Difference between revisions of "Immunology Ontologies and Their Applications in Processing Clinical Data"
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This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible. | This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible. | ||
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'''Draft Schedule''' | '''Draft Schedule''' | ||
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'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease''' | '''An Overview of Ontologies to Support Research in Immunology and Infectious Disease''' | ||
| − | :'''Morning: GO, | + | :'''Morning: GO, Reactome, IO, IEO''' |
| + | |||
| + | :Alexander Diehl (University at Buffalo) and Richard Scheuermann (University of Texas Southwestern Medical Center) | ||
| + | ::Gene Ontology and Immune System Processes | ||
| + | |||
| + | :Anna Maria Masci (Duke University) | ||
| + | ::The Immunology Ontology (with special focus on the liver) | ||
:Peter d'Eustacho (New York University) | :Peter d'Eustacho (New York University) | ||
| − | ::Immune | + | ::Immune Pathway Representations in Reactome |
:Bjoern Peters (University of California at San Diego) | :Bjoern Peters (University of California at San Diego) | ||
::Representation of immunology experiments using OBI | ::Representation of immunology experiments using OBI | ||
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB) | ::Representing epitope mapping experiments for the Immune Epitope Database (IEDB) | ||
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:'''Lunchtime talk: Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data''' | :'''Lunchtime talk: Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data''' | ||
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:'''Afternoon: The Infectious Disease Ontology (IDO) and Its Extensions''' | :'''Afternoon: The Infectious Disease Ontology (IDO) and Its Extensions''' | ||
| − | :Lindsay Cowell ( | + | :Lindsay Cowell (University of Texas Southwestern Medical Center) |
::Update on IDO-Core | ::Update on IDO-Core | ||
:::simplified definitions | :::simplified definitions | ||
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:Yu Lin (University of Michigan) | :Yu Lin (University of Michigan) | ||
::IDO Bru (Brucellosis Ontology) | ::IDO Bru (Brucellosis Ontology) | ||
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| + | :Lindsay Cowell | ||
| + | ::Overview of Current Work on IDO Extensions | ||
| + | :::IDO HIV | ||
| + | :::IDO MAL (Malaria) | ||
:Alexander C. Yu (University at Buffalo) | :Alexander C. Yu (University at Buffalo) | ||
::The Allergy Ontology | ::The Allergy Ontology | ||
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''Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm'' | ''Day 2: Tuesday, June 12, 2012: 9:00am-5:00pm'' | ||
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:'''Morning: Flow cytometry typing of normal and malignant cell types | :'''Morning: Flow cytometry typing of normal and malignant cell types | ||
| + | |||
| + | :Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo) | ||
| + | ::The Protein Ontology and Cell Type Definitions | ||
:Alexander Diehl (Buffalo) | :Alexander Diehl (Buffalo) | ||
Revision as of 10:17, 1 April 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 with a view to future coordination among ontology developers and users in this field.
- 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, followed by 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.
Registration
This meeting is free for registered participants. Space is limited and those interested in participating should contact Barry Smith as soon as possible.
Draft Schedule
Day 1: Monday, June 11, 2012: 9:00am-5:00pm
An Overview of Ontologies to Support Research in Immunology and Infectious Disease
- Morning: GO, Reactome, IO, IEO
- Alexander Diehl (University at Buffalo) and Richard Scheuermann (University of Texas Southwestern Medical Center)
- Gene Ontology and Immune System Processes
- Anna Maria Masci (Duke University)
- The Immunology Ontology (with special focus on the liver)
- Peter d'Eustacho (New York University)
- Immune Pathway Representations in Reactome
- Bjoern Peters (University of California at San Diego)
- Representation of immunology experiments using OBI
- Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
- Lunchtime talk: Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data
- Afternoon: The Infectious Disease Ontology (IDO) and Its Extensions
- Lindsay Cowell (University of Texas Southwestern Medical Center)
- Update on IDO-Core
- simplified definitions
- new approach to MIREOTing
- new terms/definitions/relations deriving from the work with Saul and potentially the work with Plant IDO
- A template for creating an IDO Extension
- Update on IDO-Core
- Albert Goldfain (Blue Highway)
- Staph Aureus (Sa) IDO
- A lattice of Sa IDO ontologies
- Sa IDO as a tool for creating interoperable clinical case report forms
- Sa IDO and Common Data Elements
- Staph Aureus (Sa) IDO
- Richard Scheuermann (Dallas)
- IDO Flu (Influenza Ontology)
- Yu Lin (University of Michigan)
- IDO Bru (Brucellosis Ontology)
- Lindsay Cowell
- Overview of Current Work on IDO Extensions
- IDO HIV
- IDO MAL (Malaria)
- Overview of Current Work on IDO Extensions
- Alexander C. Yu (University at Buffalo)
- The Allergy Ontology
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
- Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
- The Protein Ontology and Cell Type Definitions
- Alexander Diehl (Buffalo)
- 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
- Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells
- (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 (Vancouver):
- Richard Scheuermann (Dallas): Connecting results from automated FCM analysis systems with the Cell Ontology
- Cliburn Chan (Duke): 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
- noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research (includes lunch)
- 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-6pm: Working Session on the Ontology for General Medical Science (OGMS)
- Moderator: Albert Goldfain (Blue Highway / Syracuse)
- Topics to be treated will include:
- An update on OGMS
- Relations in OGMS
- 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)
- Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
- Peter d'Eustachio (New York University)
- Alex Diehl (University at Buffalo)
- Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
- Oliver He (University of Michigan)
- Yu Lin (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)
- Cathy Wu (University of Delaware, Georgetown University)
- Alex C. Yu (University at Buffalo)