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 has been involved in developing a set of approved ontologies along with a set of policies and procedures for adding new knowledge sources. BIRN knowledge sources originally included 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. The ontologies being developed by BIRN, which have been focused on the neuroscience activities of the test beds, have now been incorporated into NeuroLex. NeuroLex (http://www.neurolex.org), supported by the Neuroscience Information Framework (NIF; http://www.neuinfo.org), is a dynamic lexicon of neuroscience concepts. 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.

NeuroLex (formerly BIRNLex) — NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction. NeuroLex also includes detailed concepts for describing experimental techniques and instruments typically employed to carry out neuroscientific studies, as well as concepts for describing digital resources being created throughout the neuroscience community. Following best practices established by the Open Biological Ontology (OBO) community, NeuroLex reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources as necessary. Each concept is accompanied by a human readable definition to facilitate the application of NeuroLex to data. Each distinct domain module is represented using the Web Ontology Language (OWL). The latest information on NeuroLex is available at http://www.neuinfo.org/about/vocabularies.shtml

NeuroLex Wiki —

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