NIAID Cell Ontology Workshop Summary

NIAID-sponsored Workshop: Immune Cell Representation in the Cell Ontology (CL)

The Cell Ontology (CL: current version available at the OBO foundry ; click on the cell.obo link) includes many cells of interest to immunologists. These representations are useful, but could be improved with input from the broader immunology research community. Recently, program staff from the National Institute of Allergy and Infectious Diseases (NIAID), NIH began discussions with Dr. Alexander Diehl of the GO Consortium and a small number of investigators to further enhance the representation of the following cells in the CL: B cells, dendritic cells, macrophage, and T cells. In order to develop a consensus on the representation of these immune cells in the CL, the Division of Allergy, Immunology, and Transplantation (DAIT) of the NIAID sponsored a two-day hands-on workshop on May 13-14, 2008 in Bethesda, MD. A brief summary of this workshop is below.

The meeting began with a brief introduction by Dr. Alexander Diehl, The Jackson Laboratory, of the CL and its development. This presentation was followed by a more detailed discussion of ontologies and the OBO foundry vision of interrelated ontologies by Dr. Chris Mungall of the Berkeley Bioinformatics and Ontologies Project. Both of these presentations provided a solid context and framework to begin revisions of the current immune cell representations in the CL for the selected cell types.

Prior to the discussion of each of the selected cell types, Dr. Diehl and Dr. Richard Scheuermann, U.T. Southwestern Medical Center, gave an overview of the current representation of that cell type in the CL. Each presentation was followed by a proposal from a domain expert for improvements to the current CL representations and group discussion to finalize the recommendations. Dr. Penny Morel, University of Pittsburgh, outlined her suggested changes to the T cell CL ontology; and Dr. Martin Zand, University of Rochester, described his suggestions for improving the B cell representation in the CL. Drs. Lindsay Cowell, Duke University, and Dr. Elizabeth Gold, Institute for Systems Biology, discussed improvements to the dendritic cell and macrophage CL representations, respectively. All of the workshop participants agreed that additional subsets were required for each parent cell type and that cell surface molecules, transcription factors, and/or secreted proteins (e.g., cytokines and chemokines) needed to be used as part of the cell definitions to distinguish the subsets.

Prior to adjournment, the group developed a series of action items to ensure that the updates to the CL are completed and incorporated into the next CL version (version 1.5). Suggestions were also made to enhance the 2.0 version of the CL, which is currently in development. The action items from this workshop were:

1. Submit for publication the outcomes and implications of this workshop. This publication would minimally include the following sections:
a. Introduction to describe the fundamentals and importance of ontologies (use cases etc), including examples of the existing CL ontology and process for the changes proposed at this workshop.
b. Discussion of cell types, including the challenges/caveats for generating the current CL representations and updating as needed.
c. Invite further discussions from the broader research community (sourceforge tracker).

It is anticipated that the manuscript will be ready for submission by end of August, 2008.

2. Revise the T cell, B cell, macrophage and dendritic cell CL ontology based on workshop discussions (due date: June 30, 2008). Responsible parties are listed below.
a. T cells: Drs. Penny Morel and Alexander Diehl
b. B cells: Drs. Martin Zand and Richard Scheuermann
c. Dendritic Cells: Drs. Lindsay Cowell, Jeremy Seto (Mount Sinai School of Medicine), and Bali Puledran (Emory)
d. Macrophages: Drs. Elizabeth Gold and Anastasia Nijnik (U. of British Columbia)

3. Teleconferences to finalize the immune cell CL representations will be coordinated by NIAID program staff. The meetings will be conducted in July, 2008. Please contact Dr. Alison Deckhut Augustine (augustine at niaid.nih.gov) if you are interested in participating. Participation is open to all interested investigators, and not limited to workshop attendees.

4. Version 2.0 of CL: New relationships to be added. Dr. Chris Mungall will compose a list of these relationships, which will be sent to the meeting participants and posted on the wiki for public comment. (due date for posting: May 28, 2008; comments due by June 30, 2008)

5. Leukocyte protein list – Dr. Martin Zand has started a CD marker list, which will be the template for adding other molecules that will be used to define the immune cell subsets. Comments should be sent to Dr. Terence Meehan, The Jackson Laboratory, for final compilation and submission to the Protein Ontology. (due dates: June 30, 2008 send comments to Dr. Meehan. This document will be posted on the wiki for general comments, which are due by July 15, 2008.)