Difference between revisions of "Immunology Ontologies and Their Applications in Processing Clinical Data"
m |
|||
| Line 34: | Line 34: | ||
:Alexander Diehl | :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 | :Representative of Euroflow Consortium (to be identified): Overview of Euroflow Typing Panels | ||
| Line 46: | Line 46: | ||
:Ryan Brinkman: | :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 | :Richard Scheuermann: Connecting results from automated FCM analysis systems with the Cell Ontology | ||
Revision as of 09:01, 19 March 2012
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)