Infectious Disease Ontology 2008

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Background

The goal for the 2007 Infectious Disease Ontology workshop (IDO 2007) was to lay the foundation for a distributed, community-based approach to developing the ontology coverage needed for the infectious disease domain. The workshop had four primary outcomes:

  • Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;
  • Development of a core Infectious Disease Ontology (IDO) which is designed to serve as a consensus-based controlled vocabulary resource for annotation of data representing all entities relevant to infectious diseases generally;
  • Establishment of a method for creating a set of ontologies that can be developed in a distributed fashion yet together cover the entire infectious disease domain (the set consists of the above-described core IDO ontology plus sub-domain-specific extensions of the core, such as IDO-tuberculosis, IDO-malaria);
  • Formation of an Infectious Disease Ontology Consortium (IDOC) whose members have agreed to contribute towards continued development of the core IDO and to develop seven different sub-domain-specific ontologies.

IDO 2008

Goals

To capitalize on the above-mentioned outcomes and sustain the momentum gained from the 2007 workshop, we have scheduled a second Infectious Disease Ontology workshop in Buffalo, NY on September 16-17, 2007. The goals of this meeting are:

  • i) providing training for new consortium members,
  • ii) providing and testing a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains
  • iii) critically evaluating the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,
  • iv) identifying key application test cases, such as ontology-based natural language processing, to be developed over the coming year,
  • v) significantly expanding representation in the IDOC for sub-domains still lacking development effort, and
  • vi) involving representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.

Tentative Schedule

For each session below, one person has been designated as the session moderator. All sessions will emphasize group discussion over presentation. Moderators of the ontology evaluation sessions will be responsible for beginning the session with a brief presentation of the ontology and will be prepared to navigate and display the ontology throughout the discussion. Moderators for the remaining sessions will be responsible for jumpstarting discussion with a brief outline of discussion points.

Pre-workshop training session: Monday September 15

  • 7:00pm to 9:00pm Introduction to Principles of Ontology Development

Barry Smith and Lindsay Cowell

Day 1: Tuesday September 16

  • 9:00 am to 10:30 am
Lindsay Cowell: Presentation and Critical Evaluation of the Core Infectious Disease Ontology
  • 10:30 am to 11:00 am Coffee break
  • 11:00 am to 12:30 pm
Yongun He: Presentation and Critical Evaluation of the Vaccine Ontology
  • 12:30 pm to 2:00 pm Lunch
  • 2:00 pm to 3:00 pm
Carol Dukes-Hamilton: Presentation and Critical Evaluation of the Tuberculosis Ontology
  • 3:00 pm to 4:00 pm
Vance Fowler: Presentation and Critical Evaluation of the Staphylococcus aureus Ontology
  • 4:00 pm to 4:30 pm Coffee break
  • 4:30 pm to 5:30 pm
Sivaram Arabandi: Presentation and Critical Evaluation of the Infective Endocarditis Ontology
  • 5:30 pm to 7:00 pm Dinner
  • 7:00 pm to 9:00 pm
Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis

Day 2: Wednesday September 17

  • 9:00 am to 10:00 am
Christos Louis: Presentation and Critical Evaluation of the Vector-borne Disease Ontology
  • 10:00 am to 11:00 am
Saul Lozano-Fuentes: Presentation and Critical Evaluation of the Dengue Fever Ontology
  • 11:00 am to 11:30 am Coffee break
  • 11:30 am to 12:30 pm
Richard Scheuermann: Presentation and Critical Evaluation of the Influenza Ontology
  • 12:30 pm to 2:00 pm
Barry Smith: Refine IDO to Better Support Interoperability of Extensions (Working Lunch)
  • 2:00 pm to 3:00 pm
Alan Ruttenberg: Current Application Areas and Areas for New Development
  • 3:00 pm to 4:00 pm
Lindsay Cowell: Goals for the Coming Year

Progress

Progress has been made in the development of IDO and seven sub-domain-specific extensions of IDO. The sub-domain-specific extensions ontologies for the following diseases:

Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)
Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)
Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)
Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)
Dengue fever (Saul Lozano-Fuentes, Colorado State)
Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)

Development of IDO has continued along two fronts, expansion of content driven by development of the subdomain-specific ontologies and refinement of the approach to representing infectious disease-relevant entities ontologically.

IDO is supplemented also by a Vaccine Ontology which is being developed by Yonggun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith.

In collaboration with Dr. Carol Dukes-Hamilton at Duke University Medical Center, Drs. Cowell and Smith have begun developing a draft ontology of tuberculosis and a method for defining ISO 11179 data elements using logical constructs based on terms derived from ontologies. Dr. Dukes-Hamilton’s research group has defined eighty tuberculosis data elements and curated these into the National Cancer Institute’s metadata repository, caDSR. Definition of these data elements using ontology terms provides not only a formal method for data element definition, significantly improving the resulting definitions, but also interoperability between data elements (along with the data associated therewith) and the vast amount of biomedical data and information annotated with terms from the same or an interoperable set of ontologies.

In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a draft ontology of Staphylococcus aureus bacteremia.

Dr. Sivaram Arabandi of the Cleveland Clinic Foundation is part of a large team developing SemanticDB technology, a semantic datastore with query functionality, having primary focus on Cardiology and Cardiothoracic Surgery. A portion of this work involves developing an IDO extension ontology for infective endocarditis.

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 (http://www.vectorbase.org), an NIAID Bioinformatics Resource Center for invertebrate vectors of human pathogens, and embracing efforts to construct decision support systems for vector-borne diseases.

A group of researchers under the direction of Dr. Richard Scheuermann, University of Texas, Southwestern Medical Center, has been working to develop an influenza virus sequence and surveillance ontology to describe data generated from the Center for Influenza Research and Surveillance (CEIRS) projects. The CEIRS projects consist of two research areas, influenza virus surveillance and basic influenza virus sequence and genetic reassortment research. A list of data fields that describe influenza virus isolates and surveillance data has been created by consolidating data fields from separate CEIRS participants. The list serves as a starting point for the integration of each data field into an existing OBO Foundry ontology, including IDO, or as the basis for creation of the influenza-specific ontology. The immediate goal is to apply the Influenza Virus 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.

For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.

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