Background

Immune System GO Curation: Tackling an 'Unmet Need'

The use of high-throughput technologies, such as gene expression, and systems biology as tools to investigate innate and adaptive immunity are gaining momentum. Gene-set enrichment analysis is often used to test for the statistically significant over-representation of particular pathways and functions. Such enrichment often relies on the availability of gene function, process and subcellular location annotations produced by the Gene Ontology Consortium. Currently the dissection of immune system responses is severely hampered by the lack of functional and pathway annotation of many of the key gene products involved.

Three members of the GO Consortium, based at Mouse Genome Informatics (MGI) [external website], European Bioinformatics Institute (EBI) [external website] and University College London (UCL) [external website], in collaboration with experts at Trinity College, Dublin (TCD) [external website], plan to tackle this annotation deficit with assistance from the immunological community and associated societies. Our objective is to provide comprehensive annotation of the thousands of mammalian genes that are required for the functioning of the immune system and the successful defense against pathogens using a well established controlled vocabulary, the Gene Ontology. This focus on immunological annotation follows a recent revision of the Gene Ontology which provides a more comprehensive representation of immunologically important processes (see Diehl et al., 2007, PMID:17267433 [external website] for further details).

Figure illustrating the top level structure of the immune system processes in GO (larger version)

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Plan Of Action

1. We have created a community annotation wiki for immunology intended to allow members of the community of experimental immunologists and other interested parties to comment on existing GO annotation and guide our continuing GO annotation efforts by pointing out missing experimentally established facts about particular genes involved in the immune system that are not currently represented by GO annotation.
2. We have prepared a gene list of 3690 genes associated with the functioning of the immune system by combining and prioritizing several existing published lists of immune system genes. For further details, please see the explanation of gene prioritization on the GO wiki.
3. We have started to annotate high priority genes from the gene list in a systematic fashion, dividing the work among our team of professional GO curators. There is also documentation on how these genes will be annotated.
4. We plan to hold a series of workshops to involve experimental scientists directly in the GO annotation process, to increase the quality and quantity of annotation for immune-relevant genes. These meetings may also have guest GO tool experts to advise on enrichment analysis of high-throughput datasets with GO. The first workshop is planned for November 2008, pending funding. For more information, please contact j.deegan@ebi.ac.uk (Jennifer Deegan).

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How You Can Contribute

You can participate in this effort at many different levels.

1. Contribute to the community annotation wiki for immunology. We are particularly keen to recruit immune gene and system process experts to review our annotations using the wiki. Users may simply supply us with the PubMed identifier of a key experimental publication for curation or provide more detailed information or commentary, such as pointing out any experimental data that might be controversial (these will be discussed with our immunology advisory panel). Information regarding genes in any species is welcome. We will review information provided through the wiki on a timely basis, and notify users of how their contributions have resulted in GO annotations.
2. Suggest new GO terms related to immunology via the wiki.
3. Participate in the GO Consortium's mailing list for discussion of immunology in the context of the Gene Ontology.

All contributions are appreciated.

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Data Dissemination

All immune GO annotations generated from this project will be freely available via the Gene Ontology Consortium website, Ensembl [external website], and UniProtKB [external website] databases, and by the databases of the species-specific projects. These annotations will, de facto, be incorporated into Entrez Gene [external website] by the National Center for Biotechnology Information (NCBI) [external website].

A new dataset of annotated immune related genes, will also be created as a gene association file, the official GO Consortium format for exchange of data.

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Additional Information

• GO immunology personnel: advisory board members, annotation managers, curators, and supporting societies
• Introduction to GO Annotation: a brief introduction to GO annotation
• Case Study: Using GO Annotations to Interpret Immunology Data
• Meeting list
• Other relevant and useful links

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