A framework for community curation of interspecies interactions literature

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 re...

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Bibliographic Details
Published in:eLife 2023-07, Vol.12
Main Authors: Cuzick, Alayne, Seager, James, Wood, Valerie, Urban, Martin, Rutherford, Kim, Hammond-Kosack, Kim E
Format: Article
Language:English
Subjects:
Annotations
curation
Data Curation
Databases, Factual
Environmental conditions
Genes
Genotype
Genotype & phenotype
Genotypes
host species
Infectious diseases
Microbiology and Infectious Disease
Ontology
pathogen species
pathogen-host interactions
Pathogens
Phenotype
phenotype database
Phenotypes
PHI-base
Proteins
Virulence
Vocabularies & taxonomies
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Description
Summary: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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.84658