PHI-Canto: Introducing the concept of the metagenotype to curate information on multi-species interactions

The Canto community curation tool (Rutherford et al., (2014) doi: 10.1093/bioinformatics/btu103) was developed to enable the literature curation of biochemical and phenotype data by the publication authors with little or no curation training. We have extended Canto with configurable files to capture data for the pathogen-host interactions database PHI-base ( www.phi-base.org ) by creating PHI-Canto. PHI-Canto enables the curation of pathogen-host interaction phenotypes (i.e. alterations in pathogenicity and virulence) connected to the underlying genome-level changes. These Canto adaptations involved ‘originating’ the concept of a ‘multi-species genotype’ defined as the ‘meta-genotype’ to facilitate the capture of changes in pathogenicity observed by alterations to pathogen and host genes singly, or in combination. A second major change was the ability to handle multiple species and natural strains simultaneously and unambiguously.   A formal logically defined precomposed ontology named phipo (pathogen-host interaction phenotype ontology) is registered with the OBO foundry ( http://www.obofoundry.org/ontology/phipo.html ) and is currently being developed using the ODK (ontology development kit). These species neutral phenotype terms will be used within PHI-Canto and are described in our other poster ‘Capturing phenotypes for inclusion in a multi-species interaction database’. The PHI-canto rationale, implementation, and resulting curation workflow are described. The PomBase Canto tool is funded by the Wellcome Trust (104967/Z/14/Z). PHI-base and PHI-Canto development is supported by the UK Biotechnology and Biological Sciences Research Council (BBSRC) (BB/I/001077/1, BB/K020056/1). PHI-base receives additional support from the BBSRC as a National Capability (BB/J/004383/1).