Repositories
The Center's BioPortal repository allows users to access a variety of resources -
- A virtual library of biomedical ontologies, including ICD, the UMLS and its incorporated terminologies, and the content of the Open Biomedical Ontologies Library (OBO)
- User comments, and user ratings, and mappings among of the BioPortal ontologies
- Links between the ontologies in BioPortal and online biomedical data sets, accessible via BioPortal's Open Biomedical Resources (OBR)
- A database of manually entered annotations on experimental data summarizing key attributes such as anatomy, phenotype, and genetic features (OBD)
These components inform one another: ontologies provide terms for data annotation; the annotations provide a foundation for data query and analysis; the results of these studies inform revisions to the ontologies.
BioPortal's Ontology Content
The Center supports a large ontology library that users access via a Web application called BioPortal. In time, BioPortal will assume the ontology repository functionality of the OBO Repository at obo.sourceforge.net. BioPortal already contains current versions of all ontologies available in the OBO Library and several other important biomedical ontologies and terminologies. As ontology developers create production versions of their ontologies, they can submit them to the BioPortal repository, which provides the following features for the ontology community:
- Versioning - BioPortal maintains all versions of each ontology that is submitted so that users can track the release history of ontologies.
- Categorization and Description - BioPortal enables users to associate a variety of metadata with ontologies to describe their contents, such as the content area of the ontology, version number, submitting organization, and so on. BioPortal adopts the standard OMV format for storing metadata.
- Browsing - Users can view a list of all the ontologies in BioPortal, organized by category, and view the detailed metadata associated with each ontology, as well as the ontologies themselves.
- Search - Users can search for names of ontologies, as well as for particular terms within ontologies. Soundex facilities support search when the user knows what a term sounds like, but is unsure how to spell it.
- Alignment - BioPortal provides access to ontology-alignment tools to enable users to view differences between versions of the same ontology, or to align different but related ontologies.
- Quality and Ratings - OBO provides users with the ability to rate ontologies in terms of quality, usefulness, and other measures. Some ontologies of the ontologies in BioPortal are designated as part of the OBO Foundry, indicating that these ontologies adhere to certain design principles that are believed to promote interoperability.
Biomedical Resource Ontology
Biomedical researchers who need particular types of software tools should be able to search for those tools online, and download them easily. The Biomedical Resource Ontology provides a taxonomy of descriptive terms that describe a variety of software resources being produced by the National Centers for Biomedical Computing (NCBC) and by other NIH projects.
The purpose of this ontology is to make explicit the types of tools the NIH grantees produce and to enable workers around the world to describe their tools in the terms provided by this ontology. The Biomedical Resource Ontology thus enables indexing and search of software tools. Our long-term vision is for this ontology to continue to evolve in a variety of ways, ultimately meeting the needs of the broad biomedical research community who seek to find the tools they need among a rapidly expanding collection from which to choose.
Open Biomedical Resources
The National Center for Biomedical Ontology has developed a prototype system that is integrated with BioPortal known as Open Biomedical Resources (OBR). OBR processes the metadata-annotations of gene expression data sets, descriptions of radiology images, clinical-trial reports, as well as abstracts of Pubmed articles to annotate (or tag) them with terms from appropriate ontologies. OBR enables researchers to search for biomedical data (such as genomic data sets, medical images, clinical trials and published papers) that are associated (and annotated) with specific ontology terms.
Creating ontology-based annotations from the metadata in biomedical resources and identifying diagnoses, pathological states, and experimental agents contained in those resources allows the wide-spread indexing of the resources, enabling end users to formulate flexible searches for biomedical data that span both ontological terms and online data sets.
OBR addresses the key challenge of enabling researchers to find all the data sets relevant to their area of study—spanning the biological scales from molecular studies to clinical medicine—and bridging the research modalities from high-throughput experiments to clinical trials—by annotating the resource elements consistently to identify the biomedical concepts to which they relate.
Open Biomedical Data
Labels applied to observations of individual subjects and organisms are annotations on experimental data. These annotations include notions such as phenotype, environmental background, as well as details of the experimental assay. The annotations that are stored in OBD represent concepts drawn from any of the source ontologies stored in BioPortal. Any number of annotation terms can be associated with experimental data. In addition to storing the annotations themselves, OBD stores a reference to the ontology from which each term originates.