|Species strain||UniProtKB sequence information is commonly from a reference genome strain. This sequence may differ from the experimental strain curated in PHI-Canto.||Develop a selectable list of strains for curators to assign to the genotype (and metagenotype).||Strain selected after UniProtKB entry on gene entry page. Strain used within genotype creation.||URL1|
All phenotype annotation examples in Appendix 1 contain a ‘strain name’ within the genotype/metagenotype.
|Delivery mechanism||Pathogen–host interaction experiments use a wide array of mechanisms to deliver the treatment of choice (to cells, tissues, and host and non-host species) which are required for experimental interpretation.||Develop terms prefixed with ‘delivery mechanism’ in the Pathogen–Host Interaction Experimental Conditions Ontology (PHI-ECO).||Selection of experimental conditions whilst making a phenotype annotation to a metagenotype.||URL2|
Examples in Appendix 1 PMID:20601497, PMID:31804478 and PMID:22241993.
|Physical interaction||Physical interactions (i.e. protein–protein interactions) could only be annotated between proteins of the same species, so it was not possible to annotate interactions between a pathogen effector and its first host target.||Adapt the ‘Physical Interaction’ annotation type to store gene and species information from two organisms (instead of one).||Physical Interaction annotation type.||URL3|
|Pathogen effector||There was no available ontology term to describe a ‘class’ pathogen effector (a ‘transferred entity from pathogen to host’), because effectors have heterogeneous functions (specific enzyme inhibitors, modulating host immune responses, and targeting host gene-silencing mechanisms). Effector is not a phenotype, and so did not fit into the Pathogen–Host Interaction Phenotype Ontology (PHIPO).||Develop new Gene Ontology (GO) biological process terms (and children), to group ‘effector-mediated’ processes.||GO Biological Process annotation on a pathogen gene.||URL4|
Example in Appendix 1 PMID:31804478.
|Wild-type control phenotypes||Natural sequence variation between strains of both pathogen and host organisms can alter the phenotypic outcome within an interaction. The wild-type metagenotype phenotype needs to be curated so that the phenotype of an altered metagenotype is informative.||Allow creation of metagenotypes containing wild-type genes. Develop a new annotation extension (AE) property ‘compared to control,’ used in annotation of altered metagenotypes.||Annotation of phenotypes and AEs to metagenotypes (using the ‘PHI phenotype’ or ‘Gene for gene phenotype’ annotation type).||URL5|
Examples in Appendix 1 PMID:28715477, PMID:16517760, PMID:29020037, PMID:20601497, PMID:22241993.
|Chemistry||How to record chemicals for resistance or sensitivity phenotypes.||Follow PomBase model to pre-compose PHIPO terms to include chemical names from the ChEBI ontology.||Annotation of phenotypes to single species genotypes.||URL4|
Example in Appendix 1 PMID:22314539.
|Gene for gene interactions||Complex gene-for-gene interactions within plant pathogen–host interactions required additional detail to describe the function of the pathogen and host genes within the metagenotype (including the specified strains).||Develop the additional metagenotype curation type ‘Gene for gene phenotype.’ Develop two new AEs, ‘gene_for_gene_interaction’ and ‘inverse gene_for_gene_interaction,’ using PHIPO_EXT terms describing three components of the interaction.*||Annotation of phenotypes and AEs to metagenotypes using the ‘Gene for gene phenotype’ annotation type.||URL4|
Examples in Appendix 1 PMID:20601497 and PMID:22241993.
|Nine high-level legacy terms (from PHI-base 4)||PHI-base should incorporate legacy data from PHI-base 4 into new PHI-base 5 gene-centric pages.||Maintain the nine high level terms as ‘tags’ within the new PHI-base 5 user interface. Develop mapping methods to enable this.||Three locations described in Supplementary file 3.||Urban et al., 2015 NAR (PMID:25414340).|