A framework for community curation of interspecies interactions literature

A - Papers appearing in refereed journals

Cuzick, A., Seager, J., Wood, V., Urban, M., Rutherford, K. and Hammond-Kosack, K. E. 2023. A framework for community curation of interspecies interactions literature. eLife. 12, p. e84658. https://doi.org/10.7554/eLife.84658

AuthorsCuzick, A., Seager, J., Wood, V., Urban, M., Rutherford, K. and Hammond-Kosack, K. E.

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen–Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen–host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the ‘metagenotype,’ is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

KeywordsPathogen-host interactions; Phenotype database; PHI-base; Curation; Pathogen species; Host species
Year of Publication2023
Journal citation12, p. e84658
Digital Object Identifier (DOI)https://doi.org/10.7554/eLife.84658
PubMed IDPMID: 37401199
PubMed Central IDPMCID: PMC10319440
Web address (URL)https://elifesciences.org/articles/84658
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeDesigning Future Wheat (DFW) [ISPG]
A FAIR community resource for pathogens, hosts and their interactions to enhance global food security and human health
Growing Health [ISP]
Delivering Sustainable Wheat
Growing Health (WP1) - bio-inspired solutions for healthier agroecosystems: Understanding biointeractions
Publisher's version
Accepted author manuscript
Supplemental file
Output statusPublished
Publication dates
Online04 Jul 2023
Publication process dates
Accepted18 May 2023
PublisherElife Sciences Publications Ltd

Permalink - https://repository.rothamsted.ac.uk/item/98967/a-framework-for-community-curation-of-interspecies-interactions-literature

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