7,976 research outputs found
\u3cem\u3eJanus\u3c/em\u3e: From Workflows to Semantic Provenance and Linked Open Data
Data provenance graphs are form of metadata that can be used to establish a variety of properties of data products that undergo sequences of transformations, typically specified as workflows. Their usefulness for answering user provenance queries is limited, however, unless the graphs are enhanced with domain-specific annotations. In this paper we propose a model and architecture for semantic, domain-aware provenance, and demonstrate its usefulness in answering typical user queries. Furthermore, we discuss the additional benefits and the technical implications of publishing provenance graphs as a form of Linked Data. A prototype implementation of the model is available for data produced by the Taverna workflow system
bdbms -- A Database Management System for Biological Data
Biologists are increasingly using databases for storing and managing their
data. Biological databases typically consist of a mixture of raw data,
metadata, sequences, annotations, and related data obtained from various
sources. Current database technology lacks several functionalities that are
needed by biological databases. In this paper, we introduce bdbms, an
extensible prototype database management system for supporting biological data.
bdbms extends the functionalities of current DBMSs to include: (1) Annotation
and provenance management including storage, indexing, manipulation, and
querying of annotation and provenance as first class objects in bdbms, (2)
Local dependency tracking to track the dependencies and derivations among data
items, (3) Update authorization to support data curation via content-based
authorization, in contrast to identity-based authorization, and (4) New access
methods and their supporting operators that support pattern matching on various
types of compressed biological data types. This paper presents the design of
bdbms along with the techniques proposed to support these functionalities
including an extension to SQL. We also outline some open issues in building
bdbms.Comment: This article is published under a Creative Commons License Agreement
(http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute,
display, and perform the work, make derivative works and make commercial use
of the work, but, you must attribute the work to the author and CIDR 2007.
3rd Biennial Conference on Innovative Data Systems Research (CIDR) January
710, 2007, Asilomar, California, US
A Linked Data Approach to Sharing Workflows and Workflow Results
A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users
The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web
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
Managing the Provenance of Crowdsourced Disruption Reports
A paid open access option is available for this journal. Authors own final version only can be archived Publisher's version/PDF cannot be used On author's website immediately On any open access repository after 12 months from publication Published source must be acknowledged Must link to publisher version Set phrase to accompany link to published version (see policy) Articles in some journals can be made Open Access on payment of additional chargePublisher PD
Modelling Provenance of Sensor Data for Food Safety Compliance Checking
The research described here was funded by an award made by the RCUK IT as a Utility Network+ (EP/K003569/1) and the UK Food Standards Agency. We thank the owner and staff of Rye & Soda restaurant, Aberdeen for their support throughout the project.Postprin
A General Framework for Representing, Reasoning and Querying with Annotated Semantic Web Data
We describe a generic framework for representing and reasoning with annotated
Semantic Web data, a task becoming more important with the recent increased
amount of inconsistent and non-reliable meta-data on the web. We formalise the
annotated language, the corresponding deductive system and address the query
answering problem. Previous contributions on specific RDF annotation domains
are encompassed by our unified reasoning formalism as we show by instantiating
it on (i) temporal, (ii) fuzzy, and (iii) provenance annotations. Moreover, we
provide a generic method for combining multiple annotation domains allowing to
represent, e.g. temporally-annotated fuzzy RDF. Furthermore, we address the
development of a query language -- AnQL -- that is inspired by SPARQL,
including several features of SPARQL 1.1 (subqueries, aggregates, assignment,
solution modifiers) along with the formal definitions of their semantics
Linked Data based video annotation and browsing for distance learning
We present a pair of prototype tools that enable users to mark up video with annotations and later explore related materials using Semantic Web and Linked Data approaches. The �first tool helps academics preparing Open University course materials to mark up videos with information about the subject matter and audio-visual content. The second tool enables users, such as students or academics, to find video and other materials relevant to their study
Interrogating Capabilities of IoT Devices
This research is supported by the UK Research Councils’ Digital Economy IT as a Utility Network+ (EP/K003569/1) and the dot.rural Digital Economy Hub (EP/G066051/1).Postprin
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