Decentralized provenance-aware publishing with nanopublications

Authors : Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier

Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age.

In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a web-based bottom-up process, without top-down control of central authorities such as publishing companies.

Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data.

We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general.

Our evaluation of the current network shows that this system is efficient and reliable.

URL : Decentralized provenance-aware publishing with nanopublications

DOI : https://doi.org/10.7717/peerj-cs.78

Le catalogue des bibliothèques et ses données à l’heure du web

Auteur/Author : Raphaëlle Lapôtre

Le point de vue de cet article est de décrire la logique du web et du web de données à la lumière des enseignements de Michel Foucault, tels qu’on peut les lire, notamment, dans Les Mots et les Choses (1966).

Dans un premier temps, les données sur le web jouent le rôle que jouait au XVIIe siècle la monnaie : à la fois représentation des richesses, substitution dans le cadre d’échange différés et mesure de la valeur, en l’occurrence, de l’attention que leur attribuent les acteurs du web.

Du point de vue de la gestion de l’attention, deux visions économiques s’affrontent sur le web : l’une, plutôt utilitariste, s’attache à définir la valeur du point de vue de la subjectivité humaine et du besoin, l’autre, plutôt physiocrate, cherche à transformer l’abondance d’information pour la découper et la synthétiser.

Le Web de données quant à lui, reflète ces deux logiques au sein même du langage qui sert à l’exprimer : le RDF reproduit à sa manière l’attribution qui est le principe du lien hypertexte, tandis que les ontologies donnent à lire une classification du monde et des données qui le représentent.

D’une certaine manière, la logique épistémologique des données massives bouleversent quelque peu la logique représentationnelle du web, leur principe fondamental n’étant plus l’analyse ou la critique, mais bien la recherche de corrélation, la mise en parallèle, le commentaire.

URL : https://halshs.archives-ouvertes.fr/halshs-01331753v1

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Authors : Andra Waagmeester,  Martina Kutmon, Anders Riutta, Ryan Miller,  Egon L. Willighagen, Chris T.  Evelo , Alexander R. Pico

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data.

The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org.

Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries.

In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web.

WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development.

We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

URL : Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

DOI : http://dx.doi.org/10.1371/journal.pcbi.1004989

Linking Libraries to the Web: Linked Data and the Future of the Bibliographic Record

« The ideas behind Linked Data and the Semantic Web have recently gained ground and shown the potential to redefine the world of the web. Linked Data could conceivably create a huge database out of the Internet linked by relationships understandable by both humans and machines. The benefits of Linked Data to libraries and their users are potentially great, but so are the many challenges to its implementation. The BIBFRAME Initiative provides the possible framework that will link library resources with the web, bringing them out of their information silos and making them accessible to all users. »

URL : http://microblogging.infodocs.eu/wp-content/uploads/2015/02/gonzales2014.pdf

DOI : 10.6017/ital.v33i4.5631

Le mouvement Open Data dans la…

Le mouvement  » Open Data  » dans la grande transformation des intelligences collectives et face à la question des écritures, du web sémantique et des ontologies :

« Le capitalisme cognitif a deux caractéristiques principales, l’intelligence collective et l’utilisation intensive des technologies de l’information, fondées sur la numérisation du contenu, des procédures et des écritures. Dans cet article, nous essayons d’examiner le mouvement Open Data face à la transformation des intelligences collectives et analysons ce processus dans le cadre de l’action publique, de la science, de l’intelligence logicielle, de la stratégie. Nous montrons comment ce mouvement s’articule avec la question du web sémantique, des ontologies, avec la montée de l’algorithmique. Dans ce cadre, l’émergence du  » data mining » se présente comme « récit impérial », comme le récit des sociétés performatives. S’ouvre également la possibilité de nouveaux modes de gouvernance, l’émergence de nouvelles façons de penser le politique et l’espace public. »

« Cognitive capitalism has two main characteristics, collective intelligence and the intensive use of information technology, based on the digitization of content, procedures and writings. In this paper, we try to examine the Open Data movement faced with the transformation of collective intelligence. We analyze this process in the context of public policy, science, intelligence software. We show how this movement articulates with the issue of semantic web ontologies and with the rise of algorithmic. We emphasize, indirectly but strong, on the emergence of « data mining » as « imperial narrative, » as the story of performative societies in the context of anthropological stratum Internet. We outline the possibility of new modes of governance and the emergence of new ways of thinking about politics and public space. The future of democratic societies is partly at stake. »

URL : http://archivesic.ccsd.cnrs.fr/sic_00759618

Effective Enabling of Sharing and Reuse of Knowledge…

Effective Enabling of Sharing and Reuse of Knowledge On Semantic Web by Ontology in Date Fruit Model :

« Since Organizations have recognized that knowledge constitutes a valuable intangible asset for creating and sustaining competitive advantages, knowledge sharing has a vital role in present society. It is an activity through which information is exchanged among people through different media. Many problems face the area of knowledge sharing and knowledge reuse. Currently, knowledge sharing between entities is achieved in a very ad-hoc fashion, lacking proper understanding of the meaning of the data. Ontologies can potentially solve these problems by facilitating knowledge sharing and reuse through formal and real-world semantics. Ontologies, through formal semantics, are machine-understandable. A computer can process data, annotated with references to ontologies, and through the knowledge encapsulated in the ontology, deduce facts from the original data. The date fruit is the most enduring symbol of the Sultanate’s rich heritage. Creating ontology for dates will enrich the farming group and research scholars in the agro farm area. »

URL : http://arxiv.org/abs/1207.2232