A framework for community curation of interspecies interactions literature

Abstract

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.

A conserved fungal Knr4/Smi1 protein is vital for maintaining cell wall integrity and host plant pathogenesis

“…Disruption of the gene resulting in a reduced virulence phenotype reinforces the potential of ZtKnr4 as a candidate target for fungicide development, emphasising its significance in combating Z. tritici infections and mitigating agricultural losses. Despite the ever present global importance of STB disease for many decades (Dean et al, 2012; Savary et al, 2019) Z. tritici has far fewer functionally characterised genes, with only 99 genes with a characterised phenotype within the Pathogen Host-Interactions database and only 50 of these genes associated with a loss in pathogenicity or reduced virulence (Urban et al, 2022; Cuzick et al, 2023). The reduced virulence phenotype observed in the ZtKnr4 mutant therefore marks a valuable contribution to the characterisation of one of the >9000 core genes across the known Z. tritici pangenomes (Badet et al, 2020; Chen et al, 2023).…”

“…Annotation from PHI-base was obtained by mapping genes to version PHI-base (v4.16) annotation using UniProt gene IDs and any through Decypher Tera-Blast™ P (TimeLogic, Inc. Carlsbad, California, USA) (E-value = 0 ) against the PHI-base (v4.16) BLAST database (Cuzick et al, 2023).…”

PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability

“…Canto has now been deployed for several other communities, including PHI-base for pathogen–host interaction phenotypes ( Urban et al . 2017 ; Cuzick et al . 2023 ), FlyBase for phenotype annotation of Drosophila melanogaster , and the S. japonicus MOD JaponicusDB as described above.…”