kotoulas", url: "", company: "VU University Amsterdam", companyURL: "http://www.vu.nl"},
{name: "Antonis Loizou", url: "", company: "VU University Amsterdam", companyURL: "http://www.vu.nl"},
{name: "Valery Tkachenko", url: "", company: "RSC", companyURL: "http://www.rsc.org"},
{
name: "Andra Waagmeester",
url: "",
company: "Maastricht University",
companyURL: "http://www.maastrichtuniversity.nl"
},
{name: "Sune Askjaer", url: "", company: "Lundbeck, ", companyURL: "www.lundbeck.com"},
{
name: "Steve Pettifer",
url: "",
company: "University of Manchester",
companyURL: "http://www.manchester.ac.uk"
},
{name: "Lee Harland", url: "", company: "Pfizer/CD", companyURL: "http://connecteddiscovery.com"},
{
name: "Carina Haupt",
url: "",
company: "Uni Bonn / Fraunhofer",
companyURL: "http://www3.uni-bonn.de/die-universitaet/events-und-veranstaltungen/deutschlandfest/angebote_stadtgebiet/fraunhofer-institute-im-b-it"
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{name: "Colin Batchelor", url: "", company: "RSC", companyURL: "http://www.rsc.org"},
{name: "Miguel Vazquez", url: "", company: "CNIO", companyURL: "http://www.cnio.es"},
{name: "José María Fernández", url: "", company: "CNIO", companyURL: "http://www.cnio.es"},
{
name: "Jahn Saito",
url: "",
company: "Maastricht University",
companyURL: "http://www.maastrichtuniversity.nl/"
},
{name: "Andrew Gibson", url: "", company: "LUMC", companyURL: "http://www.lumc.nl"},
{name: "Louis Wich", url: "", company: "DTU", companyURL: "http://www.dtu.dk"},
{name: "Jesse van Dam", url: "", company: "Wageningen UR", companyURL: "https://www.wageningenur.nl/"},
{
name: "Mark Wilkinson",
url: "http://wilkinsonlab.info",
company: "Technical University of Madrid",
companyURL: "http://upm.es"
},
],
// authors, add as many as you like.
// This is optional, uncomment if you have authors as well as editors.
// only "name" is required. Same format as editors.
//authors: [
// { name: "Your Name", url: "http://example.org/",
// company: "Your Company", companyURL: "http://example.com/" },
//],
// name of the WG
//wg : "In Charge Of This Document Working Group",
// URI of the public WG page
//wgURI : "http://example.org/really-cool-wg",
// name (without the @w3c.org) of the public mailing to which comments are due
wgPublicList: "spec-writers-anonymous",
// URI of the patent status for this WG, for Rec-track documents
// !!!! IMPORTANT !!!!
// This is important for Rec-track documents, do not copy a patent URI from a random
// document unless you know what you're doing. If in doubt ask your friendly neighbourhood
// Team Contact.
wgPatentURI: "",
orguri: "http://www.nanopub.org/",//"http://www.openphacts.org/specs/",
orgicon: "<a href='http://www.nanopub.org/'><img height='70' src='figures/logo.svg' alt='nanopublication logo'/></a>",
customorg: "Nanopublications",
customcss: "./css/ops.css",
specStatus: "WD",
shortName: "guidelines",
// publishDate: "2013-12-15",
previousMaturity: "WD",
previousPublishDate: "2012-04-30",
previousURI: "http://www.nanopub.org/guidelines/1.8",
copyrightStart: "2013",
overrideCopyright: "<p class='copyright'>This document is licensed under a <a class='subfoot' href='http://creativecommons.org/licenses/sa-by/3.0/' rel='license'>Creative Commons ShareAlike Attribution 3.0 License</a>.</p>",
};
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<script type="text/turtle">
@prefix prov: <http://www.w3.org/ns/prov#> .
<http://www.nanopub.org/2013/WD-guidelines-20131215/> prov:wasDerivedFrom <https://github.com/Nanopublication/Guidelines/commit/6d7ec9f4b87f6dcc6694fbe0b87146c142c76bb5>.
</script>
</head>
<body>
<section id='abstract'>
<p>This document specifies the general format of nanopublications.</p>
</section>
<section>
<h3>Introduction</h3>
<p>
Good descriptions of data are essential to finding, understanding and ultimately reusing data.
Here, we describe nanopublications [1,2,3], a community-driven approach to representing structured data along
with its provenance as small self-contained and citable entities. A nanopublication consists of an assertion,
the provenance of the assertion (simply called "provenance"), and the provenance of the whole nanopublication
(called "publication info"). Nanopublication are implemented in and aligned with Semantic Web technologies, such
as RDF, OWL, and SPARQL. The different levels of provenance enable users to assess the trustworthiness of data
and provides a mechanism by which authors and institutions may be acknowledged for their contribution to the
global knowledge graph. Nanopublications may be used to expose quantitative and qualitative data, as well as
hypotheses, claims, negative results, and opinions that usually go unpublished. With nanopublications, it is
possible to disseminate individual data as independent publications with or without an accompanying research
article.
</p>
<p>
This document describes the structure of a nanopublication. It offers guidelines in their composition,
implementation, and use. Related code can be found on <a href="https://github.com/Nanopublication/">Github</a>.
</p>
</section>
<section id="conformance">
<!-- This includes standard text about conformance -->
</section>
<section>
<h3>Basic Elements</h3>
<p>
Each of the three parts of a nanopublication (i.e. the assertion, provenance, and publication info) is
represented as an <a href="https://www.w3.org/RDF/">RDF</a> graph [4]. An RDF graph is a collection of RDF
triples, which comprise of subject-predicate-object tuples.
We recommend using <a href="http://www.w3.org/TR/trig/">TriG</a> syntax for writing nanopublications.
The <strong>assertion graph</strong> of the nanopublication contains such statements that form the main claim of
the nanopublications. Examples of assertions include:
</p>
<pre class='example'>
:assertion {
ex:trastuzumab ex:is-indicated-for ex:breast-cancer .
}
</pre>
<pre class='example'>
:assertion {
ex:BRCA1-gene ex:is-involved-in ex:breast-cancer .
ex:BRCA1-gene ex:encodes ex:BRCA1-protein .
ex:BRCA1-protein ex:is-expressed-in ex:breast .
}
</pre>
<p>
The <strong>provenance graph</strong> of the nanopublication contains one or more RDF triples that provide
information about the <strong>assertion</strong>. The provenance graph of a nanopublication MUST contain a link
to the assertion graph identifier. Provenance means "how this came to be" and may include any statement that
discusses how the assertion was generated, who generated it, when was it generated, where was the assertion
obtained from, and any other similar information. Examples of assertional provenance include:
</p>
<pre class='example'>
:provenance {
:assertion prov:wasDerivedFrom :experiment .
:assertion prov:wasAttributedTo orcid:0000-0003-3934-0072 .
}
</pre>
<p>
The <strong>publication information graph</strong> contains one or more RDF triples that offer provenance
information regarding the nanopublication itself. In this case, the subject of the triples in the
publicationInfo graph MUST be the nanopublication URI and SHOULD contain attribution and timestamp. Examples of
the nanopublication provenance include:
</p>
<pre class='example'>
:pubinfo {
: dct:creator orcid:0000-0003-0183-6910 .
: dct:created "2020-07-10T10:20:22.382+02:00"^^xsd:dateTime .
}
</pre>
<p>
The nanopublication itself has its own identifier (here denoted by <code>:</code>) and is linked to its parts
via triples in an additional <strong>head graph</strong>:
</p>
<pre class='example'>
:Head {
: a np:Nanopublication .
: np:hasAssertion :assertion .
: np:hasProvenance :provenance .
: np:hasPublicationInfo :pubinfo .
}
</pre>
</section>
<section>
<h3>Nanopublication Ontology</h3>
<p>
The structure of a nanopublication is defined by the following ontology using the Web Ontology Language (OWL).
The namespace <code><a href="http://www.nanopub.org/nschema">http://www.nanopub.org/nschema</a></code>.
</p>
<pre>
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix rdfg: <http://www.w3.org/2004/03/trix/rdfg-1/>.
@prefix owl: <http://www.w3.org/2002/07/owl#>.
@prefix np: <http://www.nanopub.org/nschema#>.
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.
</pre>
</section>
<section>
<h3>Well-formed Nanopublications</h3>
<p>A nanopublication MUST comply with all of the following criteria to be considered well-formed:</p>
<ul>
<li>A nanopublication consists of a set of RDF quads (i.e. subject-predicate-object + context)</li>
<li>The context (i.e. graph) of each triple has to be specified as a valid URI (i.e. no null values)</li>
<li>There is exactly one quad of the form '[N] rdf:type np:Nanopublication [H]', which identifies [N] as the
nanopublication URI, and [H] as the head URI
</li>
<li>Given the nanopublication URI [N] and its head URI [H], there is exactly one quad of the form '[N]
np:hasAssertion [A] [H]', which identifies [A] as the assertion URI
</li>
<li>Given the nanopublication URI [N] and its head URI [H], there is exactly one quad of the form '[N]
np:hasProvenance [P] [H]', which identifies [P] as the provenance URI
</li>
<li>Given the nanopublication URI [N] and its head URI [H], there is exactly one quad of the form '[N]
np:hasPublicationInfo [I] [H]', which identifies [I] as the publication information URI
</li>
<li>The URIs for [N], [H], [A], [P], [I] must all be different</li>
<li>All triples must be placed in one of [H] or [A] or [P] or [I]</li>
<li>Triples in [P] have at least one reference to [A]</li>
<li>Triples in [I] have at least one reference to [N]</li>
</ul>
<p>
This is an example of a well-formed nanopublication in TriG notation:
</p>
<pre class="example">
@prefix : <http://example.org/pub1/> .
@prefix ex: <http://example.org/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix orcid: <https://orcid.org/> .
:Head {
: a np:Nanopublication .
: np:hasAssertion :assertion .
: np:hasProvenance :provenance .
: np:hasPublicationInfo :pubinfo .
}
:assertion {
ex:trastuzumab ex:is-indicated-for ex:breast-cancer .
}
:provenance {
:assertion prov:wasDerivedFrom :experiment .
:assertion prov:wasAttributedTo orcid:0000-0003-3934-0072 .
}
:pubinfo {
: dct:creator orcid:0000-0003-0183-6910 .
: dct:created "2020-07-10T10:20:22.382+02:00"^^xsd:dateTime .
}
</pre>
</section>
<section>
<h3>Query Template</h3>
<p>
To extract an entire nanopublication from a triple store, the following SPARQL query template can be used:
</p>
<pre class="example">
prefix np: <http://www.nanopub.org/nschema#>
prefix : <...>
select ?G ?S ?P ?O where {
{graph ?G {: a np:Nanopublication}} union
{graph ?H {: a np:Nanopublication {: np:hasAssertion ?G} union {: np:hasProvenance ?G} union {: np:hasPublicationInfo ?G}}}
graph ?G {?S ?P ?O}
}
</pre>
</section>
<section>
<h3>Integrity Key</h3>
<p>
The goal of the integrity key is to establish an identifier that can be used to check if a nanopublication has
changed, thus enforcing the immutability of nanopublications.
Trusty URIs [5] are the recommended way of assigning integrity keys to nanopublications.
This is the exemplary nanopublication from Section 5 after generating and attaching a trusty URI:
</p>
<pre class="example">
@prefix this: <http://example.org/pub1/RA-0Yc_l8rK3_Ts8y7kPuZvg6FqzaOSSq0yMSS9Sg4R9I> .
@prefix sub: <http://example.org/pub1/RA-0Yc_l8rK3_Ts8y7kPuZvg6FqzaOSSq0yMSS9Sg4R9I#> .
@prefix ex: <http://example.org/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix orcid: <https://orcid.org/> .
sub:Head {
this: np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo;
a np:Nanopublication .
}
sub:assertion {
ex:trastuzumab ex:is-indicated-for ex:breast-cancer .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0003-3934-0072;
prov:wasDerivedFrom sub:experiment .
}
sub:pubinfo {
this: dct:created "2020-07-10T10:20:22.382+02:00"^^xsd:dateTime;
dct:creator orcid:0000-0003-0183-6910 .
}
</pre>
</section>
<section><h3>Further Information</h3>
Please check <a href="http://www.nanopub.org">http://www.nanopub.org</a> for further guides and community
information.
</section>
<section><h3>References</h3>
<ul>
<li>[1] Paul Groth, Andrew Gibson, and Jan Velterop. <a href="https://doi.org/10.3233/ISU-2010-0613">The Anatomy
of a Nanopublication</a>. Information Services & Use 30: 51-56. 2010.
<li>[2] Barend Mons et al. <a href="https://doi.org/10.1038/ng0411-281">The value of data</a>. Commentary,
Nature Genetics 43: 281-283. 2011.
<li>[3] Tobias Kuhn, Paolo Emilio Barbano, Mate Levente Nagy, and Michael Krauthammer. <a
href="http://www.tkuhn.ch/pub/kuhn2013eswc.pdf">Broadening the Scope of Nanopublications</a>. In
Proceedings of the 10th Extended Semantic Web Conference (ESWC). Springer, 2013.
<li>[4] Jeremy J. Carroll, Christian Bizer, Pat Hayes, and Patrick Stickler. <a
href="https://doi.org/10.1145/1060745.1060835">Named graphs, provenance and trust</a>. In Proceedings of
the 14th international conference on World Wide Web. 2005.
<li>[5] Tobias Kuhn and Michel Dumontier. <a href="https://doi.org/10.1007/978-3-319-07443-6_27">Trusty URIs:
Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data</a>. In Proceedings of the 11th
Extended Semantic Web Conference (ESWC). Springer, 2014.
</ul>
</section>
</body>
</html>