GO Annotation for the Renal System

Background

The overall objective of the Renal GO Annotation Initiative is to provide a unique public resource for the international renal research community by generating high quality, detailed functional GO annotation for mammalian gene products implicated in renal development, functional processes and disease. Renal research has generated much valuable information regarding the genes and processes involved in renal development, function and disease. So much published data is available that it is difficult and time-consuming for researchers to comprehensively review current knowledge. High-throughput genomics and systems biology are particularly powerful tools for the investigation of multi-factorial phenotypes, such as renal disease. However, at the moment, systems biology approaches to dissect relevant information are severely hampered by the lack of functional annotation of many of the key gene products likely to be involved.

Consequently this initiative will support a concentrated effort to improve the manual annotation of genes involved in the renal system using the Gene Ontology. The improved annotation of these genes will ensure that the investment in genome sequencing along with the accumulated knowledge of renal processes and disease can be exploited to the full, for the benefit of researchers seeking to alleviate renal diseases. The Renal GO Annotation Initiative is supported by Kidney Research UK.

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Plan of Action

1. A priority list of genes with association to renal processes has been prepared and can be viewed online; the current GO annotations for these can be viewed via the QuickGO browser.
2. Targets for annotation will be selected in close consultation with an expert advisory panel. Gene products will be prioritized based on criteria such as the volume of biomedical literature available, involvement in renal development or disease and requests from the renal community.
3. Annotation of the genes has begun in a systematic fashion selecting targets that are highly investigated proteins involved in a particular process or pathway that is important for the maintenance of acid-base homeostasis in the kidney.

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Collaborations

1. Improvements are being made to the ontology by reviewing existing renal-related GO terms as well as creating new terms associated with nephrogenesis, in collaboration with the GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Edinburgh group and the GO editorial team. See the kidney development ontology wiki page for more details.
2. A collaboration has been initiated to curate proteins that are implicated in the development and function of the Loop of Henle across 4 species: human, mouse, Xenopus and chicken.

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How you can contribute

You can participate in this effort on different levels.

• Use the UniProtKB-GOA User Survey to suggest proteins that you would like to see prioritized for manual annotation, to suggest references or GO terms to be included in the GO annotation, or to join our expert panel to review a specified set of fully manually-annotated proteins.
• We are keen to recruit renal scientists to review the annotations; these can be viewed online using QuickGO.
• Suggest new GO terms related to renal processes.

All contributions will be appreciated.

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Data Dissemination

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

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Personnel

Renal Annotation Committee

• Chairs: Dr. Rolf Apweiler, European Bioinformatics Institute, Cambridge, UK ; Dr. Emily Dimmer, European Bioinformatics Institute, Cambridge, UK.
• Collaborator: Professor Peter Scambler, UCL Institute of Child Health, London, UK.
• Renal GO Curator: Dr. Yasmin Alam-Faruque, European Bioinformatics Institute, Cambridge, UK.

International Scientific Advisory Panel

• Professor Peter Scambler, UCL Institute of Child Health, London, UK.
• Professor Steven Potter, Children's Hospital Research Foundation, Cincinnati, OH, USA.
• Professor Andrey Shaw, Washington University, St. Louis, MO, USA.
• Dr. Ruth Lovering, University College London, London, UK.
• Professor Adrian Woolf, University of Manchester, Manchester, UK.
• Professor Jamie Davies, University of Edinburgh, Edinburgh, UK.
• Dr. Mark Dockrell, St. Helier Hospital, Carshalton, Surrey, UK.
• Professor Judith Blake, Jackson Laboratories, Bar Harbor, ME, USA.
• Professor Nicholas Topley, Cardiff University, Cardiff, UK.

Bioinformatics Support

• Tony Sawford, European Bioinformatics Institute, Cambridge, UK.

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Newsletter

The April 2012 Renal GO Annotation Initiative newsletter is now available online. You can also download previous editions from the Renal Annotation Initiative website.

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Publications

Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. The impact of focused gene ontology curation of specific Mammalian systems. PLoS ONE. 2011;6(12):e27541. PMID:22174742 doi:10.1371/journal.pone.0027541

Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. The renal gene ontology annotation initiative. Organogenesis. Apr 2010;6(2):71–5. PMID:20885853

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