Canto (gene curation tool)

Canto is a web-based tool that encourages community curation of genes. The tool allows professional curators and published authors alike to collaborate and increase inclusion in public biological database.[1] Canto is developed as part of the PomBase project,[2] which looked at Schizosaccharomyces pombe (fission yeast), and funded by the Wellcome Trust. Currently, Canto is used for Schizosaccharomyces pombe, Komagataella pastoris, and Generic Gene Ontology Implementation. However, it can be configured to use gene identifiers for any species or ontology, making it a diverse program.

Canto
Canto logo
Content
DescriptionCanto is a web-based community curation tool for gene sequences
Data types
captured		Various
OrganismsVarious
Contact
Research centerUniversity of Cambridge

University College London

Babraham Institute
Primary citationPMID 24574118
Access
Websitecuration.pombase.org
Miscellaneous
Bookmarkable
entities		yes

Curation using ontology terms

The majority of Canto curation use bio-ontologies: current CANTO uses Gene Ontology (GO)[3] and PSI-MOD.[4] Other ontologies can also be substituted to the user's needs. In order to simplify the navigation process, complex ontology structures are hidden and browsing is via search strings. Users can type in their searches and select the general term of interest, which directs them to the most specific term. With these terms, the ancestry and context can be found through external ontology browsers. Canto guides the user through the curation process with prompts for evidence, phenotype annotations, and other relevant data. Annotations can also be transferred from one gene to another efficiently due to the lack of free-text and syntax errors. Despite that, users can still add comments to certain aspects of the annotation or the entire article.

Aside from gene ontology terms, users can curate physical and genetic interactions. Canto has also allowed users to export their data in JSON format.

See also

References
  1. Rutherford, K. M., Harris, M. A., Lock, A., Oliver, S. G., & Wood, V. (2014). Canto: an online tool for community literature curation. Bioinformatics (Oxford, England), 30(12), 1791–1792. doi:10.1093/bioinformatics/btu103
  2. Lock, A., Rutherford, K., Harris, M. A., & Wood, V. (2018). PomBase: The Scientific Resource for Fission Yeast. Methods in molecular biology (Clifton, N.J.), 1757, 49–68. doi:10.1007/978-1-4939-7737-6_4
  3. Gene Ontology Consortium, Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., … Westerfield, M. (2013). Gene Ontology annotations and resources. Nucleic acids research, 41(Database issue), D530–D535. doi:10.1093/nar/gks1050
  4. Montecchi-Palazzi, L., Beavis, R., Binz, P. A., Chalkley, R. J., Cottrell, J., Creasy, D., ... & Garavelli, J. S. (2008). The PSI-MOD community standard for representation of protein modification data. Nature biotechnology, 26(8), 864.
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