Organizations and Academic Departments With a Special Focus on Developing and Using Semantic Biomedical Ontologies

[list in process] Please send your comments and suggestions to Dr. Maryann Martone or Bill Bug.

• National Center for Biomedical Ontology (cBiO)
• "The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center's tools to enhance scientific discovery."
• "The Center's resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this biomedical information in research. "
• "The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center."
• National Center for Ontological Research (NCOR)
• "The University at Buffalo and Stanford University have established the National Center for Ontological Research (NCOR), with Buffalo and Stanford as the two principal sites, together with a number of partner institutions drawn from academia, government, and industry."
• "NCOR has the goal of advancing ontological investigation within the United States."
• "...will serve as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities in its two principal sites and in its partner institutions."
• "A special focus will be on the establishment of tools and measures for quality assurance of ontologies."
• "NCOR will provide coordination, infrastructure, and other forms of support for investigators working in the United States on theoretical ontology and on applications in fields such as ontology of the sciences, spatial and cognitive ontology, terminological systems, enterprise ontology and in a variety of defense- and homeland security-related projects."
• "It will also provide US researchers working in ontology-related areas with specialized support in seeking external funding and in assembling collaborative, interdisciplinary teams both nationally and internationally."
• "It will aid the coordination of ontological projects being pursued by its partner institutions and also develop resources for the implementation and evaluation of ontologies."
• "The Center will also engage in outreach endeavors that are designed to broaden the range of institutions and individuals accepting the goals of high quality ontology in both theory and practice."
• Bio-ontologies Special Interest Group at the Annual Intelligent Systems in Molecular Biology (ISMB) Conference
• Standards and Ontologies for Functional Genomics (SOFG)
  • "...web site provides a community resource for the development of ontologies and other controlled vocabularies relevant to biology and biological experimentation."
  • "...established as a result of the first conference on Standards and Ontologies for Functional Genomics (SOFG), which was held at the Wellcome Trust Genome Campus, Hinxton, UK, 17-20 November 2002."
  • "...bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments."

• Network of Excellence ("NoE") in Semantic Interoperability and Data Mining in Biomedicine
  • "...aim...is to establish Europe as the international scientific leader in medical and biomedical informatics. The long-term goal of the network will be the development of generic methods and tools supporting the critical tasks of the field; data mining, knowledge discovery, knowledge representation, abstraction and indexing of information, semantic-based information retrieval in a complex and high-dimensional information space, and knowledge-based adaptive systems for provision of decision support for dissemination of evidence based medicine. The "NoE" is a response to the strategic objectives addressed in the IST call 1, areas "eHealth" and "Semantic-based Knowledge Systems."
  • "...partnership of 25 participants from 11 European countries with 110 identified researchers (25 female) and 31 associated Ph.D. students (10 female)."
  • "...coordinated by Linköpings universitet, Sweden."