1,256 research outputs found
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
WormBase 2012: more genomes, more data, new website
Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community
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A linked data compliant framework for dynamic and web-scale consumption of web services
The While Semantic Web Services (SWS) research aims at automating Web service tasks such as discovery, orchestration and execution, its take-up is very limited so far. This is due to several reasons, such as inherent complexity of existing SWS frameworks and the considerable costs involved in creating correct SWS descriptions. In addition, while semantics are in use to enable tasks such as discovery, interaction between service consumers, providers and brokering environments is still not supported by semantic message descriptions. On the other hand, the Linked Data approach has produced a set of established principles for sharing and describing data, such as RDF as representation language and the integral use of dereferencable URIs. In this paper we propose to apply those principles to expose Web services and Web APIs and introduce a framework in which service registries as well as services contribute to the automation of service discovery, and hence, workload is distributed more efficiently. This is achieved by developing a Linked Data compliant Web services framework with that communicate with semi-centralised registries but compute their suitability for a given request themselves. All communications among different framework components are using RDF-based message protocols including service input and output. This framework aims at optimizing load balance and performance by dynamically assembling services at run time in a massively distributed Web environment
Research and Development Workstation Environment: the new class of Current Research Information Systems
Against the backdrop of the development of modern technologies in the field
of scientific research the new class of Current Research Information Systems
(CRIS) and related intelligent information technologies has arisen. It was
called - Research and Development Workstation Environment (RDWE) - the
comprehensive problem-oriented information systems for scientific research and
development lifecycle support. The given paper describes design and development
fundamentals of the RDWE class systems. The RDWE class system's generalized
information model is represented in the article as a three-tuple composite web
service that include: a set of atomic web services, each of them can be
designed and developed as a microservice or a desktop application, that allows
them to be used as an independent software separately; a set of functions, the
functional filling-up of the Research and Development Workstation Environment;
a subset of atomic web services that are required to implement function of
composite web service. In accordance with the fundamental information model of
the RDWE class the system for supporting research in the field of ontology
engineering - the automated building of applied ontology in an arbitrary domain
area, scientific and technical creativity - the automated preparation of
application documents for patenting inventions in Ukraine was developed. It was
called - Personal Research Information System. A distinctive feature of such
systems is the possibility of their problematic orientation to various types of
scientific activities by combining on a variety of functional services and
adding new ones within the cloud integrated environment. The main results of
our work are focused on enhancing the effectiveness of the scientist's research
and development lifecycle in the arbitrary domain area.Comment: In English, 13 pages, 1 figure, 1 table, added references in Russian.
Published. Prepared for special issue (UkrPROG 2018 conference) of the
scientific journal "Problems of programming" (Founder: National Academy of
Sciences of Ukraine, Institute of Software Systems of NAS Ukraine
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine
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Collaborative analysis of multi-gigapixel imaging data using Cytomine
Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries.
Results: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications
brat: a Web-based Tool for NLP-Assisted Text Annotation
We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss several case studies of real-world annotation projects using pre-release versions of BRAT and present an evaluation of annotation assisted by semantic class disambiguation on a multicategory entity mention annotation task, showing a 15 % decrease in total annotation time. BRAT is available under an opensource license from
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