Viral term WebEx meeting june 3 2009

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3pm GMT/9am CT/10am ET

WebEx and Conference Call:

from US only: 888 727 6732
pass: 601425#

from Europe: 719 867 3417
pass: 601425#


The latest version of the ontology file can be downloaded here

Present: Jane, Michelle, Alex, Candace, Marcus, Ariane, Brenley, Fiona

  • Discussion of latest structure without the lysis/lysogeny split. Now all viral reproduction assumed to be lytic, with latency as a possible part. Lysogeny - which is phage-specific - is a child of a generic 'viral latency' term. Everyone was happy with these changes.
  • Jane was keen to import the 'phage lysogeny' branch from MeGO into GO. It's unclear how this import would work logistically, wrt keeping the two ontologies in sync, id spaces etc.
  • Some discussion of top-level term names and whether 'viral reproduction encompassed all viral processes. Perhaps use 'viral-host interaction' instead? Although there were some examples given for viral processes that occurred while the virus was outside the host. It was also felt that we didn't necessarily need a term to group all these processes.
  • There was some discussion of the annotation of 'abnormal' processes - generally the annotation of host gps to viral processes e.g. host receptor to 'viral attachment'. The group as a whole generally felt that this was okay (even Alex!), and that viral-host interactions were not 'abnormal' but like any other interaction between organisms. This is different to current GO annotation policy.
  • Michelle felt that for many of these terms, it was unnecessary to have a specific 'viral' term - for example 'viral transcription' - because the process is essentially the same as 'transcription'. Others argued that the process is fundamentally different because the host's machinery is being co-opted, the direction is often different (RNA->DNA) and sometimes the virus supplies some of its own polymerase (+ other proteins? Candace, you gave a example here I think?).
  • Marcus pointed out that by making 'viral [process] X' terms GO would be violating its own principal of not including taxonomic information in its terms.
  • Alex stressed that having 'viral' in the term name would make things a lot easier for annotation of viral terms, but Michelle pointed out that the same could be said for 'bacterial', but that would mean losing species neutrality.
  • The group came round to the idea that the 'viral' terms could be of the multi-organism process (MOP) node, and be of the form 'xxx process by symbiont in host'. It was decided that Jane should try to integrate these terms into the MOP node, and see whether specific viral terms were necessary.

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