Coordination of the OBO Foundry

The coordinating editors of the OBO Foundry are Michael Ashburner (GO), Chris Mungall (GO, BIRN, modENCODE, BBOP), Suzanna Lewis (GO, BIRN, modENCODE, BBOP), Alan Ruttenberg (ORG, Immport), Richard H. Scheuermann (IRD, ViPR, Immport, CTSA), and Barry Smith (NCBO, ORG, Immport). Melissa Haendel (OHSU)

The intention is to provide light-weight management, although the growth of OBO may, in the future, necessitate a more formal structure. It is appropriate to view these people as facilitators who assist independent ontology developers: by organizing meetings, making introductions between different groups, offering comments when requested, engaging in email discussions, making resources available, and other means. They work to ensure that the ontologies being developed are mutually compatible, expandable, and correctable in line with advances in biomedical science. Ontologies are tools of communication, and their utility depends on the network effects that come with wide acceptance. Experience thus far confirms that adherence to OBO principles is largely self-policing because of the positive benefits that accrue to individual members. The task of the OBO coordinators is to help to build this community.

Affiliations

Gene Ontology (GO)

The GO project provides a controlled vocabulary for describing gene and gene product attributes in any organism. Members of the GO Consortium supply annotations of gene products using this vocabulary, which can be viewed and downloaded via the GO website.

Immunology Database and Analysis Portal (ImmPort)

The ImmPort system provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT. It serves as a long-term, sustainable archive of data generated by investigators funded through the NIAID/DAIT and access to the system is currently limited (except for Reference Data Queries) to those investigators per NIAID/DAIT approval. The functionality of the ImmPort system will be expanded continuously over the life of the BISC Phase II contract to accommodate the needs of the NIAID/DAIT-funded research community.

Biomedical Informatics Research Network (BIRN)

The Biomedical Informatics Research Network (BIRN) is a geographically distributed virtual community of shared resources offering tremendous potential to advance the diagnosis and treatment of disease. BIRN enhances the scientific discoveries of biomedical scientists and clinical researchers across research disciplines.
BIRN: hosts a collaborative environment rich with tools that permit uniform access to hundreds of researchers, enabling cooperation on multi-institutional investigations; synchronizes developments in wide area networking, multiple data sources, and distributed computing; designs, tests, and releases new integrative software tools that enable researchers to pose questions and share knowledge across multiple animal models (mouse, human, and non-human primate); receives funding from the National Institutes of Health's National Center for Research Resources (NCRR), established in 2001.

ENCyclopedia Of DNA Elements (modENCODE)

The National Human Genome Research Institute (NHGRI) model organism ENCyclopedia Of DNA Elements (modENCODE) Project will try to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes. Both computational and experimental approaches are being applied by modENCODE investigators to study the genomes of these organisims. An added benefit of studying functional elements in model organisms is the ability to biologically validate the elements discovered using methods that cannot be applied in humans. The comprehensive dataset that is expected to result from the modENCODE Project will provide important insights into the biology of D. melanogaster and C. elegans as well as other organisms, including humans.

Clinical and Translational Science Awards (CTSA)

The Clinical and Translational Science Awards is a consortium that is transforming how clinical and translational research is conducted, ultimately enabling researchers to provide new treatments more efficiently and quickly to patients. The consortium is designed to encourage the development of new methods and approaches to clinical and translational research, improve training and mentoring to ensure that new investigators can navigate the increasingly complex research system, design new and improved clinical research informatics tools, assemble interdisciplinary teams that cover the complete spectrum of medical research and forge new partnerships with private and public health care organization.

Ontology Research Group (ORG)

The ORG is located in the New York State Center of Excellence in Bioinformatics and Life Sciences in Buffalo. It is engaged in foundational ontology research and in biomedical ontology development in the domain of biology and clinical medicine. A special focus of research is electronic health records.

Berkeley Bioinformatics Open Source Project (BBOP)

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems.

National Center for Biomedical Ontology (NCBO)

The NCBO is a National Center for Biomedical Computing whose participants intend to develop technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form.

Influenza Research Database (IRD)

The Influenza Research Database is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in- protected "workbench" spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.

The Virus Pathogen Database and Analysis Resource (ViPR)

The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR contains information for human pathogenic viruses belonging to the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae and Togaviridae families, with plans to support additional virus families in the future. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. Analytical and visualization tools for metadata- driven statistical sequence analysis, multiple sequence alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination are also provided. Data filtering and analysis workflows can be combined and the results saved in personal "Workbenches" for future use. ViPR tools and data are available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.