=Paper=
{{Paper
|id=Vol-2537/paper-09
|storemode=property
|title=Extending the Use of Nanopublications: Retrieval, Citation and Statement Verification
|pdfUrl=https://ceur-ws.org/Vol-2537/paper-09.pdf
|volume=Vol-2537
|authors=Erika Fabris
|dblpUrl=https://dblp.org/rec/conf/fdia/Fabris19
}}
==Extending the Use of Nanopublications: Retrieval, Citation and Statement Verification==
https://ceur-ws.org/Vol-2537/paper-09.pdf
Extending the Use of Nanopublications:
Retrieval, Citation and Statement Verification
Erika Fabris[0000−0003−1991−3267]
Department of Information Engineering, University of Padua, Padua, Italy
erika.fabris@unipd.it
Abstract. In a scenario where data is as central as publications are, a
novel model to represent scientific results has been proposed, the nanop-
ublication model. This model has enormous potential for the represen-
tation of “atomic” scientific results allowing interoperability, data in-
tegration and exchange of scientific findings by using a structure that
can easily be interpreted by machines. We present our contribution to
overcome the lack of a citation standard for this model by defining a
framework to automatically generate citations for nanopublications and
to widen their use of by specifying methods and tools to ease their access,
usability and comprehension also to non-expert users.
Keywords: nanopublication · data citation · statement verification
1 Introduction
The number of scholarly publications and available scientific data and results is
growing continuously, as evidenced in [1] where the publishing rate is estimated
of one new paper every 20 seconds. Thus, nowadays, researchers have to deal
with an overwhelming amount of information and data to carry out a research
project, to find relevant information for their research or to keep up to date.
Moreover, in recent years we have seen a shift in the nature of science due to
the increasing use of data which has led to a change in the nature of scientific
publications as well. This change has made it necessary to adapt the infrastruc-
ture for managing the growing amount of scientific data [2], led to the definition
and adoption of open access policies for the access to scholarly data, to new
concepts of data scholarship [3] and sanctioned the transition to data-intensive
research where data are as essential as scientific publications [4].
In this scenario, a new model of publication, the nanopublication model, has
been proposed to overcome the increasing difficulties introduced from the grow-
ing amount of scientific results and data in founding, connecting and curating
scientific statements and in determining their provenance [5]. The model is based
on the idea that the data and atomic statements are themselves a publication
Copyright ©c 2019 for this paper by its authors. Use permitted under Creative Com-
mons License Attribution 4.0 International (CC BY 4.0). FDIA 2019, 17-18 July
2019, Milan, Italy.
and it aims to represent scientific statements in a machine-readable format to-
gether with attribution and provenance metadata and to make them accessible,
uniquely identifiable, citable and attributable and to promote interoperability
among scientific results, data integration and sharing of scientific results.
However, since the concept of nanopublication is relatively novel, some facets
of the topic have been already consolidated – e.g. their structure and storing –, on
the other hand, there are diverse unresolved open challenges related to nanopub-
lications – e.g. how to properly cite a nanopublication or a set of nanopublications
referenced within a scientific publication? How can nanopublications be used by
users who do not know their structure to access some pieces of specific informa-
tion? How to display information within a nanopublication so that it is under-
stood by human users? Is it possible to verify statements by using data from the
existing nanopublications? How to allow non-expert users to retrieve statements
from the published nanopublications relative or similar to a given statement?
Our work tackles these open challenges by defining a framework which out-
lines methods and tools to ease the access, the usability and the comprehension
of nanopublication also to non-expert users.
2 Background
Nanopublication Nanopublication is a novel publishing model to represent
minimal scientific assertions or statements together with its attribution and
provenance information [6]. A nanopublication is essentially a single assertion
in the form of an atomic statement (subject, predicate and object) associ-
ated with its provenance, which contains how its origin and generation process,
and with publication information metadata about the creation and publication.
The nanopublication schema is formally structured by making use of Seman-
tic Web technologies as three W3Cs Resource Description Framework (RDF)
graphs, which are the assertion, the provenance graph and publication informa-
tion graph, containing information serialized as RDF triples. Each RDF triple
can be represented as a node-arc-node link of an RDF graph and consists of a
subject, a predicate and an object. Each element is represented by means of an
Internationalized Resource Identifier (IRI) or an ontology term (specified using
Web Ontology Language (OWL) semantics).
The nanopublication model was introduced to be used in scholarly communi-
cation, based on the idea that scientific results can be split into atomic sentences.
The model aims to overcome the difficulties due to the growing amount of scien-
tific results, to promote data interoperability, data integration, the exchange of
scientific results, to provide a machine-readable format of representing scientific
results, and to enable the distribution of scientific statements as independent
publications even without the related research article.
Today more than 10 M nanopublications are freely available on a server net-
work and other 200 M are available as independent private datasets1 . The major-
ity of them was generated by performing automatic extraction of atomic assertion
1
http://nanopub.org/wordpress/?page_id=749
from scientific publications, the others are manually created. Nanopublications
come from several domains: so far mostly from Life Sciences domain such as
pharmacology, genomics and proteinomics, and minor datasets coming from hu-
manities domain such as philosophy, archaeology and musicology.
Several management tools are provided to perform different tasks such as the
validation of nanopublication structure, the access to subsets of nanopublications
by performing SPARQL queries or the access to specific nanopublication from
its identifier and the publication of new nanopublications. It is worth noting that
all the provided tools are addressed to expert users and in order to make use of
those tools, a full knowledge of the nanopublication anatomy, RDF structures
and OWL semantics is required. Yet not every related aspect has been already
consolidated: neither a standard and structured way for the citation nor easy
access and inspection tools for non-expert users have been provided so far.
Data Citation Citations are one of the main ‘driving force’ for the scientific
progress, to promote the diffusion of knowledge, to ensure the transparency
and reproducibility of the scientific findings, to verify research conclusions and
support the reuse of the scientific results, to assure proper attribution and credit.
Since we were witnessing a radical change in the nature of science towards
the fourth paradigm of science, which made data to be considered crucial for
scientific progress, data citation is gaining importance [8, 9]. Two are the main
aspects of data citation that have been highlighted and studied: the definition
of data citation principles and the development of solutions for computational
problems related to the generation of citation.
In particular, two international initiatives promote the definition of standard
principles for data citation: CODATA (Committee on Data of the Interna-
tional Council for Science) [13] and FORCE 11 (The Future of Research Com-
munications and e-Scholarship) [14]. Until now, several solutions to automati-
cally generate data citation snippets have been proposed mostly dealing with
databases, considering provided queries and relying on views to generate a
citation [10, 11, 12]. Unfortunately, none of these solutions can be applied to
nanopublications. Moreover, even if the property of being citable is a preroga-
tive of the nanopublications, nowadays the only way to cite them is by means of
their identifiers or referring to the whole dataset. It is worth noting that, given
that nanopublication are publications in their own right, citing a specific set of
nanopublications is important to give credit to the people who contributed to
their creation and to allow the reproducibility of works that rely on single or a
finite set of nanopublications.
3 Objectives
Our work provides the solutions to the lack of a citation standard for the
nanopublication model and some tools to extend the use of nanopublications.
Firstly we design a citation framework to automatically create human- and
machine-readable reference snippets of a single nanopublication and, afterwards,
Nanopublication
server Ontologies Web sources
Query Nanopublications Metadata
Policies
Operations
Nanopublication
ID Dereferencing Metadata
+ Mapping Metadata Citation Snippet
Enrichment
Set of
Nanopublication
IDs Landing Page
Serialization
Fig. 1: Nanopublications Citation System framework workflow.
we extend the framework to handle a more common demand: the citation for
a set of nanopublications. Then we develop the above frameworks and provide
a citation system to be used to obtain nanopublications citation to be included
in the reference list, to obtain machine-readable citation metadata and to get
a visual picture of the content of nanopublications. Moreover, to widen the us-
ability of nanopublications, our work presents the structure of a knowledge base
with interlinked existing nanopublications as its base components and methods
for access and retrieval purposes. In addition, our work provides a tool to verify
if a given statement contradicts existing assertions within the nanopublication
databases by making use of the just mentioned knowledge base.
4 Methods
Nanopublication Citation
We propose a framework, the Nanocitation framework, to automatically generate
citation snippet by considering as the only input from the user the identifier of
the nanopublication. Figure 1 shows the main components of the framework.
The key idea is that every IRI defining an element of the RDF triple in the
nanopublication can be dereferenced and other related details and information
can be extracted by requesting them to external sources. The process starts from
the user citation request, the raw nanopublication undergoes a dereferencing
and enrichment process by which the information contained in the form of
IRI identifiers is transformed into human-readable form and additional relative
details are sought. Afterwards, through the metadata mapping process, the data
within the output of the latter process (the enriched nanopublication) are
integrated to form a structured human-readable entity, so-called metadata, that
embodies more information than the original nanopublication. The semantics
and constraints of the metadata are specified in an ad-hoc formal representation.
In order to generate the reference snippet, some relevant metadata fields need
to be selected and optionally modified. The operations to be undertaken at this
point for the creation of the reference follow the policies formally defined by
the administrator database through relational algebra constructs which include
three possible types of operations: selection and sorting (which field of metadata
to integrate in the reference snippet and in what order), single-field operations
(optional operations to be performed for each field) and presentation (reference
rendering, e.g. comma/semicolon between elements).
Note that, as long as reasonable policies are used, generated references can be
concise enough to be included in the reference list of a publication, furthermore,
it allows the reader to identify the nanopublication and understand its content.
At the end of the procedure, to make up for the lack of a human-readable
visualization of nanopublications and understandable by both expert and non-
expert user, a way to access to more complete and specific information about the
relative nanopublications is provided to the user: a web page which we call ‘land-
ing page’ which provides a full picture of the nanopublication content in both a
human- and machine-readable form. The purpose of this page is to support the
user in the in-depth exploration of the nanopublication content and to obtain a
metadata citation serialization. It is worth noting that given a nanopublication
or a specific set, the system always returns the same landing page. The process
to obtain a citation reference of a set of nanopublication differs by the need to
define operations that allow to aggregate multiple citation metadata to obtain
single metadata which identifies and describes the set at a certain level of com-
pleteness. These operations, as for the policies, need to be defined by the system
administrator in a formal representation.
We implemented the Nanocitation framework [7] and publish it as a web
application (http://nanocitation.dei.unipd.it) with a simple user interface
and a RESTful API enables programmatic requests of citation snippets and
serializations.
Knowledge base of Nanopublications and Statement Verification
We plan to create a knowledge graph considering the nanopublications as the
base elements and interlinking elements by considering both relationships be-
tween information embedded in the RDF triples and both relationships between
elements obtained from the procedure of deference and enrichment of the data
within nanopublication. These relationships are formally created and maintained
by an automatic linker to be executed just after some changes in the knowledge
base such as the introduction of a new element.
Together with the knowledge base, as results of crawling and reasoning
within the data in the knowledge base, we will provide tools to get: (i) all
nanopublications containing relevant information about a given input; (ii) all
scientific statements published that are similar to a statement inserted by the
user or that contain similar or relevant elements. Moreover, we plan to design a
system which can be used by researchers to automatically or semi-automatically
verify if an input statement contradicts existing assertions in the knowledge base.
5 Final Remarks
With this ongoing work, we will provide solutions to some of the open challenges
related to the novel model to publish and represent atomic scientific statements.
We contribute to the research in the field of data citation by providing Nanoc-
itation, a general framework to obtain nanopublications citation, by outlining
a formal procedure and by providing a web app where to automatically get ci-
tation snippets and a human-readable visual representation of the information
contained in a nanopublication. Our implemented citation system embeds poli-
cies and operations that aim to create citation snippets which are short enough
to be included in a paper reference list, but, on the other hand, satisfy the data
citation requirements (identification and access of the source, persistence, ci-
tation completeness and interoperability). Besides, our platform will be useful
for researchers for the retrieval and verification of scientific results. Our cita-
tion platform, knowledge base platform and methods will make up for the lack
of a human-readable visualization and lack of a system of citation, access and
search, thus we think that our work outcome will greatly extend the usability of
nanopublications and will promote their use.
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