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Cilia. 2017 Nov 16;6:10. doi: 10.1186/s13630-017-0054-8. eCollection 2017.

The Gene Ontology of eukaryotic cilia and flagella.

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK.
2
The Gene Ontology Consortium, http://geneontology.org.
3
Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
4
Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
5
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
6
Fakultät Biowissenschaften, Universität Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany.
7
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
8
Present Address: Centre for Cardiovascular Genetics, University College London, London, WC1E 6JF UK.
9
Present Address: SciBite Limited, BioData Innovation Centre, Wellcome Genome Campus, Cambridge, CB10 1DR UK.
#
Contributed equally

Abstract

Background:

Recent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO.

Methods:

Members of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools.

Results:

So far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative 'before and after' analyses of representative ciliary datasets, improve enrichment results significantly.

Conclusions:

Our work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO.

KEYWORDS:

Axoneme; Basal body; Ciliopathy; Cilium; Flagellum; Gene Ontology; Microscopy image annotation; Systems biology

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