PHI-Canto

PHI-Canto is a web application used for the annotation of pathogen–host interactions. PHI-Canto is an extension of Canto, a genome annotation tool developed and maintained by PomBase. PHI-Canto is currently used by PHI-base to assist with curation of pathogen–host literature.

Note that PHI-Canto shares almost all of its source code with Canto. Development on PHI-Canto is managed on the Canto repository on the PomBase GitHub organization (pombase/canto). All issues and pull requests related to PHI-Canto should be directed to the Canto issue tracker. This repository is used primarily to allow PHI-Canto's source code to be cited directly in publications.

Installation

PHI-Canto runs in a Docker container, so Docker must be installed (see instructions).

The following commands will download PHI-Canto's source code and set up the environment:

# Note that the path to the canto-space directory cannot contain spaces.
mkdir canto-space
cd canto-space
mkdir data import_export logs

git clone https://github.com/PHI-base/canto.git

Run the following command to create a database for PHI-Canto and generate the main configuration file (canto_deploy.yaml).

./canto/script/canto_start_docker --initialise /data

Run the following command from the canto-docker folder to start PHI-Canto:

./canto/script/canto_start_docker

Publications

Alayne Cuzick, James Seager, Valerie Wood, Martin Urban, Kim Rutherford, and Kim E. Hammond-Kosack (2023) A framework for community curation of interspecies interaction literature. eLife2023;12:e84658 DOI: https://doi.org/10.7554/eLife.84658