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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. |
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| | UPDATE: This work is now published (http://www.ncbi.nlm.nih.gov/pubmed/26215368). |
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| | ==Status - July 2012== |
| | * [[Virus_ontology_devt_July_2012]] |
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| ==People== | | ==People== |
| Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl, Fiona McCarthy, Marcus Chibucos | | * Jane Lomax, Rebecca Foulger, Brenley McIntosh - July 2012 |
| | ** Michelle Gwinn Giglio, Candace Collmer, Ariane Toussaint, Alexander Diehl, Fiona McCarthy, Marcus Chibucos |
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| ==Mailing List== | | ==Mailing List== |
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| viruses at geneontology.org
| | * Now deprecated. Instead use the general go-discuss list (go-discuss@lists.stanford.edu), and precede subject with VIRUSES |
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| Subscribe to this list [http://fafner.stanford.edu/mailman/listinfo/viruses here]<br>
| | * The archive of the old list is available [http://fafner.stanford.edu/pipermail/viruses/ here] |
| View the archive [http://fafner.stanford.edu/pipermail/viruses/ here]
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| ==Download== | | ==Download== |
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| [http://gocwiki.geneontology.org/images/6/60/Kwvirus2.pdf kwvirus2] | | [http://gocwiki.geneontology.org/images/6/60/Kwvirus2.pdf kwvirus2] |
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| ==Meetings== | | ==Meetings== |
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| *[[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]] | | *[[viral term WebEx meeting august 21 2009|August 21 2009 WebEx meeting]] |
| | *[[Virus call 2013-11-27|Nov 27 2013]] |
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| ==Discussion== | | ==Discussion== |
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| 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? |
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| Biological process terms:
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| GO:0019084 (delayed) early viral mRNA transcription
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| GO:0046737 active induction of cell-mediated immune response in host by virus
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| GO:0046732 active induction of host immune response by virus
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| GO:0046736 active induction of humoral immune response in host by virus
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| GO:0046738 active induction of innate immune response in host by virus
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| GO:0046781 dispersion by virus of host splicing factors
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| GO:0051215 DNA virus induced gene silencing
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| GO:0046802 egress of viral procapsid from host cell nucleus
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| GO:0046788 egress of virus within host cell
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| GO:0046718 entry of virus into host cell
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| GO:0019043 establishment of viral latency
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| GO:0030683 evasion by virus of host immune response
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| GO:0019049 evasion of host defenses by virus
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| GO:0046815 genome retention in viral capsid
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| GO:0060146 host gene silencing in virus induced gene silencing
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| GO:0019085 immediate early viral mRNA transcription
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| GO:0019088 immortalization of host cell by virus
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| GO:0006948 induction by virus of cell-cell fusion in host
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| GO:0019051 induction by virus of host apoptosis
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| GO:0046793 induction by virus of modification of host RNA polymerase II
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| GO:0046730 induction of host immune response by virus
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| GO:0019059 initiation of viral infection
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| GO:0046801 intracellular transport of viral capsid in host cell
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| GO:0019060 intracellular transport of viral proteins in host cell
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| GO:0046784 intronless viral mRNA export from host nucleus
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| GO:0019086 late viral mRNA transcription
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| GO:0019042 latent virus infection
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| GO:0019044 latent virus maintenance
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| GO:0019045 latent virus replication
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| GO:0019078 lytic viral budding
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| GO:0046756 lytic viral exocytosis
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| GO:0030068 lytic viral life cycle
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| GO:0019077 lytic viral release
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| GO:0046757 lytic virus budding from ER membrane
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| GO:0046758 lytic virus budding from Golgi membrane
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| GO:0046759 lytic virus budding from plasma membrane
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| GO:0019055 modification by virus of host cell cycle regulation
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| GO:0019054 modification by virus of host cellular process
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| GO:0046778 modification by virus of host mRNA processing
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| GO:0046783 modification by virus of host polysomes
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| GO:0043921 modulation by host of viral transcription
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| GO:0019056 modulation by virus of host transcription
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| GO:0043922 negative regulation by host of viral transcription
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| GO:0050687 negative regulation of defense response to virus
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| GO:0050689 negative regulation of defense response to virus by host
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| GO:0045869 negative regulation of retroviral genome replication
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| GO:0045071 negative regulation of viral genome replication
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| GO:0046725 negative regulation of viral protein levels in host cell
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| GO:0048525 negative regulation of viral reproduction
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| GO:0032897 negative regulation of viral transcription
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| GO:0046754 non-lytic viral exocytosis
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| GO:0046753 non-lytic viral release
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| GO:0046755 non-lytic virus budding
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| GO:0046762 non-lytic virus budding from ER membrane
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| GO:0046760 non-lytic virus budding from Golgi membrane
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| GO:0046761 non-lytic virus budding from plasma membrane
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| GO:0046734 passive induction of cell-mediated immune response in host by virus
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| GO:0046731 passive induction of host immune response by virus
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| GO:0046733 passive induction of humoral immune response in host by virus
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| GO:0046735 passive induction of innate immune response in host by virus
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| GO:0043923 positive regulation by host of viral transcription
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| GO:0060139 positive regulation of apoptosis by virus
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| GO:0002230 positive regulation of defense response to virus by host
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| GO:0045870 positive regulation of retroviral genome replication
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| GO:0060141 positive regulation of syncytium formation by virus
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| GO:0045070 positive regulation of viral genome replication
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| GO:0046726 positive regulation of viral protein levels in host cell
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| GO:0048524 positive regulation of viral reproduction
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| GO:0050434 positive regulation of viral transcription
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| GO:0032359 provirus excision
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| GO:0019047 provirus integration
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| GO:0032360 provirus maintenance
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| GO:0019046 reactivation of latent virus
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| GO:0019065 receptor mediated endocytosis of virus by host
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| GO:0050688 regulation of defense response to virus
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| GO:0050691 regulation of defense response to virus by host
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| GO:0050690 regulation of defense response to virus by virus
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| GO:0019057 regulation of host mRNA translation by virus
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| GO:0045091 regulation of retroviral genome replication
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| GO:0045069 regulation of viral genome replication
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| GO:0046719 regulation of viral protein levels in host cell
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| GO:0050792 regulation of viral reproduction
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| GO:0046782 regulation of viral transcription
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| GO:0019076 release of virus from host
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| GO:0043330 response to exogenous dsRNA
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| GO:0045090 retroviral genome replication
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| GO:0051214 RNA virus induced gene silencing
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| GO:0008167 sigma virus replication
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| GO:0046739 spread of virus within host
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| GO:0046740 spread of virus within host, cell to cell
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| GO:0046741 spread of virus within host, tissue to tissue
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| GO:0046779 suppression by virus of expression of host genes with introns
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| GO:0019050 suppression by virus of host apoptosis
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| GO:0046792 suppression by virus of host cell cycle arrest
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| GO:0046791 suppression by virus of host complement neutralization
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| GO:0046775 suppression by virus of host cytokine production
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| GO:0019053 suppression by virus of host extracellular antiviral response
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| GO:0019052 suppression by virus of host intracellular antiviral response
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| GO:0046780 suppression by virus of host mRNA splicing
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| GO:0046773 suppression by virus of host termination of protein biosynthetic process
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| GO:0046774 suppression by virus of intracellular interferon activity in host
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| GO:0046776 suppression by virus of MHC class I cell surface presentation in host
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| GO:0060140 syncytium formation by plasma membrane fusion of virally targeted cells
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| GO:0009293 transduction
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| GO:0019087 transformation of host cell by virus
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| GO:0019066 translocation of virus into host cell
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| GO:0019089 transmission of virus
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| GO:0019061 uncoating of virus
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| GO:0019037 viral assembly intermediate
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| GO:0019067 viral assembly, maturation, egress, and release
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| GO:0019069 viral capsid assembly
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| GO:0046744 viral capsid envelopment
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| GO:0046752 viral capsid precursor localization in host cell nucleus
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| GO:0046745 viral capsid re-envelopment
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| GO:0046743 viral capsid transport in host cell cytoplasm
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| GO:0046742 viral capsid transport in host cell nucleus
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| GO:0019071 viral DNA cleavage
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| GO:0019073 viral DNA genome packaging
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| GO:0046787 viral DNA repair
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| GO:0019064 viral envelope fusion with host membrane
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| GO:0060145 viral gene silencing in virus induced gene silencing
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| GO:0019080 viral genome expression
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| GO:0019070 viral genome maturation
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| GO:0019072 viral genome packaging
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| GO:0019079 viral genome replication
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| GO:0046796 viral genome transport in host cell
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| GO:0019058 viral infectious cycle
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| GO:0019035 viral integration complex
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| GO:0046797 viral procapsid maturation
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| GO:0060153 viral process regulating host cell cycle
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| GO:0019081 viral protein biosynthetic process
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| GO:0019082 viral protein processing
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| GO:0008166 viral replication
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| GO:0046786 viral replication complex formation and maintenance
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| GO:0016032 viral reproduction
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| GO:0022415 viral reproductive process
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| GO:0019074 viral RNA genome packaging
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| GO:0046807 viral scaffold assembly and maintenance
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| GO:0019083 viral transcription
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| GO:0044009 viral transmission by vector
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| GO:0060150 viral triggering of virus induced gene silencing
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| GO:0019068 virus assembly
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| GO:0046764 virus budding from ER membrane
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| GO:0046751 virus budding from ER membrane during viral capsid envelopment
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| GO:0046748 virus budding from ER membrane during viral capsid re-envelopment
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| GO:0046763 virus budding from Golgi membrane
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| GO:0046750 virus budding from Golgi membrane during viral capsid envelopment
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| GO:0046747 virus budding from Golgi membrane during viral capsid re-envelopment
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| GO:0046771 virus budding from inner nuclear membrane during viral capsid envelopment
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| GO:0046769 virus budding from inner nuclear membrane during viral capsid re-envelopment
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| GO:0046765 virus budding from nuclear membrane
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| GO:0046749 virus budding from nuclear membrane during viral capsid envelopment
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| GO:0046746 virus budding from nuclear membrane during viral capsid re-envelopment
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| GO:0046772 virus budding from outer nuclear membrane during viral capsid envelopment
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| GO:0046770 virus budding from outer nuclear membrane during viral capsid re-envelopment
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| GO:0046766 virus budding from plasma membrane
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| GO:0046767 virus budding from plasma membrane during viral capsid envelopment
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| GO:0046768 virus budding from plasma membrane during viral capsid re-envelopment
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| GO:0009616 virus induced gene silencing
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| GO:0019075 virus maturation
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| GO:0019048 virus-host interaction
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| GO:0006926 virus-infected cell apoptosis
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| Cellular component terms:
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| GO:0019027 ambisense viral genome
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| GO:0019018 bipartite viral genome
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| GO:0019021 DNA viral genome
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| GO:0019023 dsRNA viral genome
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| GO:0019029 helical viral capsid
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| GO:0019030 icosahedral viral capsid
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| GO:0019020 multipartite viral genome
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| GO:0019026 negative sense viral genome
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| GO:0019016 non-segmented viral genome
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| GO:0019025 positive sense viral genome
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| GO:0019038 provirus
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| GO:0000943 retrotransposon nucleocapsid
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| GO:0019022 RNA viral genome
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| GO:0019017 segmented viral genome
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| GO:0019024 ssRNA viral genome
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| GO:0019019 tripartite viral genome
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| GO:0019028 viral capsid
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| GO:0019031 viral envelope
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| GO:0019015 viral genome
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| GO:0019013 viral nucleocapsid
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| GO:0046798 viral portal complex
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| GO:0046729 viral procapsid
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| GO:0019034 viral replication complex
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| GO:0031381 viral RNA-directed RNA polymerase complex
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| GO:0046806 viral scaffold
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| GO:0019033 viral tegument
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| GO:0019036 viral transcriptional complex
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| GO:0019012 virion
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| Molecular Function terms:
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| GO:0019041 viral antireceptor activity
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| GO:0001618 viral receptor activity
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| ===Also see=== | | ===Also see=== |
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:
- 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.
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