34 research outputs found

    Broadening the Scope of Nanopublications

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    In this paper, we present an approach for extending the existing concept of nanopublications --- tiny entities of scientific results in RDF representation --- to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.Comment: To appear in the Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013

    nanopub-java: A Java Library for Nanopublications

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    The concept of nanopublications was first proposed about six years ago, but it lacked openly available implementations. The library presented here is the first one that has become an official implementation of the nanopublication community. Its core features are stable, but it also contains unofficial and experimental extensions: for publishing to a decentralized server network, for defining sets of nanopublications with indexes, for informal assertions, and for digitally signing nanopublications. Most of the features of the library can also be accessed via an online validator interface.Comment: Proceedings of 5th Workshop on Linked Science 201

    Decentralized provenance-aware publishing with nanopublications

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    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

    Making Digital Artifacts on the Web Verifiable and Reliable

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    The current Web has no general mechanisms to make digital artifacts --- such as datasets, code, texts, and images --- verifiable and permanent. For digital artifacts that are supposed to be immutable, there is moreover no commonly accepted method to enforce this immutability. These shortcomings have a serious negative impact on the ability to reproduce the results of processes that rely on Web resources, which in turn heavily impacts areas such as science where reproducibility is important. To solve this problem, we propose trusty URIs containing cryptographic hash values. We show how trusty URIs can be used for the verification of digital artifacts, in a manner that is independent of the serialization format in the case of structured data files such as nanopublications. We demonstrate how the contents of these files become immutable, including dependencies to external digital artifacts and thereby extending the range of verifiability to the entire reference tree. Our approach sticks to the core principles of the Web, namely openness and decentralized architecture, and is fully compatible with existing standards and protocols. Evaluation of our reference implementations shows that these design goals are indeed accomplished by our approach, and that it remains practical even for very large files.Comment: Extended version of conference paper: arXiv:1401.577

    Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data

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    To make digital resources on the web verifiable, immutable, and permanent, we propose a technique to include cryptographic hash values in URIs. We call them trusty URIs and we show how they can be used for approaches like nanopublications to make not only specific resources but their entire reference trees verifiable. Digital artifacts can be identified not only on the byte level but on more abstract levels such as RDF graphs, which means that resources keep their hash values even when presented in a different format. Our approach sticks to the core principles of the web, namely openness and decentralized architecture, is fully compatible with existing standards and protocols, and can therefore be used right away. Evaluation of our reference implementations shows that these desired properties are indeed accomplished by our approach, and that it remains practical even for very large files.Comment: Small error corrected in the text (table data was correct) on page 13: "All average values are below 0.8s (0.03s for batch mode). Using Java in batch mode even requires only 1ms per file.

    Science Bots: a Model for the Future of Scientific Computation?

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    As a response to the trends of the increasing importance of computational approaches and the accelerating pace in science, I propose in this position paper to establish the concept of "science bots" that autonomously perform programmed tasks on input data they encounter and immediately publish the results. We can let such bots participate in a reputation system together with human users, meaning that bots and humans get positive or negative feedback by other participants. Positive reputation given to these bots would also shine on their owners, motivating them to contribute to this system, while negative reputation will allow us to filter out low-quality data, which is inevitable in an open and decentralized system.Comment: WWW 2015 Companion, May 18-22, 2015, Florence, Ital

    Pattern-based access control in a decentralised collaboration environment

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    As the building industry is rapidly catching up with digital advancements, and Web technologies grow in both maturity and security, a data- and Web-based construction practice comes within reach. In such an environment, private project information and open online data can be combined to allow cross-domain interoperability at data level, using Semantic Web technologies. As construction projects often feature complex and temporary networks of stakeholder firms and their employees, a property-based access control mechanism is necessary to enable a flexible and automated management of distributed building projects. In this article, we propose a method to facilitate such mechanism using existing Web technologies: RDF, SHACL, WebIDs, nanopublications and the Linked Data Platform. The proposed method will be illustrated with an extension of a custom nodeJS Solid server. The potential of the Solid ecosystem has been put forward earlier as a basis for a Linked Data-based Common Data Environment: its decentralised setup, connection of both RDF and non-RDF resources and fine-grained access control mechanisms are considered an apt foundation to manage distributed building data

    FAIR Convergence Matrix: Optimizing the Reuse of Existing FAIR-Related Resources

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    The FAIR principles articulate the behaviors expected from digital artifacts that are Findable, Accessible, Interoperable and Reusable by machines and by people. Although by now widely accepted, the FAIR Principles by design do not explicitly consider actual implementation choices enabling FAIR behaviors. As different communities have their own, often well-established implementation preferences and priorities for data reuse, coordinating a broadly accepted, widely used FAIR implementation approach remains a global challenge. In an effort to accelerate broad community convergence on FAIR implementation options, the GO FAIR community has launched the development of the FAIR Convergence Matrix. The Matrix is a platform that compiles for any community of practice, an inventory of their self-declared FAIR implementation choices and challenges. The Convergence Matrix is itself a FAIR resource, openly available, and encourages voluntary participation by any self-identified community of practice (not only the GO FAIR Implementation Networks). Based on patterns of use and reuse of existing resources, the Convergence Matrix supports the transparent derivation of strategies that optimally coordinate convergence on standards and technologies in the emerging Internet of FAIR Data and Services

    A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing

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    Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of organization and access. Peer reviewing is the main method of quality assessment, but these peer reviews are nowadays rarely published and their own complicated structure and linking to the respective articles is not accessible. In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent in a semantic way the elements of publications, their assessments, as well as the involved processes, actors, and provenance in general. To evaluate our approach, we present a dataset of 627 nanopublications representing an interlinked network of the elements of articles (such as individual paragraphs) and their reviews (such as individual review comments). Focusing on the specific scenario of editors performing a meta-review, we introduce seven competency questions and show how they can be executed as SPARQL queries. We then present a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful to answer their competency questions. In summary, we demonstrate that a unified and semantic publication model based on nanopublications can make scientific communication more effective and user-friendly

    Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data

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    Making available and archiving scientific results is for the most part still considered the task of classical publishing companies, despite the fact that classical forms of publishing centered 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. Here 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 for the Semantic Web in general. Evaluation of the current small network shows that this system is efficient and reliable.Comment: In Proceedings of the 14th International Semantic Web Conference (ISWC) 201
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