format-version: 1.2
subsetdef: goantislim_grouping "Grouping classes that can be excluded"
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
subsetdef: goslim_mouse "Mouse GO slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_virus "Viral GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: virus_checked "Viral overhaul terms"
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
ontology: go/subsets/goslim_virus

[Term]
id: GO:0016032
name: viral process
namespace: biological_process
alt_id: GO:0022415
def: "A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle." [GOC:bf, GOC:jl, GOC:mah]
comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_virus
synonym: "viral infection" RELATED []
synonym: "virulence" RELATED []
synonym: "virus process" EXACT [GOC:bf, GOC:jl]
xref: Reactome:REACT_6145 "Influenza Life Cycle, Homo sapiens"
xref: Reactome:REACT_6185 "HIV Infection, Homo sapiens"
xref: Reactome:REACT_6256 "HIV Life Cycle, Homo sapiens"
xref: Wikipedia:Viral_life_cycle

[Term]
id: GO:0019048
name: modulation by virus of host morphology or physiology
namespace: biological_process
alt_id: GO:0044792
def: "The process in which a virus effects a change in the structure or processes of its host organism." [GOC:bf, GOC:jl, ISBN:0781718325, UniProtKB-KW:KW-0945]
subset: goslim_virus
subset: virus_checked
synonym: "host-virus interaction" EXACT [GOC:bf, GOC:jl]
synonym: "modulation by virus of host anatomical structure or process" EXACT [GOC:bf, GOC:jl]
synonym: "modulation by virus of host anatomy or process" EXACT [GOC:bf, GOC:jl]
synonym: "viral interaction with host" EXACT []
synonym: "viral-host process" EXACT [GOC:bf, GOC:jl]
synonym: "virus-host interaction" BROAD [GOC:bf, GOC:jl]
synonym: "virus-host process" EXACT [GOC:bf, GOC:jl]
xref: Reactome:REACT_6323 "Host Interactions with Influenza Factors, Homo sapiens"
xref: VZ:886 "Vertebrate host-virus interactions"
is_a: GO:0016032 ! viral process

[Term]
id: GO:0019056
name: modulation by virus of host transcription
namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of its host's transcription." [ISBN:0781718325]
subset: goslim_virus
synonym: "modification by virus of host transcription" EXACT []
synonym: "viral perturbation of host cell transcription" EXACT []
is_a: GO:0039656 ! modulation by virus of host gene expression

[Term]
id: GO:0019057
name: modulation by virus of host translation
namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of translation of host mRNA." [ISBN:0781718325]
subset: goslim_virus
synonym: "host cell protein synthesis shutoff" BROAD []
synonym: "host cell shutoff" BROAD []
synonym: "modification by virus of host cell mRNA translation" EXACT []
synonym: "modulation of host translation by virus" EXACT [GOC:bf]
synonym: "regulation of host mRNA translation by virus" EXACT []
synonym: "regulation of host translation by virus" EXACT []
synonym: "regulation of translation in host by virus" EXACT []
synonym: "viral host shutoff protein" RELATED []
synonym: "viral perturbation of host cell mRNA translation" EXACT []
is_a: GO:0039656 ! modulation by virus of host gene expression

[Term]
id: GO:0019062
name: virion attachment to host cell
namespace: biological_process
def: "The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection." [GOC:bf, GOC:jl, UniProtKB-KW:KW-1161, VZ:956]
subset: goslim_virus
subset: virus_checked
synonym: "viral absorption" EXACT []
synonym: "viral attachment to host cell" RELATED [GOC:bf, GOC:jl]
synonym: "virion attachment to host cell surface receptor" NARROW []
xref: VZ:956 "Viral attachment to host cell"
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0019068
name: virion assembly
namespace: biological_process
alt_id: GO:0042963
def: "A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed." [ISBN:0121585336]
subset: goslim_virus
subset: virus_checked
synonym: "bacteriophage assembly" NARROW [GOC:bm]
synonym: "phage assembly" NARROW [GOC:bm]
synonym: "viral assembly" EXACT []
synonym: "viral particle assembly" EXACT []
synonym: "virion assembly and maintenance" EXACT [GOC:bf, GOC:jl]
synonym: "virion organization" EXACT [GOC:bf, GOC:jl]
synonym: "virus assembly" EXACT [GOC:dph, GOC:tb]
synonym: "virus particle assembly" EXACT []
xref: Reactome:REACT_6137 "Accumulation of M1 at the inner leaflet of the lipid bilayer, Homo sapiens"
xref: Reactome:REACT_6146 "Association of HA into rafts, Homo sapiens"
xref: Reactome:REACT_6212 "Budding, Homo sapiens"
xref: Reactome:REACT_6271 "Association of NP into rafts, Homo sapiens"
xref: Reactome:REACT_6277 "Assembly of Viral Components at the Budding Site, Homo sapiens"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0019069
name: viral capsid assembly
namespace: biological_process
def: "The assembly of a virus capsid from its protein subunits." [ISBN:0781702534, UniProtKB-KW:KW-0118]
subset: goslim_virus
is_a: GO:0016032 ! viral process
relationship: part_of GO:0019068 ! virion assembly

[Term]
id: GO:0019072
name: viral genome packaging
namespace: biological_process
def: "The encapsulation of the viral genome within the capsid." [ISBN:0121585336]
subset: goslim_virus
subset: virus_checked
xref: Reactome:REACT_6235 "Packaging of Eight RNA Segments, Homo sapiens"
xref: Reactome:REACT_6336 "RNP association, Homo sapiens"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0019068 ! virion assembly

[Term]
id: GO:0019076
name: viral release from host cell
namespace: biological_process
def: "The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane." [GOC:jl]
subset: goslim_virus
subset: virus_checked
synonym: "release of virus from host" EXACT []
synonym: "viral exit" EXACT []
synonym: "viral release" EXACT []
synonym: "viral shedding" EXACT []
synonym: "virus exit from host cell" EXACT [GOC:bf, GOC:jl]
xref: Reactome:REACT_6326 "Release, Homo sapiens"
xref: Reactome:REACT_6348 "Neuraminidase enzymatic release from sialic acid, Homo sapiens"
xref: VZ:1076 "Virus exit from host cell"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0019079
name: viral genome replication
namespace: biological_process
def: "Any process involved directly in viral genome replication, including viral nucleotide metabolism." [ISBN:0781702534]
subset: goslim_virus
synonym: "sigma virus replication" NARROW []
synonym: "viral replication" BROAD []
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0019081
name: viral translation
namespace: biological_process
def: "A process by which viral mRNA is translated into viral protein, using the host cellular machinery." [GOC:bf, GOC:jl, ISBN:0781702534]
subset: goslim_virus
subset: virus_checked
synonym: "viral protein anabolism" EXACT []
synonym: "viral protein biosynthesis" EXACT []
synonym: "viral protein biosynthetic process" EXACT [ISBN:0781702534]
synonym: "viral protein formation" EXACT []
synonym: "viral protein synthesis" EXACT []
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0019083
name: viral transcription
namespace: biological_process
def: "The process by which a viral genome, or part of a viral genome, is transcribed within the host cell." [GOC:jl, ISBN:0781702534]
subset: goslim_virus
xref: Reactome:REACT_6142 "Assembly of an Active Transcription Complex, Homo sapiens"
xref: Reactome:REACT_6152 "Influenza Viral RNA Transcription and Replication, Homo sapiens"
xref: Reactome:REACT_6210 "Elongation of viral mRNA, Homo sapiens"
xref: Reactome:REACT_6233 "Transcription of the HIV genome, Homo sapiens"
xref: Reactome:REACT_6239 "Priming and Initiation of Transcription, Homo sapiens"
xref: Reactome:REACT_6264 "Polyadenylation and Termination, Homo sapiens"
xref: Reactome:REACT_6354 "Viral Messenger RNA Synthesis, Homo sapiens"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0030683
name: evasion or tolerance by virus of host immune response
namespace: biological_process
alt_id: GO:0019052
alt_id: GO:0019053
def: "Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mah, GOC:pk]
subset: goslim_virus
synonym: "evasion by virus of host immune response" NARROW [GOC:bf, GOC:bm, GOC:jl]
synonym: "inhibition of extracellular antiviral response" EXACT []
synonym: "negative regulation by virus of extracellular antiviral response" EXACT []
synonym: "negative regulation by virus of intracellular antiviral response" EXACT []
synonym: "negative regulation of host extracellular antiviral response by virus" EXACT []
synonym: "negative regulation of host intracellular antiviral response by virus" EXACT []
synonym: "suppression by virus of host extracellular antiviral response" EXACT []
synonym: "suppression by virus of host immune response" NARROW [GOC:bf]
synonym: "suppression by virus of host intracellular antiviral response" EXACT []
synonym: "suppression of host extracellular antiviral response by virus" EXACT []
synonym: "suppression of host intracellular antiviral response by virus" EXACT []
synonym: "viral inhibition of intracellular antiviral response" EXACT []
xref: Reactome:REACT_6186 "Binding of NS1 to PKR, Homo sapiens"
xref: Reactome:REACT_6301 "Inhibition of Interferon Synthesis, Homo sapiens"
xref: Reactome:REACT_6320 "Inhibition of IFN-beta, Homo sapiens"
xref: Reactome:REACT_6339 "Binding of NS1 to dsRNA, Homo sapiens"
xref: Reactome:REACT_6350 "Inhibition of PKR, Homo sapiens"
is_a: GO:0019048 ! modulation by virus of host morphology or physiology

[Term]
id: GO:0039516
name: modulation by virus of host catalytic activity
namespace: biological_process
def: "The process in which a virus effects a change in host enzyme activity." [GOC:bf, GOC:sp]
subset: goslim_virus
subset: virus_checked
synonym: "modulation of catalytic activity of host by virus" EXACT [GOC:bf]
synonym: "regulation by virus of host catalytic activity" EXACT [GOC:bf]
synonym: "regulation of host catalytic activity by virus" EXACT [GOC:bf]
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: rfoulger
creation_date: 2011-06-16T02:59:35Z

[Term]
id: GO:0039519
name: modulation by virus of host autophagy
namespace: biological_process
def: "Any process in which a virus effect a change in the frequency, rate or extent of autophagy in the host." [GOC:bf, GOC:sp]
subset: goslim_virus
subset: virus_checked
synonym: "regulation by virus of host autophagy" EXACT [GOC:bf]
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: rfoulger
creation_date: 2011-06-22T04:19:19Z

[Term]
id: GO:0039526
name: modulation by virus of host apoptotic process
namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells." [GOC:bf, GOC:mtg_apoptosis, GOC:sp, UniProtKB-KW:KW-1119]
subset: goslim_virus
subset: virus_checked
synonym: "modulation by virus of host apoptosis" EXACT []
synonym: "modulation of host cell apoptosis by virus" EXACT [UniProtKB-KW:KW-1119]
synonym: "regulation by virus of host apoptosis" EXACT [GOC:bf]
xref: VZ:1581 "Apoptosis modulation"
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: rfoulger
creation_date: 2011-06-22T05:22:53Z

[Term]
id: GO:0039633
name: killing by virus of host cell
namespace: biological_process
def: "Any process mediated by a virus that results in the death of a cell in the host organism." [GOC:bf, GOC:bm, GOC:jl]
subset: goslim_virus
synonym: "killing by phage of host cells" NARROW [GOC:bm]
synonym: "killing by virus of host cells" EXACT []
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: rfoulger
creation_date: 2012-08-10T14:44:40Z

[Term]
id: GO:0039656
name: modulation by virus of host gene expression
namespace: biological_process
def: "The process in which a virus effects a change in gene expression in its host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:bf]
subset: goslim_virus
subset: virus_checked
synonym: "regulation by virus of host gene expression" RELATED [GOC:bf]
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: rfoulger
creation_date: 2013-06-20T15:28:26Z

[Term]
id: GO:0039674
name: exit of virus from host cell nucleus
namespace: biological_process
def: "The directed movement of the viral genome or a viral particle out of the host cell nucleus." [VZ:2177]
subset: goslim_virus
subset: virus_checked
xref: VZ:2177 "Nuclear exit of viral genome"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process
created_by: rfoulger
creation_date: 2013-09-25T13:59:41Z

[Term]
id: GO:0039707
name: pore formation by virus in membrane of host cell
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components by a virus to form a pore complex in a membrane of a host organism." [GOC:bf, GOC:jl, PMID:12972148, UniProtKB-KW:KW-1182]
subset: goslim_virus
synonym: "pore formation in membrane of host cell by virus" EXACT [GOC:bf]
synonym: "viroporin" RELATED [PMID:12972148, UniProtKB-KW:KW-1182]
is_a: GO:0016032 ! viral process
created_by: rfoulger
creation_date: 2013-11-25T15:33:33Z

[Term]
id: GO:0046718
name: viral entry into host cell
namespace: biological_process
alt_id: GO:0019063
def: "The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm." [GOC:jl]
comment: Viral attachment to the host cell is not part of viral entry in GO because virus attachment does not always lead to viral entry: attachment can also result in the virion being carried by the host cell to another location.
subset: goslim_metagenomics
subset: goslim_virus
subset: virus_checked
synonym: "entry of virus into host cell" EXACT []
synonym: "phage translocation" EXACT []
synonym: "viral penetration" EXACT []
synonym: "virion penetration" EXACT []
synonym: "virion penetration into host cell" EXACT []
synonym: "virus entry into host cell" EXACT [GOC:bf]
xref: Reactome:REACT_6232 "Binding of the influenza virion to the host cell, Homo sapiens"
xref: Reactome:REACT_6282 "Fusion and Uncoating of the Influenza Virion, Homo sapiens"
xref: VZ:936
relationship: part_of GO:0016032 ! viral process

[Term]
id: GO:0046740
name: transport of virus in host, cell to cell
namespace: biological_process
def: "The transport of a virus between adjacent cells in a multicellular organism." [GOC:bf, GOC:jl, ISBN:0781718325]
subset: goslim_virus
subset: virus_checked
synonym: "cell to cell spread of virus within host" EXACT []
synonym: "intercellular virus transport" EXACT [GOC:bf, GOC:jl]
synonym: "spread of virus in host, cell to cell" RELATED [GOC:bf, GOC:jl]
synonym: "spread of virus within host, cell to cell" EXACT []
synonym: "viral spread within host, cell to cell" EXACT []
xref: VZ:1018
is_a: GO:0016032 ! viral process

[Term]
id: GO:0046755
name: viral budding
namespace: biological_process
alt_id: GO:0046744
def: "A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space." [ISBN:0781718325, VZ:1947]
subset: goslim_virus
subset: virus_checked
synonym: "viral capsid envelopment" RELATED []
synonym: "virion budding" NARROW []
synonym: "virus budding" RELATED []
xref: VZ:1947 "Viral budding"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0019068 ! virion assembly

[Term]
id: GO:0060153
name: modulation by virus of host cell cycle
namespace: biological_process
def: "Any viral process that modulates the rate or extent of progression through the cell cycle." [GOC:dph, UniProtKB-KW:KW-1121, VZ:1636]
subset: goslim_virus
synonym: "modulation of host cell cycle by virus" EXACT [UniProtKB-KW:KW-1121]
synonym: "regulation by virus of host cell cycle" EXACT []
synonym: "regulation of host cell cycle by virus" EXACT []
synonym: "viral process regulating host cell cycle" EXACT []
xref: VZ:1636 "Modulation of host cell cycle by virus"
is_a: GO:0019048 ! modulation by virus of host morphology or physiology

[Term]
id: GO:0075509
name: endocytosis involved in viral entry into host cell
namespace: biological_process
def: "Any endocytosis that is involved in the uptake of a virus into a host cell." [GOC:bf, GOC:jl, VZ:977]
subset: goslim_virus
subset: virus_checked
synonym: "viral entry into host cell via endocytosis" RELATED [GOC:bf, GOC:jl]
synonym: "viral penetration via endocytosis followed by endosome disruption" EXACT []
synonym: "virus endocytosis by host" EXACT [UniProtKB-KW:KW-1164]
xref: VZ:977 "Virus endocytosis by host"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0046718 ! viral entry into host cell
created_by: janelomax
creation_date: 2011-07-27T11:06:34Z

[Term]
id: GO:0075528
name: modulation by virus of host immune response
namespace: biological_process
def: "The process in which a virus effects a change in the host immune response." [GOC:bf, GOC:jl]
subset: goslim_virus
subset: virus_checked
synonym: "regulation by virus of host immune system process" EXACT [GOC:jl]
is_a: GO:0019048 ! modulation by virus of host morphology or physiology
created_by: janelomax
creation_date: 2011-08-04T02:47:57Z

[Term]
id: GO:0075606
name: transport of viral material towards nucleus
namespace: biological_process
def: "The directed movement of a virus, or part of a virus, towards the host cell nucleus. The process begins after viral entry, and ends when the viral material is at the nuclear membrane." [GOC:bf, GOC:jl, VZ:990]
comment: This process does not include the viral material crossing the nuclear membrane. For transport of viral material into the nucleus, consider instead: 'viral penetration into host nucleus ; GO:0075732'.
subset: goslim_virus
subset: virus_checked
synonym: "cytoplasmic inwards viral transport" EXACT [UniProtKB-KW:KW-1176, VZ:990]
synonym: "transport of viral material to nucleus" EXACT [GOC:jl]
synonym: "viral genome transport to host cell nucleus" EXACT []
xref: VZ:990 "Cytoplasmic inwards viral transport"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process
created_by: jane
creation_date: 2009-11-05T03:33:36Z

[Term]
id: GO:0075713
name: establishment of integrated proviral latency
namespace: biological_process
alt_id: GO:0019047
def: "A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage." [GOC:jl]
subset: goslim_virus
synonym: "prophage integration" EXACT []
synonym: "provirus integration" EXACT []
xref: PHI:0000055
xref: Reactome:REACT_6918 "Integration of provirus, Homo sapiens"
xref: Reactome:REACT_8990 "Integration of viral DNA into host genomic DNA, Human immunodeficiency virus 1"
xref: VZ:980 "Viral genome integration"
is_a: GO:0016032 ! viral process
relationship: has_part GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process
created_by: jane
creation_date: 2009-05-07T02:28:41Z

[Term]
id: GO:0075732
name: viral penetration into host nucleus
namespace: biological_process
def: "The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid." [PMID:22929056, VZ:989]
subset: goslim_virus
subset: virus_checked
synonym: "viral entry into host nucleus" EXACT []
synonym: "viral import into host nucleus" EXACT []
xref: VZ:989 "Viral penetration into host nucleus"
is_a: GO:0016032 ! viral process
relationship: part_of GO:0016032 ! viral process
created_by: jane
creation_date: 2009-05-01T02:43:16Z

[Typedef]
id: ends_during
name: ends_during
namespace: external
xref: RO:0002093

[Typedef]
id: happens_during
name: happens_during
namespace: external
xref: RO:0002092
is_transitive: true
is_a: ends_during ! ends_during

[Typedef]
id: has_part
name: has_part
namespace: external
xref: BFO:0000051
is_transitive: true

[Typedef]
id: negatively_regulates
name: negatively regulates
namespace: external
xref: RO:0002212
is_a: regulates ! regulates
transitive_over: part_of ! part of

[Typedef]
id: never_in_taxon
name: never_in_taxon
namespace: external
xref: RO:0002161
expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y" []
is_metadata_tag: true
is_class_level: true

[Typedef]
id: occurs_in
name: occurs in
namespace: external
xref: BFO:0000066
holds_over_chain: part_of occurs_in
transitive_over: part_of ! part of

[Typedef]
id: part_of
name: part of
namespace: external
xref: BFO:0000050
is_transitive: true
inverse_of: has_part ! has_part

[Typedef]
id: positively_regulates
name: positively regulates
namespace: external
xref: RO:0002213
holds_over_chain: negatively_regulates negatively_regulates
is_a: regulates ! regulates
transitive_over: part_of ! part of

[Typedef]
id: regulates
name: regulates
namespace: external
xref: RO:0002211
is_transitive: true
transitive_over: part_of ! part of

[Typedef]
id: starts_during
name: starts_during
namespace: external
xref: RO:0002091