156 research outputs found

    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

    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

    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

    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.

    Provenance-Centered Dataset of Drug-Drug Interactions

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    Over the years several studies have demonstrated the ability to identify potential drug-drug interactions via data mining from the literature (MEDLINE), electronic health records, public databases (Drugbank), etc. While each one of these approaches is properly statistically validated, they do not take into consideration the overlap between them as one of their decision making variables. In this paper we present LInked Drug-Drug Interactions (LIDDI), a public nanopublication-based RDF dataset with trusty URIs that encompasses some of the most cited prediction methods and sources to provide researchers a resource for leveraging the work of others into their prediction methods. As one of the main issues to overcome the usage of external resources is their mappings between drug names and identifiers used, we also provide the set of mappings we curated to be able to compare the multiple sources we aggregate in our dataset.Comment: In Proceedings of the 14th International Semantic Web Conference (ISWC) 201

    Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature

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    Constructing a biodiversity knowledge graph will require making millions of cross links between diversity entities in different datasets. Researchers trying to bootstrap the growth of the biodiversity knowledge graph by constructing databases of links between these entities lack obvious ways to publish these sets of links. One appealing and lightweight approach is to create a "datasette", a database that is wrapped together with a simple web server that enables users to query the data. Datasettes can be packaged into Docker containers and hosted online with minimal effort. This approach is illustrated using a dataset of links between globally unique identifiers for plant taxonomic namesand identifiers for the taxonomic articles that published those names

    The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

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    Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

    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
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