Extensions

  • IDO - HIV - used in the HIV Toolbox (http://www.bio-toolkit.com)
  • IDO - Dengue fever
  • IDO - infective endocarditis - Dr. Sivaram Arabandi is developing an IDO extension ontology for infective endocarditis. Preliminary work can be found here: http://sivsmusings.wordpress.com/.
  • IDO - influenza - a collaborative group of influenza researchers have established an influenza application ontology extensible for any virus sequence and surveillance collection project which encompasses the core IDO biomedical and clinical aspects of infectious diseases for influenza. Working together Joanne Luciano (MITRE), Lynn Schriml (University of Maryland, School of Medicine), Burke Squires (University of Texas Southwestern Medical Center (UTSW)) and Richard Scheuermann (UTSW) have consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS) with the help of Eric Bortz (Mount Sinai School of Medicine) and Torsten Staab (Los Alamos National Laboratory), and the Gemina and Influenza Virus Genome Projects. The immediate goal of I-IDO is to apply the Influenza Infectious Disease Ontology to data collected as part of the CEIRS projects in an effort to enable influenza researchers to more easily elucidate the causes of influenza virulence and pathogenesis.
  • IDO - malaria and other vector-borne diseases - Dr. Christos Louis’ research group at the Institute of Molecular Biology and Biochemistry (IMBB), one of the seven institutes of the Foundation for Research and Technology – Hellas (FORTH), based in Crete, is developing an IDO extension for malaria and other vector-borne diseases. The group is working in parallel to develop an ontology of the physiological processes of disease vectors that play a direct or indirect role in disease transmission. These ontology development efforts are being pursued within the context of VectorBase, an NIAID Bioinformatics Resource Center for invertebrate vectors of human pathogens, and embracing efforts to construct decision support systems for vector-borne diseases.
  • IDO - Staphylococcus aureus bacteremia - In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Lindsay G. Cowell (Duke University Medical Center) and Barry Smith (University at Buffalo) have developed a draft ontology of Staphylococcus aureus bacteremia. The ontology is being used to analyze networks of functionally related gene products to identify host genes conferring susceptibility to Staphylococcus aureus bacteremia.
  • IDO - tuberculosis - In collaboration with Dr. Carol Dukes-Hamilton at Duke University Medical Center, Drs. Lindsay G. Cowell (Duke University Medical Center) and Barry Smith (University at Buffalo) have begun developing a draft ontology of tuberculosis. The Tuberculosis Ontology is being applied the development a tuberculosis clinical decision support system.
  • IDO - Vaccines - The Vaccine Ontology is being developed in the context of a large database and textmining effort led by Dr. Yongqn He at the University of Michigan. Drs. Lindsay G. Cowell (Duke University Medical Center) and Barry Smith (University at Buffalo) are collaborating with Dr. He on development of the Vaccine Ontology, and Dr. He is applying the ontology to the annotation of data resulting from vaccine research, to natural language processing of primary scientific literature describing the results of vaccine research, and to the management of the resulting data and information in an online public information resource called the Vaccine Investigation and Online Information Network (VIOLIN) (http://violinet.org).
  • IDO - brucellosis - The Brucellosis Ontology(BO) is being developed in Dr. Yongqun He's group as well. BO captured the terms relevant to brucellosis-specific knowledge including symptoms, pathology, virulence factors, epidemiology, diagnosis, prevention and treatment under the IDO-Core structure.(http://bo-ontology.svn.sourceforge.net/viewvc/bo-ontology/trunk/src/ontology/BO.owl)