Difference between revisions of "Immunology Ontologies and Their Applications in Processing Clinical Data"

From NCBO Wiki
Jump to navigation Jump to search
m
m
Line 1: Line 1:
The National Center for Biomedical Ontology in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) Consortia will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.  
+
The National Center for Biomedical Ontology in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) Consortia 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'''
 
'''Goals'''
Line 17: Line 17:
 
:'''Morning: GO, PRO, CL, IO, IEO'''
 
:'''Morning: GO, PRO, CL, IO, IEO'''
  
:Ideas:  
+
:Topics to be discussed:  
 
::Immune pathway representations
 
::Immune pathway representations
 
::Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells  
 
::Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells  
 
::Representation of immunology experiments using OBI
 
::Representation of immunology experiments using OBI
 
::Representing epitope mapping experiments for Immune Epitope Database (IEDB)
 
::Representing epitope mapping experiments for Immune Epitope Database (IEDB)
 +
 +
:'''Atul Butte (Stanford): Immune Receptors, Inflammation and Type 2 Diabetes"
  
 
:'''Afternoon: IDO and Its Extensions'''
 
:'''Afternoon: IDO and Its Extensions'''
  
''Days 2: Tuesday, June 12, 2012: 9:00am-5:00pm''
+
''Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm''
  
 
:'''Ontologies and Flow Cytometry Informatics'''
 
:'''Ontologies and Flow Cytometry Informatics'''
 +
 +
:'''Morning: Flow cytometry typing of normal and malignant cell types
 +
 +
Ryan Brinkman: .
 +
 +
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: FLOCK
 +
 +
Cliburn Chan: Flow cytometry analysis system
 +
 +
Topics to be discussed:
 +
::Methods to automatically link flow cytometry results to cell type identification.
  
 
''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''
 
''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''
 +
 +
:9am-noon: TBD
  
 
:'''12pm-3pm Practical Applications of Ontologies in Clinical Research with special reference to Flow Cytometry'''
 
:'''12pm-3pm Practical Applications of Ontologies in Clinical Research with special reference to Flow Cytometry'''
  
:'''3pm-6pm: Closing Session on the Ontology for General Medical Science'''
+
:'''3pm: Closing Session on the Ontology for General Medical Science'''
 
 
 
 
  
''Close, June 13, 6:00pm''
+
''Close: 6:00pm''
  
 
----
 
----

Revision as of 06:13, 19 March 2012

The National Center for Biomedical Ontology in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) Consortia 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 the field of immunology ontology, 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:
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)
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

Ryan Brinkman: .

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: FLOCK

Cliburn Chan: Flow cytometry analysis system

Topics to be discussed:

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 with special reference to Flow Cytometry
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)