5,628 research outputs found
Selected papers from the 15th Annual Bio-Ontologies special interest group meeting
© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes
A pattern-based approach to a cell tracking ontology
Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations
vSPARQL: A View Definition Language for the Semantic Web
Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages
Knowledge-infused and Consistent Complex Event Processing over Real-time and Persistent Streams
Emerging applications in Internet of Things (IoT) and Cyber-Physical Systems
(CPS) present novel challenges to Big Data platforms for performing online
analytics. Ubiquitous sensors from IoT deployments are able to generate data
streams at high velocity, that include information from a variety of domains,
and accumulate to large volumes on disk. Complex Event Processing (CEP) is
recognized as an important real-time computing paradigm for analyzing
continuous data streams. However, existing work on CEP is largely limited to
relational query processing, exposing two distinctive gaps for query
specification and execution: (1) infusing the relational query model with
higher level knowledge semantics, and (2) seamless query evaluation across
temporal spaces that span past, present and future events. These allow
accessible analytics over data streams having properties from different
disciplines, and help span the velocity (real-time) and volume (persistent)
dimensions. In this article, we introduce a Knowledge-infused CEP (X-CEP)
framework that provides domain-aware knowledge query constructs along with
temporal operators that allow end-to-end queries to span across real-time and
persistent streams. We translate this query model to efficient query execution
over online and offline data streams, proposing several optimizations to
mitigate the overheads introduced by evaluating semantic predicates and in
accessing high-volume historic data streams. The proposed X-CEP query model and
execution approaches are implemented in our prototype semantic CEP engine,
SCEPter. We validate our query model using domain-aware CEP queries from a
real-world Smart Power Grid application, and experimentally analyze the
benefits of our optimizations for executing these queries, using event streams
from a campus-microgrid IoT deployment.Comment: 34 pages, 16 figures, accepted in Future Generation Computer Systems,
October 27, 201
Common features of killer apps: A comparison with Protégé
Killer apps are highly transformative technologies that create new markets and widespread patterns of behaviour. IT generally, and the Web in particular, has benefited from killer apps creating new networks of users. The Semantic Web community on the other hand, is still unsure whether any of their applications could become a killer app. This paper sheds some light on the main aspects of killer apps in general, and compares them with the features of Protégé as a killer app for ontology curation and management
e-Social Science and Evidence-Based Policy Assessment : Challenges and Solutions
Peer reviewedPreprin
Estimating Fire Weather Indices via Semantic Reasoning over Wireless Sensor Network Data Streams
Wildfires are frequent, devastating events in Australia that regularly cause
significant loss of life and widespread property damage. Fire weather indices
are a widely-adopted method for measuring fire danger and they play a
significant role in issuing bushfire warnings and in anticipating demand for
bushfire management resources. Existing systems that calculate fire weather
indices are limited due to low spatial and temporal resolution. Localized
wireless sensor networks, on the other hand, gather continuous sensor data
measuring variables such as air temperature, relative humidity, rainfall and
wind speed at high resolutions. However, using wireless sensor networks to
estimate fire weather indices is a challenge due to data quality issues, lack
of standard data formats and lack of agreement on thresholds and methods for
calculating fire weather indices. Within the scope of this paper, we propose a
standardized approach to calculating Fire Weather Indices (a.k.a. fire danger
ratings) and overcome a number of the challenges by applying Semantic Web
Technologies to the processing of data streams from a wireless sensor network
deployed in the Springbrook region of South East Queensland. This paper
describes the underlying ontologies, the semantic reasoning and the Semantic
Fire Weather Index (SFWI) system that we have developed to enable domain
experts to specify and adapt rules for calculating Fire Weather Indices. We
also describe the Web-based mapping interface that we have developed, that
enables users to improve their understanding of how fire weather indices vary
over time within a particular region.Finally, we discuss our evaluation results
that indicate that the proposed system outperforms state-of-the-art techniques
in terms of accuracy, precision and query performance.Comment: 20pages, 12 figure
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