GO ribbon for viruses

[jrr-cpt]

Based on ribbon discussion at GOC meeting, I am suggesting the development of a virus ribbon to be applicable for NCBITaxon 10239, Viruses. That may require the development of a slim subset.

There was a virus slim back in 2015 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517558/, but I don't see it in the list anymore.

Although the multi-organism modifications to symbiont terms will likely bear on this, two 2017 papers on eukaryotic viruses (https://pubmed.ncbi.nlm.nih.gov/28207819/) and bacterial viruses (https://pubmed.ncbi.nlm.nih.gov/28545254/) would be a good place to start.

@pgaudet

[pgaudet]

Hi @jrr-cpt There was this slim - http://release.geneontology.org/2016-04-01/ontology/subsets/goslim_virus.obo

I cannot tell when/why it was retired. Would that be a good place to start? Or if you have a list of useful terms you'd like to include?

Thanks, Pascale

[pgaudet]

Virus slim from 2015

[pgaudet]

Hi @jrr-cpt

I have added the virus subset:

• GO:0001907 symbiont-mediated killing of host cell
• GO:0016032 viral process
• GO:0019049 virus-mediated perturbation of host defense response
• GO:0019058 viral life cycle
• GO:0019062 virion attachment to host cell
• GO:0019068 virion assembly
• GO:0019072 viral genome packaging
• GO:0019080 viral gene expression
• GO:0019083 viral transcription
• GO:0035891 exit from host cell
• GO:0039693 viral DNA genome replication
• GO:0044003 modulation by symbiont of host process
• GO:0044409 symbiont entry into host
• GO:0052008 symbiont-mediated disruption of host cellular anatomical entity
• GO:0075528 perturbation by virus of host immune response

According to GOA, it covers most manual annotations: GO ID- term label - number of manual annotations to viral proteins (search was restricted to taxon:10239

GO:0039689 negative stranded viral RNA replication 106 GO:0039520 induction by virus of host autophagy 62 GO:0039695 DNA-templated viral transcription 59 GO:0039696 RNA-templated viral transcription 55 GO:0039686 bidirectional double-stranded viral DNA replication 45 GO:0039693 viral DNA genome replication 37 GO:0019079 viral genome replication 35 GO:0044659 viral release from host cell by cytolysis 33 GO:0046813 receptor-mediated virion attachment to host cell 30 GO:0019073 viral DNA genome packaging 27 GO:0039694 viral RNA genome replication 24 GO:0019058 viral life cycle 22 GO:0039501 suppression by virus of host type I interferon production 21 GO:0039697 negative stranded viral RNA transcription 21 GO:0019062 virion attachment to host cell 19 GO:0075512 clathrin-dependent endocytosis of virus by host cell 18 GO:0039684 rolling circle single-stranded viral DNA replication 17 GO:0046761 viral budding from plasma membrane 17 GO:0098996 symbiont entry into host cell via disruption of host cell glycocalyx 17 GO:0046718 symbiont entry into host cell 15 GO:0019069 viral capsid assembly 14 GO:0039708 nuclear capsid assembly 14 GO:0098003 viral tail assembly 14 GO:0019068 virion assembly 13 GO:0039690 positive stranded viral RNA replication 13 GO:0039704 viral translational shunt 11 GO:0046760 viral budding from Golgi membrane 10 GO:0019065 receptor-mediated endocytosis of virus by host cell 9 GO:0019083 viral transcription 9 GO:0039687 viral DNA strand displacement replication 9 GO:0099002 symbiont genome ejection through host cell envelope, short tail mechanism 9 GO:0019064 fusion of virus membrane with host plasma membrane 8 GO:0046765 viral budding from nuclear membrane 8 GO:0075528 perturbation by virus of host immune response 8 GO:0019080 viral gene expression 7 GO:0019074 viral RNA genome packaging 6 GO:0039521 suppression by virus of host autophagy 6 GO:0039666 virion attachment to host cell pilus 6 GO:0039702 viral budding via host ESCRT complex 6 GO:0046774 suppression by virus of host intracellular interferon activity 6 GO:0019046 release from viral latency 5 GO:0019048 modulation by virus of host process 5 GO:0019076 viral release from host cell 5 GO:0019082 viral protein processing 5 GO:0039640 viral release via suppression of host peptidoglycan biosynthetic process 5 GO:0098004 virus tail fiber assembly 5 GO:0098671 adhesion receptor-mediated virion attachment to host cell 5

[pgaudet]

let me know if there are terms think are missing.

I think we can use the same subset for ribbons and for binning.

Thanks, Pascale

[pgaudet]

@pmasson55 let me know if you have any suggestions to improve this subset.

[pgaudet]

updated metadata file

• id: goslim_virus title: Virus slim short_label: Viruses status: active description: Virus-relevant terms role: Binning, Ribbon taxa:
  • id: NCBITaxon:10239 label: Viruses tracker: https://github.com/geneontology/go-ontology/issues contact:
  • email: go-ontology@lists.stanford.edu label: GO Ontology Curators tracker: https://github.com/geneontology/go-ontology/issues contributors:
  • email: go-ontology@lists.stanford.edu label: GO Ontology Curators

[jrr-cpt]

It's good for the process terms to cover the most annotated processes. There are also some cellular component terms that would expand the ribbon in a useful way. I'm not sure if the preference is to use higher level terms that can encompass more annotations to child terms (is that how the ribbon tallies?), such as virion component and host cell part, or to use more specific terms, like viral capsid (GO:0019028) and host cell nucleus (GO:0042025)?

[pgaudet]

Hi @jrr-cpt

We can add up to 15 terms and still have the ribbon quite easily displayed on a webpage.

[pgaudet]

I've added

• viral capsid GO:0019028
• host cell nucleus GO:0042025
• host cell plasma membrane
• symbiont-containing vacuole
• host cell Golgi apparatus
• host cell endoplasmic reticulum

Let me know if you think other terms should be added.

Thanks, Pascale