12,238 research outputs found
Identitas: A Better Way To Be Meaningless
It is often recommended that identifiers for ontology terms should be
semantics-free or meaningless. In practice, ontology developers tend to use
numeric identifiers, starting at 1 and working upwards. In this paper we
present a critique of current ontology semantics-free identifiers;
monotonically increasing numbers have a number of significant usability flaws
which make them unsuitable as a default option, and we present a series of
alternatives. We have provide an implementation of these alternatives which can
be freely combined.Comment: 2 pages, accepted at ICBO 201
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the
biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in
the use of models as well as the development of improved software systems and the availability of better, cheaper
computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model
repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in
these repositories should be extensively tested and encoded in community-supported and standardised formats. In
addition, the models and their components should be cross-referenced with other resources in order to allow their
unambiguous identification.
Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a
freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative
models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by
BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled
vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various
formats. Reaction network diagrams generated from the models are also available in several formats. BioModels
Database also provides features such as online simulation and the extraction of components from large scale models
into smaller submodels. Finally, the system provides a range of web services that external software systems can use to
access up-to-date data from the database.
Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by
the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the
clustering of models based upon their annotations. Model deposition to the database today is advised by several
publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying
software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU
General Public License
Mapping Big Data into Knowledge Space with Cognitive Cyber-Infrastructure
Big data research has attracted great attention in science, technology,
industry and society. It is developing with the evolving scientific paradigm,
the fourth industrial revolution, and the transformational innovation of
technologies. However, its nature and fundamental challenge have not been
recognized, and its own methodology has not been formed. This paper explores
and answers the following questions: What is big data? What are the basic
methods for representing, managing and analyzing big data? What is the
relationship between big data and knowledge? Can we find a mapping from big
data into knowledge space? What kind of infrastructure is required to support
not only big data management and analysis but also knowledge discovery, sharing
and management? What is the relationship between big data and science paradigm?
What is the nature and fundamental challenge of big data computing? A
multi-dimensional perspective is presented toward a methodology of big data
computing.Comment: 59 page
Integration of all FSSIM components within SEAMLESS-IF and a stand alone Graphical User Interface for FSSIM
Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use,
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Ontology mapping for semantically enabled applications
In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, using machine-learning technologies. We discuss challenges and solutions for better ontology mappings, as well as how to select ontologies before their application. In addition, we describe tools and algorithms for ontology mapping, including evaluation of tool capability and quality of mappings. Finally, we outline the requirements for an ontology mapping service (OMS) and the progress being made towards implementation of such sustainable services
The art of video MashUp: supporting creative users with an innovative and smart application
In this paper, we describe the development of a new and innovative tool of video mashup. This application is an easy to use tool of video editing integrated in a cross-media platform; it works taking the information from a repository of videos and puts into action a process of semi-automatic editing supporting users in the production of video mashup. Doing so it gives vent to their creative side without them being forced to learn how to use a complicated and unlikely new technology. The users will be further helped in building their own editing by the intelligent system working behind the tool: it combines semantic annotation (tags and comments by users), low level features (gradient of color, texture and movements) and high level features (general data distinguishing a movie: actors, director, year of production, etc.) to furnish a pre-elaborated editing users can modify in a very simple way
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