13,954 research outputs found
National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge
The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated
tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease
Complete Semantics to empower Touristic Service Providers
The tourism industry has a significant impact on the world's economy,
contributes 10.2% of the world's gross domestic product in 2016. It becomes a
very competitive industry, where having a strong online presence is an
essential aspect for business success. To achieve this goal, the proper usage
of latest Web technologies, particularly schema.org annotations is crucial. In
this paper, we present our effort to improve the online visibility of touristic
service providers in the region of Tyrol, Austria, by creating and deploying a
substantial amount of semantic annotations according to schema.org, a widely
used vocabulary for structured data on the Web. We started our work from
Tourismusverband (TVB) Mayrhofen-Hippach and all touristic service providers in
the Mayrhofen-Hippach region and applied the same approach to other TVBs and
regions, as well as other use cases. The rationale for doing this is
straightforward. Having schema.org annotations enables search engines to
understand the content better, and provide better results for end users, as
well as enables various intelligent applications to utilize them. As a direct
consequence, the region of Tyrol and its touristic service increase their
online visibility and decrease the dependency on intermediaries, i.e. Online
Travel Agency (OTA).Comment: 18 pages, 6 figure
NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation
Biomedical researchers use ontologies to annotate their data with ontology
terms, enabling better data integration and interoperability. However, the
number, variety and complexity of current biomedical ontologies make it
cumbersome for researchers to determine which ones to reuse for their specific
needs. To overcome this problem, in 2010 the National Center for Biomedical
Ontology (NCBO) released the Ontology Recommender, which is a service that
receives a biomedical text corpus or a list of keywords and suggests ontologies
appropriate for referencing the indicated terms. We developed a new version of
the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new
recommendation approach that evaluates the relevance of an ontology to
biomedical text data according to four criteria: (1) the extent to which the
ontology covers the input data; (2) the acceptance of the ontology in the
biomedical community; (3) the level of detail of the ontology classes that
cover the input data; and (4) the specialization of the ontology to the domain
of the input data. Our evaluation shows that the enhanced recommender provides
higher quality suggestions than the original approach, providing better
coverage of the input data, more detailed information about their concepts,
increased specialization for the domain of the input data, and greater
acceptance and use in the community. In addition, it provides users with more
explanatory information, along with suggestions of not only individual
ontologies but also groups of ontologies. It also can be customized to fit the
needs of different scenarios. Ontology Recommender 2.0 combines the strengths
of its predecessor with a range of adjustments and new features that improve
its reliability and usefulness. Ontology Recommender 2.0 recommends over 500
biomedical ontologies from the NCBO BioPortal platform, where it is openly
available.Comment: 29 pages, 8 figures, 11 table
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
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
Towards a biodiversity knowledge graph
One way to think about "core" biodiversity data is as a network of connected entities, such as taxa, taxonomic names, publications, people, species, sequences, images, and collections that form the "biodiversity knowledge graph". Many questions in biodiversity informatics can be framed as paths in this graph. This article explores this futher, and sketches a set of services and tools we would need in order to construct the graph
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