RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

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

What can be done with the Semantic Web? An overview of Watson-based applications

Thanks to the huge efforts deployed in the community for creating, building and generating semantic information for the Semantic Web, large amounts of machine processable knowledge are now openly available. Watson is an infrastructure component for the Semantic Web, a gateway that provides the necessary functions to support applications in using the Semantic Web. In this paper, we describe a number of applications relying on Watson, with the purpose of demonstrating what can be achieved with the Semantic Web nowadays and what sort of new, smart and useful features can be derived from the exploitation of this large, distributed and heterogeneous base of semantic information

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