Representing kidney development using the gene ontology

Yasmin Alam-Faruque, David P. Hill, Emily C. Dimmer, Midori A. Harris, Rebecca E. Foulger, Susan Tweedie, Helen Attrill, Douglas G. Howe, Stephen Randall Thomas, Duncan Davidson, Adrian S. Woolf, Judith A. Blake, Christopher J. Mungall, Claire O'Donovan, Rolf Apweiler, Rachael P. Huntley

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease. © 2014 Alam-Faruque et al.
    Original languageEnglish
    Article numbere99864
    JournalPLoS ONE
    Volume9
    Issue number6
    DOIs
    Publication statusPublished - 18 Jun 2014

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