48 research outputs found
Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data
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.
Making Digital Artifacts on the Web Verifiable and Reliable
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
nanopub-java: A Java Library for Nanopublications
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
Provenance-Centered Dataset of Drug-Drug Interactions
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
Decentralized provenance-aware publishing with nanopublications
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
Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data
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
Science Bots: a Model for the Future of Scientific Computation?
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