Semantic micro-contributions with decentralized nanopublication services

Authors : Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier

While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases.

Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish.

To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications.

The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments.

We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing.

URL : Semantic micro-contributions with decentralized nanopublication services


Genuine semantic publishing

Authors : Tobias Kuhn, Michel Dumontier

Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers.

This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm.

We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications.

We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead.

This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points.

URL : Genuine semantic publishing

Original location :

Semantic publishing, la sémantique dans la sémiotique des codes sources d’écrits d’écran scientifiques

Auteur/Author : Gérald Kembellec

Cet article analyse les enjeux du semantic publishing en contexte scientifique et examine sous un axe sémiotique les codes sources qui en sont le vecteur de propagation.

Sont présentés et discutés les différents signes passeurs qui rendent possible le maillage de l’écriture fragmentaire en réseau : le RDFa, les microdonnées et le JSON-LD par exemple. Leurs usages sont ici analysés et mis en relation avec les besoins et objectifs des chercheurs, qu’ils soient auteurs ou lecteurs.

Enfin, le futur du semantic publishing scientifique est anticipé de manière critique et des points de vigilance sont évoqués tant sur la gouvernance des autorités et des schémas qui étayent le linked data que sur les tentations d’user et d’abuser des bénéfices communicationnels annexes entre médiation et médiatisation.


Écrilecture : la littératie informationnelle à la croisée de l’offre et des services des intermédiaires

Auteur/Author : Evelyne Broudoux

Nous proposons ici d’observer les usages et non usages de l’offre logicielle visant l’écriture, la lecture, la préservation des données, des références, des citations et leur traitement.

Nous établissons le lien entre cette panoplie d’outils, services, plateformes, avec les acteurs de la recherche responsables de cette offre : start-ups émanant de projets de recherche, éditeurs et groupes de médias scientifiques.

Nous complétons par une exploration des services et créations logicielles liées au web de données et à l’éditorialisation sémantique des articles qui représentent des innovations notables encore à l’état de prototypes.


Réflexions sur le fragment dans les pratiques scientifiques en ligne : entre matérialité documentaire et péricope

Auteurs/Authors : Gérald Kembellec, Thomas Bottini

Cette communication propose une réflexion pluridisciplinaire (SIC, ingénierie documentaire et théorie du document numérique, informatique, « humanités numériques », histoire des pratiques savantes) sur les usages du fragment dans les pratiques documentaires scientifiques en ligne.

En prolongement de ces éléments théoriques sont proposés un modèle théorique de la segmentation des contenus en unités de sens (péricope) et des directions d’implémentation.


Automating semantic publishing

Author : Silvio Peroni

Semantic Publishing involves the use of Web and Semantic Web technologies and standards for the semantic enhancement of a scholarly work so as to improve its discoverability, interactivity, openness and (re-)usability for both humans and machines.

Recently, people have suggested that the semantic enhancements of a scholarly work should be undertaken by the authors of that scholarly work, and should be considered as integral parts of the contribution subjected to peer review. However, this requires that the authors should spend additional time and effort adding such semantic annotations, time that they usually do not have available.

Thus, the most pragmatic way to facilitate this additional task is to use automated services that create the semantic annotation of authors’ scholarly articles by parsing the content that they have already written, thus reducing the additional time required of the authors to that for checking and validating these semantic annotations.

In this article, I propose a generic approach called compositional and iterative semantic enhancement (CISE) that enables the automatic enhancement of scholarly papers with additional semantic annotations in a way that is independent of the markup used for storing scholarly articles and the natural language used for writing their content.

URL : Automating semantic publishing

Alternative location :

Biotea: semantics for Pubmed Central

Authors : Alexander Garcia​, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies.

In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.

We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language.

We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at

URL : Biotea: semantics for Pubmed Central