Ontologies specify the terms used to describe and represent areas of knowledge. They are commonly used by people, databases, and applications that have a requirement to share information about a subject. For example, the subject areas of medicine, real estate, and automobile repair all have specific ways of representing and communicating knowledge. Ontologies include computer-usable definitions of the basic terms describing the domain and the relationships between concepts. They encode knowledge within a domain and also knowledge that spans multiple domains. In this way, they make that knowledge reusable.  For comprehensive information on ontologies and their use in biomedical science, please visit the National Center for Biomedical Ontology (NCBiO).

The Biomedical Informatics Research Network (BIRN) project is creating a large capacity and high bandwidth network for linking disease-related databases created at multiple centers. Linking and navigating among distributed data sources is a key component of BIRN’s architecture. Each participating site creates individual digital databases to manage their experimental data and derived data products. These databases are being linked to permit cross querying and data integration across a series of federated databases, containing multi-dimensional and multi-scale information relevant to the understanding of human disease. To facilitate data exchange and database interoperability, each of the BIRN databases is mapping their schema and data to shared knowledge sources.

It is BIRN policy to use existing ontologies wherever possible and extend them as necessary if the coverage of concepts is not sufficient. New ontologies will be developed, only if and when they are needed to achieve the type of data integration and interoperability needed. New ontologies may be required if no existing ontology covers a required area or if existing ontologies provide a substantially different conceptual view of a field that cannot be reconciled with BIRN's view. The OTF recommends that any ontological endeavor within the BIRN be aligned with concurrent efforts and document links to the appropriate source ontology or to the Unified Medical Language System (UMLS). This policy applies equally to the development of lexical tools and formalisms within BIRN.

A controlled terminology is a fundamental requirement for assuring the inter-operability of the unique and diverse knowledge sources that make up BIRN's shared environment. In order to enhance collaboration across BIRN's open, fluid, and diverse infrastructure, we have adopted structured procedures to support enhanced interoperability. Specifically, BIRN is developing a set of approved ontologies along with a set of policies and procedures for adding new knowledge sources. BIRN knowledge sources include the UMLS, Gene Ontology (GO), Logical Observations Identifiers Names and Codes (LOINC), Systematized Nomenclature of Medicine Ontology (SNOMED), and NeuroNames. Mapping between these sources is provided by UMLS. Extensions to these can be handled by BIRN's Bonfire tool. The OTF is developing a set of criteria for including ontologies as BIRN knowledge sources. At least some of these criteria will align with those of the OBO Foundry, e.g., ontologies must be orthogonal to existing ontologies, and they must have unique identifiers and definitions for concepts. The OTF will assume an oversight role for the addition of ontologies to the BIRN knowledge sources, ensuring that proposed ontologies meet a basic set of criteria.

BIRNLex — In order to reduce the complexity of working with multiple ontologies, and to ensure coverage of BIRN-relevant vocabulary, the OTF is creating BIRNLex, a controlled lexicon for annotating BIRN data sources. BIRN’s data sources include structural and functional magnetic resonance imaging (MRI) databases from human subjects involved in studies of Alzheimer's disease and schizophrenia, and multiscale image databases from mouse models of human neurological disease using MRI, light, and electron microscopic imaging. The BIRNLex provides standardized terms to describe subject information, neuroanatomy, molecular species, behavioral and cognitive processes, experimental practice and design, and associated elements of primary data provenance.  The on-going development of BIRN's uniform lexicon is essential for large-scale data integration across disparate experimental studies. The latest version of BIRNLex is available to the public on the BIRN OTF public Wiki.

Bonfire — The BIRN has created Bonfire, a software tool for browsing, extending, or assembling a set of existing ontologies/terminologies for use within the BIRN environment.  Bonfire currently includes the latest version of the UMLS and NeuroNames terminologies, along with proposed extensions for the BIRN community.  The Unified Medical Language System (UMLS) facilitates the development of computer systems that can ‘understand’ the meaning of the biomedical language. NeuroNames, maintained by the University of Washington, is a structured system of neuroanatomical terminology that provides a comprehensive representation of virtually all human and nonhuman primate brain structures.

The use of Bonfire currently requires a BIRN account because these terminology resources are covered by licensing agreements. The BIRNLex will contain a subset of the vocabularies that are most relevant to BIRN data with cross references to the parent source.

BIRN FACT Sheets: Summaries of existing ontologies have been created by the OTF to describe the scope and utility of available ontologies within the BIRN context. Available sheets:

1. Gene Ontology (GO)
2. Systematized Nomenclature of Medicine Ontology (SNOMED)
3. NeuroNames
4. Mammalian Phenotype Ontology

National Center for Biomedical Ontologies: A national center for biomedical computing established to develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-readable form. The Center's resources include the Open Biomedical Ontologies (OBO) and Open Biomedical data (OBD), Web resources containing structured vocabularies for shared use across different biological and medical domains.

FuGO — The Functional Genomics Investigation Ontology is being developed to model functional genomics domains such as Proteomics.

PATO — Phenotype and Trait Ontology. A reference ontology of biological qualities.

2006

On January 26-27, the first Ontology Boot Camp was hosted at the BIRN Coordinating Center at UCSD's School of Medicine. See the Welcome PowerPoint, Concept Based Queries PowerPoint and Ontology Boot Camp Report.

BIRNLex curation sessions: The BIRN OTF is holding multiple BIRNLex curation sessions. The schedule is posted on the Wiki.

The ontologies task force was initiated by the BIRN Executive Committee to review the issue of different ontological reference interpretations by audience: anatomists, clinicians, genomics, pathologists, diagnosticians, and neurologists. The task force will recommend a process for mapping between each of these vocabularies.

Goals

• Develop policies and procedures for BIRN participants regarding ontologies.
• Keep abreast of major meetings where BIRN ontology efforts should be represented.
• Develop and maintain contact with major ontology groups.
• Educate BIRN participants on the use, development and importance of ontologies.
• Promote and develop cross test bed ontologies for animal models and human disease.

Maryann Martone (UCSD), Chair
Amarnath Gupta (UCSD)
Bill Bug (Drexel)
Christine Fennema-Notestine (UCSD)
Jessica Turner (UCI)
Jeff Grethe (UCSD)
David Kennedy (Harvard's Center for Functional Neuroimaging Technologies at Massachusetts General Hospital)
Daniel Rubin (National Center for Biomedical Ontologies)

*Carol Bean (NIH), Chair Emeritus

The BIRN Ontology Task Force has recently created a new public wiki. View