NCG PHI Base - The Pathogen-Host Intercations database

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NCG PHI Base - The Pathogen-Host Intercations 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. Genes not affecting the disease interaction phenotype are also curated. Viruses are not included. Other data types included are (1) direct targets of pathogen effector proteins in experimental and natural host organisms and (2) target sites of some anti-infective chemistries. A PHIB-BLAST search function is provided. The latest release of PHI-base ver. 4.3 (May 2017) contains information from 2330 manually curated references. The data provide information on 4775 genes from 264 pathogens tested on 173 hosts in 8610 interactions. Pro- and eukaryotic pathogens are represented in almost equal numbers. Host species belong ~70% to plants and 30% to other species of medical and/or environmental importance. Each entry in PHI-base is curated by domain experts and is supported by strong experimental evidence (e.g. gene disruption and gene complementation experiments), as well as literature references. To facilitate data interoperability, gene/protein IDs are annotated using controlled vocabularies and linked to external sources (Uniprot, Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). Urban et al. (2017) Nucleic Acids Research doi:10.1093/nar/gkw1089 Objectives 1. To curate relevant literature on pathogens and the pathogenic process 2. To identify missing ontologies / controlled vocabularies 3. To connect the PHI-base phenotypic data to the pathogen genomes in ENSEMBL and PhytoPath 4. To provide two data releases per year 5. To provide a BLAST function 6. To become more integrated with the UK node of the ELIXIR 'Data for Life 'project 7. To promote PHI-base use by the UK, European and international research communities

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