Canto is a web-based tool to support the curation of gene-specific scientific data, by both professional biocurators and publication authors.
Rutherford, K. M., Harris, M. A., Lock, A., Oliver, S. G., & Wood, V. (2014). Canto: an online tool for community literature curation. Bioinformatics, 30(12), 1791–1792. doi:10.1093/bioinformatics/btu103 Canto was developed as part of the

PomBase PomBase is a model organism database that provides online access to the fission yeast Schizosaccharomyces pombe genome sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase webs ...

project,
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 and is funded by the

Wellcome Trust The Wellcome Trust is a charitable foundation focused on health research based in London, in the United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Henry Wellcome (founder of one of the predecessors of Glaxo ...

. Canto enables experts (biocurators and publication authors) to provide detailed, standardized, sharable annotation from research publications and was originally created for the fission yeast community. Canto is a generic tool that can be readily configured for use with other organisms and other databases and now supports pathogen-host interactions for

PHI-base The Pathogen-Host Interactions database (PHI-base) is a biological database that contains curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database is maintained by researchers at Rotha ...

(

Rothamsted research Rothamsted Research, previously known as the Rothamsted Experimental Station and then the Institute of Arable Crops Research, is one of the oldest agricultural research institutions in the world, having been founded in 1843. It is located at Harp ...

) and the curation of phenotypes and genetic interactions at

FlyBase FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, ''Drosophila melanogaster'', a wide range of ...

(

University of Cambridge , mottoeng = Literal: From here, light and sacred draughts. Non literal: From this place, we gain enlightenment and precious knowledge. , established = , other_name = The Chancellor, Masters and Schola ...

), and all gene-specific datatypes for the emerging model species ''Schizosaccharomyces japonicus'' in JaponicusDB.

Curation using ontology terms

Canto supports the use of bio-ontologies (including the

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

, Protein Ontology, The Fission Yeast Phenotype Ontology FYPO, and the

Sequence Ontology The Sequence Ontology (SO) is an ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped int ...

to describe attributes of gene products. Complex ontology structures are hidden by an intuitive search, browse, and drill-down workflow. Canto workflow guides the user through the curation process with prompts for required qualifiers and metadata (for example evidence (provenance), annotation extensions, and experimental conditions). Prompts are tailored to different data types, and their individual specific domains and ranges.

Community Curation

Canto has been successful in supporting community curation, and most of the new curation in PomBase is provided by the community of researchers who use the fission yeast

Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically meas ...

as a

model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...

. The PomBase team demonstrate that co-curation by publication authors and professional curators provides higher quality curation to maximise the value and impact of scientific research.
Lock, A., Harris, M. A., Rutherford, K. M., Hayles J & Wood, V. (2020). Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications Database (Oxford). 2020; 2020: baaa028. doi: 10.1093/database/baaa028

References

{{Reflist Genetics databases Genetics in the United Kingdom Science and technology in Cambridgeshire South Cambridgeshire District