=Paper=
{{Paper
|id=Vol-1114/Poster_Lopes
|storemode=property
|title=Exploring Nanopublishing with COEUS
|pdfUrl=https://ceur-ws.org/Vol-1114/Poster_Lopes.pdf
|volume=Vol-1114
|dblpUrl=https://dblp.org/rec/conf/swat4ls/LopesSO13
}}
==Exploring Nanopublishing with COEUS==
https://ceur-ws.org/Vol-1114/Poster_Lopes.pdf
Exploring nanopublishing with COEUS
Pedro Lopes*, Pedro Sernadela, José Luís Oliveira
DETI/IEETA, University of Aveiro, Aveiro, Portugal
{pedrolopes,sernadela,jlo}@ua.pt
Abstract. A nanopublication represents the smallest unit of publishable infor-
mation. This schema enhances attribution and ownership of specific data ele-
ments. With these guidelines for relating atomic data with its authors, accessing
and exchanging knowledge becomes a more streamlined process. Nanopublica-
tions are particularly relevant in the scientific domain, where scientific publica-
tion, validation and ownership of data are essential.
The COEUS semantic web application framework delivers, in a single package,
all the tools required to rapidly build a new semantic knowledge base from
scratch, including multiple data integration algorithms and interoperability ser-
vices.
This work introduces the combination of COEUS’ integration and interoperabil-
ity features with the nanopublications standard. This results in a unique na-
nopublishing pipeline, where collections of annotated data can be modeled and
integrated, stored in a semantic knowledge base, and published through COEUS
API. These improvements to the COEUS framework greatly benefit the scien-
tific community, where creating and publishing nanopublications is still cum-
bersome.
Keywords: Semantic Web, nanopublications, data integration, application
framework.
1 Introduction
The Semantic Web [1] paradigm introduces multiple technologies and strategies
that are a perfect fit to represent real-world relationships in digital information sys-
tems, namely in the life sciences. Semantic Web standards tackle challenges in the
most diverse domains, from data heterogeneity to service interoperability (or lack
thereof) [2]. The cornerstone of this flexibility is the concept of nanopublications, a
simple micro attribution strategy enabling the creation of machine-readable
knowledge assertions, empowering a new structure level for the huge amounts of
information flooding the scientific field [3, 4].
With this standard still its infancy, new tools are required to streamline the na-
nopublications generation and publishing process. Nowadays, this process is still
manual, based on ad-hoc tools tailored to niche use cases.
This work introduces a strategy that exploits COEUS' [5] features to streamline the
creation, storage and publishing of nanopublications. This new pipeline starts with a
translation process, integrating data from existing datasets into a semantic knowledge
base, and modeling it according to the nanopublications standard. Aggregated
knowledge is made available through COEUS' API, including REST services, a
SPARQL endpoint, LinkedData interfaces and a nanopublications URI interface.
2 Background
Migrating systems to a Semantic Web environment is no different than the transi-
tion to previous paradigms. New technologies, algorithms and development strategies
are introduced, making this transition a cumbersome task. The COEUS framework
was built to overcome these challenges. The COEUS platform improves four key
features in the development of new Semantic Web applications: (1) the transition
from primitive to semantically enhanced systems; (2) the integration and triplification
of data; (3) the sharing of knowledge through interoperable interfaces; (4) the de-
ployment of a knowledge federation layer.
COEUS' flexible integration engine improves traditional data warehousing Extract-
Transform-Load tasks, enabling the acquisition of data from heterogeneous resources
(in CSV, JSON, XML, SQL, SPARQL, RDF and LinkedData) and its translation to a
semantic data abstraction. The latter organizes knowledge in a cohesive structure,
based on Entity-Concept-Item relationships. COEUS' API comprises various methods
to access data (REST services, SPARQL endpoint, LinkedData interface, Java meth-
ods), making them easily available for querying and integration in external systems.
Nanopublications expand existing Semantic Web strategies to standardize how one
can attribute provenance, authorship, publication information and further relation-
ships, always with the intention to stimulate information reuse. In a sense, nanopubli-
cations are a natural response to the exploding number and complexity behind scien-
tific data. With this standard, we can summarize published knowledge to a set of
thoroughly individualized list of assertions - the nanopublication.
In summary, nanopublications are composed of three sections, each detailing asser-
tion information, authorship and provenance, for elaborate knowledge statements [6]
– Figure 1. Nanopublications are serializable through the interoperable RDF format,
Nanopublication ID
Assertion
Subject Predicate Object
Provenance
Publication Info
Fig. 1. Basic nanopublication structure: the unique nanopublication identifier is connected to
Assertion, Provenance and Publication Information objects. Each of these contains a set of
axioms representing the nanopublication metadata.
opening the door to many new knowledge exchange possibilities and fostering their
retrieval and use. Moreover, with universal nanopublications identifiers, each na-
nopublication can be cited and their impact tracked, encouraging compliance with
open semantic web standards. In addition to normalized positive assertions, Semantic
Web's expressiveness can also be leveraged to expose negative knowledge assertions
3 Methods
The rational behind this work is to extend the base COEUS framework with sup-
port for nanopublications. This will enable a new nanopublishing pipeline where all
tasks are automated. This process includes three general steps: (1) configuring the
data abstraction to a semantic model - Figure 2-1; (2) integrating & translating data
from external resources into the internal knowledge base - Figure 2-2; (3) sharing the
nanopublications dataset - Figure 2-3. Adding nanopublishing support to COEUS
leverages on its flexibility.
Before the actual integration process, we need to setup where the data comes from
and how it will be represented according to the nanopublications format. COEUS
setup allows organizing data according to a predefined hierarchy, based on an Entity-
Concept-Item structure. With the nanopublication extension, two new properties were
added to COEUS’ configuration to enable the automated creation of nanopublications.
COEUS integration engine was updated to detect these settings and proceed accord-
ingly. The setup configuration changes are detailed next.
• coeus:isNanopublication. This predicate can be applied to the Concept configura-
tion metadata, defining the base data imports for creating new nanopublications.
Where this property is enabled, COEUS’ integration engine automatically gener-
ates new nanopublications and their respective URIs autonomously.
• coeus:np_element. This predicate can be applied to the Resource configuration
COEUS
Knowledge Base
1 2 3
COEUS Knowledge Nanopublications
Configuration Integration & Translation Access
Fig. 2. Nanopublishing pipeline activities. (1) Configuration: data translations, from primi-
tive formats to the nanopublications standard, are defined. (2) Integration and translation:
COEUS access configured resources on-the-fly and automatically generates a nanopublica-
tions knowledge base. (3) Access: the nanopublications dataset can be queried through any
of the available methods in the COEUS API.
metadata (for external resources associated with a nanopublication Concept), defin-
ing the type of data being loaded: a new assertion, provenance or publication in-
formation object.
In addition to these nanopublications-specific elements, the already existing dynamic
properties can still be used to add any predicate from any ontology to the newly gen-
erated nanopublications.
4 Conclusion
Nanopublications arise as a new strategy to cope with knowledge provenance,
ownership and sharing issues. The standard enables publishing comprehensive da-
tasets, featuring large datasets, as a collection of rich individual assertions.
This work introduces an innovative nanopublishing pipeline. By extending
COEUS, we enable a new semantic web framework to flexibly generate nanopublica-
tions dataset. These results streamline the translation of data in primitive formats to a
semantic environment and, consequently, its delivery through open web interfaces.
Furthermore, COEUS is now a “turn-key” nanopublishing solution, making the na-
nopublications dataset generation process much more agile.
Acknowledgments. The research leading to these results has received funding
from the European Community (FP7/2007-2013) under ref. no. 305444 – the
RD-Connect project, and from the QREN "MaisCentro" program, ref.
CENTRO-07-ST24-FEDER-00203 – the CloudThinking project.
References
1. Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Sci Am 284, 34 - 43 (2001)
2. Ruttenberg, A., Clark, T., Bug, W., Samwald, M., Bodenreider, O., Chen, H., Doherty, D.,
Forsberg, K., Gao, Y., Kashyap, V., Kinoshita, J., Luciano, J., Marshall, M.S., Ogbuji, C.,
Rees, J., Stephens, S., Wong, G.T., Wu, E., Zaccagnini, D., Hongsermeier, T., Neumann,
E., Herman, I., Cheung, K.-H.H.: Advancing translational research with the Semantic
Web. BMC Bioinformatics 8, S2-S2 (2007)
3. Velterop, J.: Nanopublications*: the future of coping with information overload. LOGOS:
The Journal of the World Book Community 21, 3-4 (2010)
4. Mons, B., van Haagen, H., Chichester, C., den Dunnen, J.T., van Ommen, G., van
Mulligen, E., Singh, B., Hooft, R., Roos, M., Hammond, J.: The value of data. Nature
genetics 43, 281-283 (2011)
5. Lopes, P., Oliveira, J.L.: COEUS:“semantic web in a box” for biomedical applications.
Journal of Biomedical Semantics 3, 1-19 (2012)
6. Groth, P., Gibson, A., Velterop, J.: The anatomy of a nanopublication. Information
Services and Use 30, 51-56 (2010)