Renal Gene Ontology Annotation Initiative

This project was completed in April 2012. If you have any questions regarding this project, please contact goa@ebi.ac.uk.

The Renal Gene Ontology Annotation Initiative is a 3 year project funded by Kidney Research UK. This initiative, headed by Dr. Rolf Apweiler of the PANDA group at the EBI and Prof. Peter Scambler of the Institute of Child Health, UCL, aims to provide a unique public resource for renal research by generating high-quality, detailed functional GO annotation for mammalian gene products implicated in renal development 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. This is a particular problem for the interpretation of high-throughput experiments where the absence of annotations greatly reduces the ability of researchers to effectively interpret results.

The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using the GO to curate scientific literature and by integrating results from high-quality high-throughput experiments we will create an information-rich resource for the renal research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research.

Targets for annotation will be selected in close consultation with an expert advisory panel. Gene products will be prioritised based on criteria such as the volume of biomedical literature available, involvement in renal development or disease and requests from the renal community. A preliminary list of targets is shown below. If you have any suggestions for additional targets or corrections to the list, please email goa@ebi.ac.uk .

Scientific Advisory Panel:


Prof Peter Scambler , Head of Molecular Medicine, Room 211, MMU, UCL-ICH, 30 Guilford St. London UK.

Prof. Steven Potter , Division of Developmental Biology, Children's Hospital Research Foundation Cincinnati, Ohio, USA.

Prof. Andrey Shaw , Unanue Professor of Pathology and Immunology, Head of the Division of Immunobiology, Investigator at the Howard Hughes Medical Institute, Washington University, St. Louis, USA.

Dr. Ruth Lovering , Division of Cardiovascular Genetics, BHF Laboratories, University College London, London, UK.

Prof. Adrian Woolf , Biomedical Research Centre Chair in Paediatric Science, Professor of Paediatric Science, University of Manchester, Manchester, UK.

Prof. Jamie Davies , Professor of Experimental Anatomy, Centre for Integrative Physiology, University of Edinburgh, UK.

Dr. Mark Dockrell , Principal Investigator. South West Thames Institute for Renal Research, St Helier Hospital, Carshalton, Surrey, UK.

Prof. Judith Blake , Associate Professor, The Jackson Laboratory, Principal Investigator, The Gene Ontology Consortium, Co-Principal Investigator and Project Leader, Mouse Genome Informatics Project. Jackson Laboratories, Bar Harbour, Maine, USA.

Prof. Nicholas Topley , Institute of Nephrology, Wales College of Medicine, Cardiff University, Cardiff, UK .

Gene Ontology Annotator


Dr. Yasmin Alam-Faruque , EBI.

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 GUDMAP Edinburgh Group and the GO editorial Team.The kidney development ontology web page can be viewed at http://wiki.geneontology.org/index.php/Kidney_Development

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).

3. Dr Herbert Schramek of Innsbruck Unversity has provided a list of differentially expressed proteins in response to neuropilin genes

4. Professor Moin Saleem of Bristol University has provided a list of proteins associated with the function of podocyte cells within the glomerulus (the main filtration unit of the kidney).

Further information on this Initiative is available at http://www.geneontology.org/GO.renal.shtml?all . There is 'renal interest' mailing list that has been set up ( renal@ebi.ac.uk ) mainly intended for sending out newsletters. It will be low traffic and it would be a more convenient way of sending out information relating to the Renal GOA Initiative. So, if you are interested in continuing to receive these newsletters please could you sign up to it at http://listserver.ebi.ac.uk/mailman/listinfo/renal . You can also use this list for discussion of any issues relating to the Renal GOA Initiative.

Newsletter

 

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. Epub 2011 Dec 9.

abstract full text

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

abstract full text

Target List

The current list of proteins being prioritised for annotation by the UniProt Renal Gene Ontology Initiative is located here .