Virus terms (Completed 2012)

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Aim

The aim of this project is to completely overhaul all the terms related to viruses in GO, mainly processes. Term phrasing and tree structures will be standardized, and new terms will be added with the aim of giving a broad coverage for all species of virus.


Status - July 2012

People

  • Jane Lomax, Rebecca Foulger, Brenley McIntosh - July 2012
    • Michelle Gwinn Giglio, Candace Collmer, Ariane Toussaint, Alexander Diehl, Fiona McCarthy, Marcus Chibucos

Mailing List

  • Now deprecated. Instead use the general go-discuss list (go-discuss@lists.stanford.edu), and precede subject with VIRUSES
  • The archive of the old list is available here

Download

The most recent file of terms is available to download here:

http://www.geneontology.org/scratch/virus_terms.obo


The keyword mappings from SIB are available here:

host-virus

kwvirus2


Meetings

We should probably aim for several virtual meetings via WebEx and phone, and perhaps one face-to-face meeting, budget allowing in 2009.

Discussion

Agreed Principles

The discussion can be viewed in the meeting minutes and on the mailing list archive, but we have so far all agreed to the following principles for developing the viral terms in GO:

  1. viruses should be classed as organisms
  2. virus-host interactions should be classed as symbiotic interactions, even when they result in the demise of the host
  3. viral-host processes should be regarded as 'normal' from the perspective of both the host and the virus

Issues

  • Are viruses organisms or not? This is important because it will determine whether the virus will live under the multi-organism process node or not.

I disagree. The Gene Ontology is about classifying gene function. Viruses have genes, therefore these viral gene products should be included in the GO. However, if you really need to decide if viruses are "organisms" then I would say that they contain genetic material and are capable of reproducing, evolving and responding to their environment. They are organisms without baggage. - Fiona

The developers of the Infectious Disease Ontology favor defining viruses as organisms, and would like the GO to do so as well, to ensure that this issue is handled in the same way across the OBO Foundry ontologies, so that IDO can import GO terms without modification in their ontological placements. - Alex

  • Most of the existing virus terms in GO were added for the annotation of HPV1, so the existing structure may not be optimal for organising all viral processes. We may need to obsolete many of these terms (note: there are very few annotations to these terms because the HPV1 annotation file went out of date).
  • It is not always obvious with these terms whether they describe the host or the symbiont process or both. We'll need to make sure that's made clear.

SF items

Existing viral terms

This is a list of all the terms currently in GO relating to viruses. I've removed the obsolete terms, and the molecular function terms.

Ariane: some of the 'component' terms are in fact SO terms (provirus and the genomes). Where should virion (and phage in my case) fit with a sequence/nucleic acid AND proteins?

Biological process terms:

GO:0019084	(delayed) early viral mRNA transcription
GO:0046737	active induction of cell-mediated immune response in host by virus
GO:0046732	active induction of host immune response by virus
GO:0046736	active induction of humoral immune response in host by virus
GO:0046738	active induction of innate immune response in host by virus
GO:0046781	dispersion by virus of host splicing factors
GO:0051215	DNA virus induced gene silencing
GO:0046802	egress of viral procapsid from host cell nucleus
GO:0046788	egress of virus within host cell
GO:0046718	entry of virus into host cell
GO:0019043	establishment of viral latency
GO:0030683	evasion by virus of host immune response
GO:0019049	evasion of host defenses by virus
GO:0046815	genome retention in viral capsid
GO:0060146	host gene silencing in virus induced gene silencing
GO:0019085	immediate early viral mRNA transcription
GO:0019088	immortalization of host cell by virus
GO:0006948	induction by virus of cell-cell fusion in host
GO:0019051	induction by virus of host apoptosis
GO:0046793	induction by virus of modification of host RNA polymerase II
GO:0046730	induction of host immune response by virus
GO:0019059	initiation of viral infection
GO:0046801	intracellular transport of viral capsid in host cell
GO:0019060	intracellular transport of viral proteins in host cell
GO:0046784	intronless viral mRNA export from host nucleus
GO:0019086	late viral mRNA transcription
GO:0019042	latent virus infection
GO:0019044	latent virus maintenance
GO:0019045	latent virus replication
GO:0019078	lytic viral budding
GO:0046756	lytic viral exocytosis
GO:0030068	lytic viral life cycle
GO:0019077	lytic viral release
GO:0046757	lytic virus budding from ER membrane
GO:0046758	lytic virus budding from Golgi membrane
GO:0046759	lytic virus budding from plasma membrane
GO:0019055	modification by virus of host cell cycle regulation
GO:0019054	modification by virus of host cellular process
GO:0046778	modification by virus of host mRNA processing
GO:0046783	modification by virus of host polysomes
GO:0043921	modulation by host of viral transcription
GO:0019056	modulation by virus of host transcription
GO:0043922	negative regulation by host of viral transcription
GO:0050687	negative regulation of defense response to virus
GO:0050689	negative regulation of defense response to virus by host
GO:0045869	negative regulation of retroviral genome replication
GO:0045071	negative regulation of viral genome replication
GO:0046725	negative regulation of viral protein levels in host cell
GO:0048525	negative regulation of viral reproduction
GO:0032897	negative regulation of viral transcription
GO:0046754	non-lytic viral exocytosis
GO:0046753	non-lytic viral release
GO:0046755	non-lytic virus budding
GO:0046762	non-lytic virus budding from ER membrane
GO:0046760	non-lytic virus budding from Golgi membrane
GO:0046761	non-lytic virus budding from plasma membrane
GO:0046734	passive induction of cell-mediated immune response in host by virus
GO:0046731	passive induction of host immune response by virus
GO:0046733	passive induction of humoral immune response in host by virus
GO:0046735	passive induction of innate immune response in host by virus
GO:0043923	positive regulation by host of viral transcription
GO:0060139	positive regulation of apoptosis by virus
GO:0002230	positive regulation of defense response to virus by host
GO:0045870	positive regulation of retroviral genome replication
GO:0060141	positive regulation of syncytium formation by virus
GO:0045070	positive regulation of viral genome replication
GO:0046726	positive regulation of viral protein levels in host cell
GO:0048524	positive regulation of viral reproduction
GO:0050434	positive regulation of viral transcription
GO:0032359	provirus excision
GO:0019047	provirus integration
GO:0032360	provirus maintenance
GO:0019046	reactivation of latent virus
GO:0019065	receptor mediated endocytosis of virus by host
GO:0050688	regulation of defense response to virus
GO:0050691	regulation of defense response to virus by host
GO:0050690	regulation of defense response to virus by virus
GO:0019057	regulation of host mRNA translation by virus
GO:0045091	regulation of retroviral genome replication
GO:0045069	regulation of viral genome replication
GO:0046719	regulation of viral protein levels in host cell
GO:0050792	regulation of viral reproduction
GO:0046782	regulation of viral transcription
GO:0019076	release of virus from host
GO:0043330	response to exogenous dsRNA
GO:0045090	retroviral genome replication
GO:0051214	RNA virus induced gene silencing
GO:0008167	sigma virus replication
GO:0046739	spread of virus within host
GO:0046740	spread of virus within host, cell to cell
GO:0046741	spread of virus within host, tissue to tissue
GO:0046779	suppression by virus of expression of host genes with introns
GO:0019050	suppression by virus of host apoptosis
GO:0046792	suppression by virus of host cell cycle arrest
GO:0046791	suppression by virus of host complement neutralization
GO:0046775	suppression by virus of host cytokine production
GO:0019053	suppression by virus of host extracellular antiviral response
GO:0019052	suppression by virus of host intracellular antiviral response
GO:0046780	suppression by virus of host mRNA splicing
GO:0046773	suppression by virus of host termination of protein biosynthetic process
GO:0046774	suppression by virus of intracellular interferon activity in host
GO:0046776	suppression by virus of MHC class I cell surface presentation in host
GO:0060140	syncytium formation by plasma membrane fusion of virally targeted cells
GO:0009293     transduction
GO:0019087	transformation of host cell by virus
GO:0019066	translocation of virus into host cell
GO:0019089	transmission of virus
GO:0019061	uncoating of virus
GO:0019037	viral assembly intermediate
GO:0019067	viral assembly, maturation, egress, and release
GO:0019069	viral capsid assembly
GO:0046744	viral capsid envelopment
GO:0046752	viral capsid precursor localization in host cell nucleus
GO:0046745	viral capsid re-envelopment
GO:0046743	viral capsid transport in host cell cytoplasm
GO:0046742	viral capsid transport in host cell nucleus
GO:0019071	viral DNA cleavage
GO:0019073	viral DNA genome packaging
GO:0046787	viral DNA repair
GO:0019064	viral envelope fusion with host membrane
GO:0060145	viral gene silencing in virus induced gene silencing
GO:0019080	viral genome expression
GO:0019070	viral genome maturation
GO:0019072	viral genome packaging
GO:0019079	viral genome replication
GO:0046796	viral genome transport in host cell
GO:0019058	viral infectious cycle
GO:0019035	viral integration complex
GO:0046797	viral procapsid maturation
GO:0060153	viral process regulating host cell cycle
GO:0019081	viral protein biosynthetic process
GO:0019082	viral protein processing
GO:0008166	viral replication
GO:0046786	viral replication complex formation and maintenance
GO:0016032	viral reproduction
GO:0022415	viral reproductive process
GO:0019074	viral RNA genome packaging
GO:0046807	viral scaffold assembly and maintenance
GO:0019083	viral transcription
GO:0044009	viral transmission by vector
GO:0060150	viral triggering of virus induced gene silencing
GO:0019068	virus assembly
GO:0046764	virus budding from ER membrane
GO:0046751	virus budding from ER membrane during viral capsid envelopment
GO:0046748	virus budding from ER membrane during viral capsid re-envelopment
GO:0046763	virus budding from Golgi membrane
GO:0046750	virus budding from Golgi membrane during viral capsid envelopment
GO:0046747	virus budding from Golgi membrane during viral capsid re-envelopment
GO:0046771	virus budding from inner nuclear membrane during viral capsid envelopment
GO:0046769	virus budding from inner nuclear membrane during viral capsid re-envelopment
GO:0046765	virus budding from nuclear membrane
GO:0046749	virus budding from nuclear membrane during viral capsid envelopment
GO:0046746	virus budding from nuclear membrane during viral capsid re-envelopment
GO:0046772	virus budding from outer nuclear membrane during viral capsid envelopment
GO:0046770	virus budding from outer nuclear membrane during viral capsid re-envelopment
GO:0046766	virus budding from plasma membrane
GO:0046767	virus budding from plasma membrane during viral capsid envelopment
GO:0046768	virus budding from plasma membrane during viral capsid re-envelopment
GO:0009616	virus induced gene silencing
GO:0019075	virus maturation
GO:0019048	virus-host interaction
GO:0006926	virus-infected cell apoptosis

Cellular component terms:

GO:0019027	ambisense viral genome
GO:0019018	bipartite viral genome
GO:0019021	DNA viral genome
GO:0019023	dsRNA viral genome
GO:0019029	helical viral capsid
GO:0019030	icosahedral viral capsid
GO:0019020	multipartite viral genome
GO:0019026	negative sense viral genome
GO:0019016	non-segmented viral genome
GO:0019025	positive sense viral genome
GO:0019038	provirus
GO:0000943	retrotransposon nucleocapsid
GO:0019022	RNA viral genome
GO:0019017	segmented viral genome
GO:0019024	ssRNA viral genome
GO:0019019	tripartite viral genome
GO:0019028	viral capsid
GO:0019031	viral envelope
GO:0019015	viral genome
GO:0019013	viral nucleocapsid
GO:0046798	viral portal complex
GO:0046729	viral procapsid
GO:0019034	viral replication complex
GO:0031381	viral RNA-directed RNA polymerase complex
GO:0046806	viral scaffold
GO:0019033	viral tegument
GO:0019036	viral transcriptional complex
GO:0019012	virion

Molecular Function terms:

GO:0019041	viral antireceptor activity
GO:0001618	viral receptor activity

Also see

  • Suggestion from Fiona for structuring the process terms:
Hi Jane,
I see that you are involved with editing the viral GO terms. For viral
genome replication it would make the most biological sense to have
children based on the type of genome because (1)this will affect
functionality, including is a's for all the child terms and (2) it is how
virologists think of the function. For example:
1. dsDNA viruses 
2. ssDNA viruses (+)sense DNA
3. dsRNA viruses 
4. ssRNA viruses
 4.1. (+)ssRNA viruses (+)sense RNA
 4.2. (-)ssRNA viruses (-)sense RNA (includes the "ambisense" viruses like bunyaviruses)
5. ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle
6. dsDNA-RT viruses
So instead of having a child term "Flaviridae viral genome replication"
you would want to have "positive sense, single stranded RNA genome
replication" and etc. Then I think you will find that all these terms will
just fall out naturally and you will be able to make child terms to these
in a very systematic way. The ds DNA viruses (Pox & Herpes) will be a part
of regular DNA replication but they also have rolling circle replication,
exactly as you would describe for plasmids. Etc, etc.
Anyway, my 2 cents.
Fiona

Useful Links

  • Here's a link to the phage and plasmid protein database ACLAME where you shall see a link to the MeGO ontology. The phage ontology PhiGO is now part of MeGO.


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