Part I: dual taxon annotation

1. Part I: dual taxon annotation • Proposal agreed at content meeting 2005 • Some unresolved issues before implementation • now resolved/postponed • Now ready to go

2. Interaction between organisms • New node added after content meeting I: ‘interaction between organisms ; GO:0051704’ • An annotation scheme to complement these terms proposed in content meeting II • captures taxon of both species involved in interaction • A form of this system actually already in place before interaction terms created, but never used!

3. Interaction between organisms • The documentation for the taxon field in the annotation file was changed to: For cardinality 1, the ID of the species encoding the gene product. For cardinality 2, to be used only in conjunction with terms that have the term 'interaction between organisms' as an ancestor. The first taxon id should be that of the organism encoding the gene or gene product, and the taxon id after the pipe should be that of the other organism in the interaction. this field is mandatory, cardinality 1, 2; for cardinality 2 use a pipe to separate entries (e.g. taxon:1|taxon:1000)

4. Interaction between organisms • First taxon id that of organism encoding gp, second of other organism in interaction • Dual taxon only used with child terms of interaction between organisms • can’t take a ‘normal’ term from the ontology e.g. regulation of ethylene biosynthesis and use dual annotation • instead use a new term ‘regulation of ethylene biosynthesis in host’ • Reason for this mostly clarity - makes it easy to understand what the process is, easy to understand ontology • Also allows more granular terms to be used

5. Interaction between organisms • Will require the addition of lots of new terms in the interaction between organisms node • GO representatives visit PAMGO group later this year for development meeting

6. Teaching • Add detailed documentation • Guidance document (Amelia’s poster) • Announce on annotation list/website • Include in annotation camp • Proactively add terms for annotation

7. Part II: capturing host side of interactions • GO does not annotate pathogenic processes, except where the process is normal i.e. for the pathogen • “A gene product should be annotated with terms reflecting its normal activity and location…For example, many viruses use host proteins to carry out viral processes. The host protein is then doing something abnormal from the perspective of the host, but completely normal from the perspective of the virus…”

8. Capturing host side of interactions • So a process where e.g. a virus binds a host receptor, the virus will be annotated to ‘virion attachment to host cell surface receptor’ but the host protein will get no reciprocal annotation • This is inconsistent with the way we annotate symbioses

9. Capturing host side of interactions • In creating the symbiosis terms, we decided ‘symbiosis’ is a gradient ranging from mutually beneficial interactions to pathogenic interactions • impossible to determine ‘good’ and ‘bad’ interactions • For mutually beneficial interactions, be annotate both the host and the symbiont • We also annotate defense responses • So by this rationale, we should annotate the host in pathogenic interactions • limited to pathogenic processes where more than one organism involved