ImmPort Ontology Conference: Difference between revisions
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The goal of this meeting is to show how work in standards and ontologies can support NIAID-DAIT funded information-driven science. We will work with immunologists who have data which pose special problems for handling in a resource such as ImmPort, and develop strategies to address these problems. | The goal of this meeting is to show how work in standards and ontologies can support NIAID-DAIT funded information-driven science. We will work with immunologists who have data which pose special problems for handling in a resource such as ImmPort, and develop strategies to address these problems. | ||
Subgoals | '''Subgoals''' | ||
*providing examples of success stories in the use of standards and ontologies to support immunological research | *providing examples of success stories in the use of standards and ontologies to support immunological research | ||
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*provide an overview of ontology resources of particular interest to the ImmPort / HIPC and related communities | *provide an overview of ontology resources of particular interest to the ImmPort / HIPC and related communities | ||
*identifying strategies for data retrieval based on natural language processing | *identifying strategies for data retrieval based on natural language processing | ||
'''Background''' | |||
[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies An overview of ontologies proposed by ImmPort for use across the immunology research community] | |||
== <u>Wednesday, September 4, 2013</u> == | == <u>Wednesday, September 4, 2013</u> == | ||
Revision as of 12:48, 18 June 2013
Where: Stanford University
When: September 4-5, 2013
Audience: The conference is divided into two parts. Day 1 is intended for all those engaged in information-driven immunology research who have an interest in ontology and data standardization; Day 2 is intended also to provide training for those interested in acquiring skills needed for working with ontologies to solve specific problems.
Participation: There is a limited number of places available for this meeting. If you are interested in attending please contact Barry Smith as soon as possible.
Goals (tentative)
The goal of this meeting is to show how work in standards and ontologies can support NIAID-DAIT funded information-driven science. We will work with immunologists who have data which pose special problems for handling in a resource such as ImmPort, and develop strategies to address these problems.
Subgoals
- providing examples of success stories in the use of standards and ontologies to support immunological research
- identifying obstacles to the sharing of immunology research data and building strategies to overcome them
- identifying the ontology and data standardization needs of DAIT-funded experimental scientists
- provide an overview of ontology resources of particular interest to the ImmPort / HIPC and related communities
- identifying strategies for data retrieval based on natural language processing
Background
An overview of ontologies proposed by ImmPort for use across the immunology research community
Wednesday, September 4, 2013
8:30 Registration and Continental Breakfast
9:00 What Benefits Can Ontology Bring to the DAIT Research Community?
- Overview by Barry Smith
10:15 Break
10:30 ImmPort Ontologies
12:00 Lunch
13:00 Flow Cytometry and CyTOF Data Using the Cell Ontology
- Courtot/Brinkman: http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf The Cytometry-Ontology Framework]
- PRO, CL and CyTOF
15:00 Break
15:30 Shai Shen-Orr (Technion Israel Institute of Technology): Ontology, NLP and the Semantic Enhancement of Immunology Research Literature
16:30 Lindsay Cowell: Immunology Ontology and NLP
Thursday, September 5, 2013
8:30 Continental Breakfast
9:00 An Introduction to Ontology for Immunology
10:00 Immunology in the Gene Ontology (Alexander Diehl)
10:30 VDJServer (Lindsay Cowell)
11:00 Further Use Cases
12:00 Lunch
13:00 Further Use Cases
16:00 Close
Participants (* = tentative)
- Ryan Brinkman (Vancouver, BC)
- Lindsay Cowell (UT Southwestern, Dallas)
- Melanie Courtot (Vancouver, BC)
- Alexander Diehl (ImmPort / Buffalo)
- Sanda Harabagiu (UT Southwestern, Dallas)
- Nikesh Kotecha (Stanford)
- *Anna Maria Masci (Duke)
- Yannick Pouliot (ImmPort / Stanford)
- Alan Ruttenberg (ImmPort / Buffalo)
- Ravi Shankar (ImmPort / Stanford)
- Shai Shen-Orr (ImmPort / Technion Institute)
- Barry Smith (ImmPort / Buffalo)
- *Christian Stoeckert (Penn)
- *Representatives of institutions supplying data to ImmPort
- *Representatives of companies selling (for example) analytes
Plus participants from Stanford area
