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==Aim==
==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.
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.
UPDATE: This work is now published (http://www.ncbi.nlm.nih.gov/pubmed/26215368).
==Status - July 2012==
* [[Virus_ontology_devt_July_2012]]


==People==
==People==
Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl, Fiona McCarthy, Marcus Chibucos (who else?)
* 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 [http://fafner.stanford.edu/pipermail/viruses/ here]
 
==Download==
 
The most recent file of terms is available to download here:
 
[http://www.geneontology.org/scratch/virus_terms.obo http://www.geneontology.org/scratch/virus_terms.obo]
 
 
 
The keyword mappings from SIB are available here:
 
[http://gocwiki.geneontology.org/images/2/2a/Host-virus.pdf host-virus]
 
[http://gocwiki.geneontology.org/images/6/60/Kwvirus2.pdf kwvirus2]
 
 


==Meetings==
==Meetings==
Line 10: Line 38:
*Initial [[first email for virus-term overhaul, march 09|email]], March 2009
*Initial [[first email for virus-term overhaul, march 09|email]], March 2009
*[[viral term WebEx meeting june 3 2009|June 3 2009 WebEx meeting]]
*[[viral term WebEx meeting june 3 2009|June 3 2009 WebEx meeting]]
*[[viral term WebEx meeting august 21 2009|August 21 2009 WebEx meeting]]
*[[Virus call 2013-11-27|Nov 27 2013]]
==Discussion==


==Issues==
===Agreed Principles===
 
The discussion can be viewed in the meeting minutes and on the [http://fafner.stanford.edu/pipermail/viruses/ mailing list archive], but we have so far all agreed to the following principles for developing the viral terms in GO:
 
#viruses should be classed as organisms
#virus-host interactions should be classed as symbiotic interactions, even when they result in the demise of the host
#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.
* 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''
''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 [http://www.infectiousdiseaseontology.org/Home.html 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).
* 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.
* 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==
===SF items===
*transduction [https://sourceforge.net/tracker2/index.php?func=detail&aid=2532011&group_id=36855&atid=440764 SF:2532011]
*transduction [https://sourceforge.net/tracker2/index.php?func=detail&aid=2532011&group_id=36855&atid=440764 SF:2532011]
*viral genome replication [https://sourceforge.net/tracker2/?func=detail&aid=1774586&group_id=36855&atid=440764 SF:1774586]
*viral genome replication [https://sourceforge.net/tracker2/?func=detail&aid=1774586&group_id=36855&atid=440764 SF:1774586]
*recombinases [https://sourceforge.net/tracker2/?func=detail&aid=1742920&group_id=36855&atid=440764 SF:1742920]
*recombinases [https://sourceforge.net/tracker2/?func=detail&aid=1742920&group_id=36855&atid=440764 SF:1742920]
*children of viral genome replication [https://sourceforge.net/tracker2/index.php?func=detail&aid=1883849&group_id=36855&atid=440764 SF:1883849]
*children of viral genome replication [https://sourceforge.net/tracker2/index.php?func=detail&aid=1883849&group_id=36855&atid=440764 SF:1883849]
*obsolete 'provirus' [https://sourceforge.net/tracker/index.php?func=detail&aid=2930856&group_id=36855&atid=440764 SF:2930856]


==Existing viral terms==
===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.
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.
Line 31: Line 74:
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?
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:
===Also see===
 
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:
*Suggestion from Fiona for structuring the process terms:
Line 260: Line 102:
  Fiona
  Fiona


* Here's a link to the phage and plasmid protein database [[http://aclame.ulb.ac.be ACLAME]] where you shall see a link to the MeGO ontology. The phage ontology PhiGO is now part of MeGO.
==Useful Links==
*Here's a link to the phage and plasmid protein database [http://aclame.ulb.ac.be ACLAME] where you shall see a link to the MeGO ontology. The phage ontology PhiGO is now part of MeGO.





Latest revision as of 13:44, 10 January 2018

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.

UPDATE: This work is now published (http://www.ncbi.nlm.nih.gov/pubmed/26215368).

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?

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.


Back to Ontology Development main page