The National Center for Biomedical Ontology

Springer eBooks, 2013

2008

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a Web-based system that serves as a repository for biomedical ontologies. BioPortal defines relationships among those ontologies and between the ontologies and online data resources such as PubMed, ClinicalTrials.gov, and the Gene Expression Omnibus (GEO). BioPortal supports not only the technical requirements for access to biomedical ontologies either via Web browsers or via Web services, but also community-based participation in the evaluation and evolution of ontology content. BioPortal enables ontology users to learn what biomedical ontologies exist, what a particular ontology might be good for, and how individual ontologies relate to one another. BioPortal is available online at http://bioportal.bioontology.org.

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural- language processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a Web-based system that serves as a repository for biomedical ontologies. Bio- Portal denes relationships among those ontologies and between the ontologies and online data resources such as PubMed, Clin- icalTrials.gov, and the Gene Expression Omnibus (GEO). Bio- Portal supports not only the technical requirements for access to biomedical ontologies either via Web browsers or via Web services, but also community-based participation in the evalu- ation and evolution of ontology content. BioPortal enables on- tology users to learn what biomedical ontologies exist, what a particular ontology might be good for, and how individual on- tologies relate to one another. BioPortal is available online at http://alpha.bioontology.org.

2009

Ontologies are being used in a variety of ways by researchers in almost every life science discipline, and their use in annotation of both clinical and experimental data is now a common technique in integrative translational research. When data from different sources are described using shared, logically structured, controlled vocabularies such as the Gene Ontology (GO), this makes the data more easily retrievable and navigable, and it also enhances the degree to which they can be analyzed and combined to serve new purposes. Two major international conferences on Standards and Ontologies for Functional Genomics (SOFG), held at the Wellcome Trust Genome Campus in Hinxton, UK in 2002 and at the University of Pennsylvania School of Medicine in Philadelphia, PA in 2004, have thus far been devoted to the topic of biomedical ontology. They served to bring together researchers involved in the development and use of ontologies in addressing the data annotation needs created by the new high-throughput experimental techniques and new applications of comparative genomics in the investigation of human biology and disease. In the years since SOFG, the number of applications of ontologies in biomedicine has expanded greatly, and so also has the range and functionality of associated software tools. The Web Ontology Language (OWL) serves as a central enabling technology of the Semantic Web, which is itself increasingly being used to serve computational biomedical research in reflection of the growth of the Internet as a medium for data exchange. Ontologies are now being used in almost every domain of biomedical research, including translational medicine, drug discovery, clinical trials, neuroimaging, environmental studies, evolutionary biology, and many other fields. Ontologies have been developed to describe data at all scales, from molecular pathways to mammalian anatomy and from protein modifications to infectious disease. Increasingly, it is recognized that these different ontologies need to work together in order to maximize the degree to which they can serve the needs of researchers and clinicians, and it is the recognition of this need that led to the organization of the International Conference on Biomedical Ontology (ICBO) in Buffalo on July 24-26, 2009. ICBO brings together scientists and informaticians developing and using ontologies across the entire spectrum of biology and clinical and translational medicine. It represents a continuation not only of the SOFG series but also of multiple dissemination events organized under the auspices of the National

Nucleic Acids Research, 2011

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology .org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http:// www.bioontology.org/wiki/index.php/NCBO_REST_ services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

Omics A Journal of Integrative Biology, 2006

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. This paper is part of the special issue of OMICS on data standards.

2008

Ontologies are becoming critical to e-Science, but there are challenges for the community to find the ontologies relevant to their work, to declare mappings among related ontologies, and to provide feedback or critiques to ontology developers. We have created BioPortal, a Web portal to a virtual library of ontologies on the Semantic Web and a tool set enabling the community to access, critique, and improve ontologies. The BioPortal library contains over 50 ontologies from the biological and medical domains. In addition to a Web interface enabling researchers in cyberspace to locate these knowledge resources, BioPortal provides a suite of Web services, including ontology categorization, term search, graphical ontology visualization, and ontology version histories. As development of the knowledge resources in e-Science is increasingly collaborative, we are also creating novel tools in BioPortal to enable the community to create mappings between classes in related ontologies and to critique ontology content, providing feedback to ontology developers. Preliminary user experience with BioPortal has been extremely positive. BioPortal appears promising for unifying and disseminating ontology content on the Semantic Web, and it is providing tools needed by the research community to exploit these rich resources.

2010

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage?

2010

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion.

2008

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called 'top-level ontologies' to address this issue, and to establish strategies among leaders in the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration.