Immunology Ontologies and Their Applications in Processing Clinical Data
The National Center for Biomedical Ontology (NCBO) in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012. Day 1 will provide a survey of current ontology-based research in immunology and infectious disease; Day 2 will be focused on flow cytometry; Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, and a session on the Ontology for General Medical Science.
Goals
Provisional goals of the meeting are:
To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and other fields.
Draft Schedule
Day 1: Monday, June 11, 2012: 10:00am-5:00pm
An Overview of Ontologies to Support Research in Immunology and Infectious Disease
- Morning: GO, PRO, CL, IO, IEO
- Topics to be discussed will include:
- Immune pathway representations
- Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells
- Representation of immunology experiments using OBI
- Representing epitope mapping experiments for Immune Epitope Database (IEDB)
- Lunchtime talk: Atul Butte (Stanford): Immune Receptors, Inflammation and Type 2 Diabetes
- Afternoon: IDO and Its Extensions
Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm
Ontologies and Flow Cytometry Informatics
- Morning: Flow cytometry typing of normal and malignant cell types
- Alexander Diehl
- Overview of Hematopoietic Cell Types in the Cell Ontology
- An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes
- Representative of Euroflow Consortium (to be identified): Overview of Euroflow Typing Panels
- (To be identified): Clinical Flow Cytometry in HIV
- Discussion of the ontological treatment of typing panels.
- Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology
- Ryan Brinkman:
- 1. Overview of the representation of flow cytometry assays in OBI
- 2. Overview of Flow Cap Competition & flowMeans
- Richard Scheuermann: Connecting results from automated FCM analysis systems with the Cell Ontology
- Cliburn Chan: Flow cytometry analysis system
- Topics to be discussed will include:
- Methods to automatically link flow cytometry results to cell type identification.
Day 3: Wednesday, June 13, 2012:9:00am-6:00pm
- 9am-noon: TBD
- 12pm-3pm Practical Applications of Ontologies in Clinical Research
- Topics to be discussed will include:
- Current work on Neurological Disease Ontology
- Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease
- The HIV Ontology
- 3pm: Closing Session on the Ontology for General Medical Science
- Close: 6:00pm
Relevant ontology efforts
- GO-IP Gene Ontology -- Immunological Process (Alex Diehl)
- CL Cell ontology immune branches (e.g. for dendritic cells)
- PRO Protein Ontology
- IO Immunology Ontology (Lindsay Cowell and Alex Diehl)
- IEO Immune Epitope Ontology (Bjoern Peters)
- MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
- OGMS Ontology for General Medical Science (Albert Goldfain)
- IDO Infectious Disease Ontology (Lindsay Cowell)
- Vaccine Ontology (Oliver He)
- AO Allergy Ontology (Alex C. Yu)
- ND Neurological Disease Ontology (Alex Diehl)
Participants will include
- Ryan Brinkman (University of British Columbia, June 11-12)
- Atul Butte (Stanford University)
- Cliburn Chan (Duke University, June 11-12)
- Lindsay Cowell (University of Texas Southwestern Medical Center)
- Peter d'Eustachio (New York University, June 11-12)
- Alex Diehl (University at Buffalo)
- Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
- Oliver He (University of Michigan)
- Anna Maria Masci (Duke University)
- Darren Natale (Georgetown University)
- Dave Parrish (Digital Infuzion)
- Bjoern Peters, (University of California at San Diego)
- Alan Ruttenberg (University at Buffalo)
- Richard Scheuermann (University of Texas Southwestern Medical Center)
- Stanley A. Schwartz (University at Buffalo)
- Barry Smith (University at Buffalo)
- Alex C. Yu (University at Buffalo)
- Cathy Wu (University of Delaware, Georgetown University)