PHI-base: Capturing phenotypes for inclusion in a multi-species interaction database 

The pathogen-host interactions database PHI-base ( www.phi-base.org ) is a knowledge database. It contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. The recent release of PHI-base version 4.6 contains information from >3000 manually curated references. The data provides information on 6438 genes from 263 pathogens tested on 194 hosts in 11340 interactions. Pro- and eukaryotic pathogens are represented in almost equal numbers. Viruses are not included. Host species belong ~65% to plants and 35% to other species of medical and/or environmental importance. Phenotypes are assigned to each interaction. Genes not affecting the disease interaction phenotype are also curated. Historically nine high level controlled language phenotypes have been used in PHI-base. These are now being extended into a formal logically defined precomposed ontology named phipo (pathogen host interaction phenotype ontology) using the ODK (ontology development kit) and registered with the OBO foundry ( http://www.obofoundry.org/ontology/phipo.html ). PHI-base is a multi-species database, therefore we are aiming to develop a species neutral vocabulary for maximum data comparability. We are also developing a Community curation tool called PHI-Canto to enable authors to curate their own data and annotate genotypes with phipo terms. PHI-base continues to use and openly provide data with a variety of resources encouraging maximum data interoperability. In Urban et al., 2017 (doi: 10.1093/nar/gkw1089) and our other poster on PHI-Canto, the development of a community author curation tool is explained. This work 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).