Biomedical Ontology: Semantic Web

Resource:  The National Center for Biomedical Ontology
Information from:  www.bioontology.org

The goal of the Center is to support biomedical researchers in their knowledge-intensive work, by providing online tools and a Web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of our work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.

The Center is organized into six core components:

The Center is truly a National center, assembling the expertise of leading investigators from across the country.

Organization of the Center
The Core 1 computer-science research and the Core 2 bioinformatics research involves the participation of Stanford University, Lawrence Berkeley National Laboratory, Mayo Clinic, University of Victoria, and University of Buffalo. Two Driving Biological Projects involve investigation of model-organism databases (FlyBase and ZFIN), while the third involves analysis of clinical-trial data stored in TrialBank.

The computer-science research in Core 1 delivers tools for accessing and unifying ontologies, and Core 2 concentrates on creating tools for using these ontologies to annotate large biomedical data sets, enabling data-set analysis and integration. These tools enable the driving biological projects in Core 3. There is a direct flow of tools and technologies from Core 1 to Core 2 to Core 3, while the projects in Core 3 motivate our Center’s research activities at all levels.

The Center achieves its objectives by advancing standards of good practice, by creating tools and theories that support a wide range of driving biological projects and collaborative research activities, and by training computational biologists, specialists in informatics, and computer scientists in the use of ontologies and of the Center’s technologies in support of their research.

The Center is funded by the National Institutes of Health (NIH) and is part of the network of National Centers for Biomedical Computing.

Collaboration
A major objective of our Center is to reach out to the scientific community to provide investigators with tools and methodologies to stimulate biomedical research, and in working with these scientists, to drive future development of the Center’s resources and technologies.

 Call for Driving Biological Projects
We are seeking applications for biomedical investigations that will drive development of our Center’s technologies as well as enabling the work of the researcher and the broader biomedical community.

NIH Collaborative R01 and R21 Program
The NIH sponsors a Collaborative RO1 and R21 program designed to support projects that interact with the National Centers for Biomedical Computing. Current projects span a broad range of biomedicine and informatics technology development, and have the common theme of using ontology to enable their work. Please see NIH Collaborative R01 and R21 Program for further information on how to collaborate.

Other Collaborations
In addition, our Center seeks a variety of collaborations both with academia and industry to advance the development and use of ontologies in biology and medicine and to benefit the broader scientific community. Please see Other Collaborations for further information.

Driving Biological Projects
The Center currently supports three driving biological projects that serve as test beds for the Center’s technology and that provide feedback on our work. Please see Driving Biological Projects for further information.

Resources

We are developing algorithms and tools for accessing, visualizing, and analyzing biomedical knowledge and data. The Center’s technologies address the needs of a diverse community of users.

Core Technologies

As part of the Center’s activities, we are producing the following resources for the biomedical community:

  • An integrated library of open biomedical ontologies (OBO)
  • A database of annotations on experimental data summarizing key attributes such as anatomy, phenotype, and genetic features (OBD)
  • A Web portal (BioPortal) for accessing, visualizing, and analyzing experimental data informed using ontologies and annotations.
  • A prototype system (Ontrez) integrated with BioPortal enabling researchers to search for biomedical data associated (annotated) with specific ontology terms.
  • A tool for annotating and storing biomedical phenotypes using terms from multiple ontologies (Phenote)
  • Tools to assist biomedical investigators in the annotation of experimental data using ontologies accessible through BioPortal.Medical Researcher Tools:
BioPortal  BioPortalA public Web portal that provides access to the Center’s repositories as well as open-source ontology management, query, and visualization tools  Phenote  PhenoteA tool for annotating and storing biomedical phenotypes using terms from multiple ontologies
       
OBO Converter OBO ConverterA tool for converting OBO format files into OWL files and vice-versa    
Jambalaya JambalayaA Protégé plug-in for visualizing Protege, OWL, and RDFS ontologies and knowledge bases  LexGrid  LexGridSupport for a distributed network of lexical resources such as terminologies and ontologies
          
OBO-Edit  OBO EditA graph-based editor for OBO ontologies  Prompt  PromptA set of tools for versioning, mapping, merging, and partitioning ontologies
          
Protege  ProtégéDomain-independent ontology editor and knowledge-acquisition platform      

The Center is currently collaborating with several outside centers and communities:

  • OBO - The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who have established a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.
  • NCI - A component of the NIH, NCI conducts and supports research, training, health information dissemination, and other programs with respect to the cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and the continuing care of cancer patients and their families.
  • W3C Health Care Life Sciences Interest Group - HCLSIG is chartered to develop and support the use of Semantic Web technologies and practices to improve collaboration, research and development, and innovation adoption in the of Health Care and Life Science domains.
  • BIRN - Among other things, BIRN hosts a collaborative environment rich with tools that permit uniform access to hundreds of researchers seeking to advance diagnosis and treatment of disease, enabling communication and cooperation on multi-institutional investigations.
  • Distributed Annotation System (DAS) - DAS defines a communication protocol used to exchange biological annotations. DAS is heavily used in the genome bioinformatics community.
  • CTSA informatics community - The CTSA is a consortium that is transforming how clinical and translational research is conducted, ultimately enabling researchers to provide patients with new treatments more quickly and efficiently.

Reference:
Bioontology.org (2008). The National Center for Biomedical Ontology. Retrieved May 16, 2008, from http://www.bioontology.org/about.html.

Bioontology.org (2008). The National Center for Biomedical Ontology: Resources tools.  Retrieved May 16, 2008, from http://www.bioontology.org/tools.html