LiteFold/GO huggingface dataset:
symbiont-mediated disruption of host cell PML body (GO:0075342)
Namespace: biological_process
Definition: The process in which an organism effects a change that impairs the structure or function of the host PML body. A PML body is a nuclear body that reacts against SP100 auto-antibodies (PML = promyelocytic leukemia). The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: catabolism by symbiont of host cell PML body; degradation by symbiont of host cell PML body; disassembly by symbiont of host cell PML body; disassembly by symbiont of host cell PML body during symbiotic interaction; disassembly by symbiont of host cell PML NB; disassembly by symbiont of host cell PML nuclear body; disruption by symbiont of host cell PML body
obsolete modulation by symbiont of host protein levels (GO:0075344)
Namespace: biological_process
Definition: OBSOLETE. The alteration by an organism of protein levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it is a readout, and annotations should be made to more informative terms.
obsolete modification by symbiont of host protein (GO:0075345)
Namespace: biological_process
Definition: OBSOLETE. The covalent alteration by an organism of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it represents a molecular function.
obsolete modification by symbiont of host protein by ubiquitination (GO:0075346)
Namespace: biological_process
Definition: OBSOLETE. The process in which an organism adds one or more ubiquitin groups to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: modification by symbiont of host protein by ubiquitinylation; modification by symbiont of host protein by ubiquitylation
Comment: This term was obsoleted because it represents a molecular function.
endosome membrane permeabilization involved in viral entry into host cell (GO:0075502)
Namespace: biological_process
Definition: Induction of endosome membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with the capsid. Occurs after internalization of the virus through the endosomal pathway, and results in delivery of the virus contents into the host cell cytoplasm.
Synonyms: viral entry into host cell via caveolae-mediated endocytosis followed by endosome membrane; viral entry into host cell via clathrin-mediated endocytosis followed by endosome membrane permeabilization
fusion of virus membrane with host macropinosome membrane (GO:0075503)
Namespace: biological_process
Definition: Fusion of a viral membrane with a host macropinosome membrane, that occurs after internalization of the virus through the endosomal pathway, and results in release of the viral contents into the host cell cytoplasm.
Synonyms: viral entry into host cell via macropinocytosis followed by membrane fusion with the endosome membrane; viral entry into host cell via macropinocytosis followed by membrane fusion with the host macropinosome membrane
macropinosomal membrane permeabilization involved in viral entry into host cell (GO:0075504)
Namespace: biological_process
Definition: Induction of macropinosome membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with the capsid. Occurs after internalization of the virus in a macropinosome, and results in release of the viral contents from the macropinosome into the host cell cytoplasm.
Synonyms: viral entry into host cell via macropinocytosis followed by macropinosomal membrane permeabilization
entry of intact viral capsid into host nucleus through nuclear pore complex (GO:0075505)
Namespace: biological_process
Definition: Viral penetration into the host nucleus where a viral capsid passes intact through the host nuclear pore complex (NPC).
Comment: This mechanism is used by viruses with capsids small enough to cross the nuclear pore complex, such as the single-stranded (ss) DNA viruses Parvoviridae, Circoviridae and Geminiviridae.
entry of viral genome into host nucleus through nuclear pore complex via importin (GO:0075506)
Namespace: biological_process
Definition: Viral penetration into the host nucleus where the viral genome passes through the nuclear pore complex (NPC) using the cellular importin transport machinery.
Synonyms: entry of viral genome into host nucleus via cellular importin transport through the nuclear pore complex
Comment: This mechanism is used by some RNA viruses (e.g. Orthomyxoviridae), some dsDNA viruses (e.g. Polyomaviridae) and some ssRNA viruses (e.g. Lentivirus).
entry of viral genome into host nucleus via docking of viral capsid to the nuclear pore complex and injection of viral genome (GO:0075507)
Namespace: biological_process
Definition: Viral penetration into the host nucleus where the where a viral capsid docks on the cytoplasmic side of the nuclear pore complex (NPC) and ejects the viral genome through the pore into the nucleoplasm.
Comment: This mechanism is used by viruses such as Herpesvirales whose capsid is too large to enter the nuclear pore complex (NPC) pore.
entry of viral genome into host nucleus via retainment of capsid in nuclear pore complex and release of genome into nucleoplasm (GO:0075508)
Namespace: biological_process
Definition: Viral penetration into the host nucleus where a viral capsid enters the host nuclear pore complex (NPC) but remains attached to the pore on the nuclear side. The capsid then disassembles, releasing the viral genome into the nucleoplasm.
Synonyms: entry of viral genome into host nucleus via attachment of capsid to nuclear pore complex and release of genome into nucleoplasm
Comment: This mechanism is used by viruses such as Hepadnaviridae whose capsids enter the NPC but are too big to pass intact into the nucleus.
endocytosis involved in viral entry into host cell (GO:0075509)
Namespace: biological_process
Definition: Any endocytosis that is involved in the uptake of a virus into a host cell.
Synonyms: viral entry into host cell via endocytosis; viral penetration via endocytosis followed by endosome disruption; virus endocytosis by host
macropinocytosis involved in viral entry into host cell (GO:0075510)
Namespace: biological_process
Definition: Any macropinocytosis that is involved in the uptake of a virus into a host cell.
Synonyms: viral entry into host cell via macropinocytosis
macropinosome lysis involved in viral entry into host cell (GO:0075511)
Namespace: biological_process
Definition: Viral-induced lysis of the macropinosome involved in the uptake of a virus into a host cell. Occurs after internalization of the virus in a macropinosome, and results in the release of viral contents from the macropinosome into the host cell cytoplasm.
clathrin-dependent endocytosis of virus by host cell (GO:0075512)
Namespace: biological_process
Definition: Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
Synonyms: clathrin-mediated endocytosis of virus by host cell; viral entry into host cell via clathrin-mediated endocytosis; viral entry into host cell via clathrin-mediated endocytosis followed by endosome lysis; viral penetration via clathrin-mediated endocytosis
caveolin-mediated endocytosis of virus by host cell (GO:0075513)
Namespace: biological_process
Definition: Any caveolin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins when material is taken up into plasma membrane caveolae - specialized lipid rafts that form 50-70 nm flask-shaped invaginations of the plasma membrane - which then pinch off to form endocytic caveolar carriers containing the virus.
Synonyms: viral entry into host cell via caveolae-mediated endocytosis; viral entry into host cell via caveolin-mediated endocytosis; viral penetration via caveolae-mediated endocytosis followed by endosome disruption
endosome lysis involved in viral entry into host cell (GO:0075514)
Namespace: biological_process
Definition: Viral-induced lysis of the endosome involved in uptake of a virus into a host cell. Occurs after internalization of the virus through the endosomal pathway, and results in release of the viral contents from the endosome into the host cell cytoplasm.
Synonyms: viral entry into host cell via caveolae-mediated endocytosis followed by endosome lysis
obsolete viral entry into host cell via caveolin-mediated endocytosis followed by genetic injection through the endosome membrane (GO:0075515)
Namespace: biological_process
Definition: OBSOLETE. The uptake of a virus into a host cell that begins when material is taken up into plasma membrane caveolae which then pinch off to form endocytic caveolar carriers containing the virus. The caveolar carriers then deliver their viral content to early endosomes, and the process ends when viral nucleic acid is released into the host cytoplasm by its injection through the endosome membrane.
Synonyms: viral entry into host cell via caveolae-mediated endocytosis followed by genetic injection through the endosome membrane; viral entry into host cell via caveolin-mediated endocytosis followed by genetic injection through the endosome membrane
Comment: This term was made obsolete because it doesn't represent a genuine process. The term injection is mostly used for prokaryotic viruses where there is no endocytosis.
microtubule-dependent intracellular transport of viral material (GO:0075519)
Namespace: biological_process
Definition: The directed movement of the viral genome or viral particle within the host cell cytoplasm along host microtubules. Microtubule-dependent transport involves motor proteins like dynein and kinesin and is mostly used by viruses that target their genomes to the nucleus.
actin-dependent intracellular transport of virus (GO:0075520)
Namespace: biological_process
Definition: The directed movement of a virus, or part of a virus, within the host cell cytoplasm via the host's actin filaments. Actin-dependent transport is induced by viral proteins that interact with actin and/or host cell motor proteins like myosins or that promotes actin polymerization/depolymerization reactions.
Synonyms: actin-dependent intracellular transport of viral material
microtubule-dependent intracellular transport of viral material towards nucleus (GO:0075521)
Namespace: biological_process
Definition: The directed movement of a virus, or part of a virus, towards the host cell nucleus using host microtubules.
Synonyms: microtubule-dependent intracellular transport of viral material to nucleus
IRES-dependent viral translational initiation (GO:0075522)
Namespace: biological_process
Definition: Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
viral translational frameshifting (GO:0075523)
Namespace: biological_process
Definition: A process which occurs during viral translation, which involves a translational recoding mechanism called programmed ribosomal frameshifting. This causes the ribosome to alter its reading of the mRNA to an a different open reading frame to produce alternate viral proteins.
Synonyms: ribosomal frameshifting involved in viral translation
Comment: This term is intended to annotate gene products involved in the process of viral translational frameshifting, not viral proteins produced by this translation process.
ribosomal skipping (GO:0075524)
Namespace: biological_process
Definition: A translation process in which a specific viral peptide prevents the ribosome from covalently linking a new inserted amino acid, and lets it continue translation, thereby cleaving the nascent protein while allowing translation to continue.
Comment: This term is intended to annotate gene products involved in the process of ribosomal skipping, not viral proteins produced by this translation process.
viral translational termination-reinitiation (GO:0075525)
Namespace: biological_process
Definition: A process which occurs as part of viral mRNA translation which allows expression of a downstream open reading frame (ORF) in a dicistronic mRNA. In this process, ribosomes translate the upstream ORF but following termination, a proportion of 40S subunits remain tethered to the mRNA and go on to re-initiate translation at the start codon of the downstream ORF.
Synonyms: termination reinitiation involved in viral translation; viral translation involving termination re-initiation; viral translation involving termination-reinitiation; viral translation involving translational stop-start
Comment: This term is intended to annotate gene products involved in the process of viral translational termination-reinitiation, not viral proteins produced by this translation process.
cap snatching (GO:0075526)
Namespace: biological_process
Definition: A transcription initiation process during which a nucleotide sequence between 10 and 20 nucleotides in size is cleaved from the 5' end of host mRNAs by a viral RNA-dependent polymerase. The capped leader sequence obtained is subsequently used to prime transcription on the viral genome, which ultimately leads to the synthesis of capped, translatable viral mRNAs.
Synonyms: cap snatching involved in viral mRNA transcription
viral RNA editing (GO:0075527)
Namespace: biological_process
Definition: The process by which bases in viral mRNA are chemically altered during viral transcription. This is usually the incorporation of 1 - 6 additional nucleotides, which shifts the reading frame, allowing the generation of different protein products or through a specific nucleotide change that eliminates the termination codon.
Synonyms: RNA editing involved in viral mRNA transcription
obsolete perturbation by virus of host immune response (GO:0075528)
Namespace: biological_process
Definition: OBSOLETE. A process in which a virus effects a change in the host immune response.
Synonyms: regulation by virus of host immune system process
Comment: This term was obsoleted because it represents the same process as symbiont-mediated suppression of host innate immune response ; GO:0052170.
establishment of latency as a circular episome (GO:0075529)
Namespace: biological_process
Definition: A process by which a virus establishes a latent state within its host as an episome, where the viral genome remains silent in the cytoplasm or nucleus as a circular structure.
Synonyms: establishment of circular plasmid latency; establishment of latency as a circular plasmid
establishment of latency as a linear episome (GO:0075530)
Namespace: biological_process
Definition: A process by which a virus establishes a latent state within its host as an episome, where the viral genome remains silent in the cytoplasm or nucleus as linear structure.
Synonyms: establishment of latency as a linear plasmid; establishment of linear plasmid latency
transport of viral material towards nucleus (GO:0075606)
Namespace: biological_process
Definition: 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.
Synonyms: cytoplasmic inwards viral transport; transport of viral material to nucleus; viral genome transport to host cell nucleus
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'.
obsolete viral entry into host cell via clathrin-mediated endocytosis followed by genetic injection through the endosome membrane (GO:0075705)
Namespace: biological_process
Definition: OBSOLETE. The uptake of a virus into a host cell that begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicles containing the virus. The vesicle then delivers its viral content to early endosomes, and the process ends when the viral nucleic acid is released into the host cytoplasm by its injection through the endosome membrane.
Synonyms: viral entry into host cell via clathrin-mediated endocytosis followed by genetic injection through the endosome membrane; viral penetration via endocytosis followed by genetic injection through the endosome membrane
Comment: This term was made obsolete because it doesn't represent a genuine process. The term injection is mostly used for prokaryotic viruses where there is no endocytosis.
establishment of integrated proviral latency (GO:0075713)
Namespace: biological_process
Definition: A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
Synonyms: prophage integration; provirus integration
establishment of episomal latency (GO:0075720)
Namespace: biological_process
Definition: A process by which a virus establishes a latent state within its host as an episome, where the viral genome remains silent in the cytoplasm or nucleus as a distinct genetic entity.
Synonyms: establishment as a plasmid prophage; establishment of plasmid latency
viral penetration into host nucleus (GO:0075732)
Namespace: biological_process
Definition: The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
Synonyms: viral entry into host nucleus; viral import into host nucleus
intracellular transport of virus (GO:0075733)
Namespace: biological_process
Definition: The directed movement of a virus, or part of a virus, within the host cell.
Synonyms: egress of virus within host cell; intracellular transport of viral material; intracellular virion transport; movement of virus within host cell; viral egress; viral genome transport in host cell
mucilage extrusion from seed coat (GO:0080001)
Namespace: biological_process
Definition: The process in which seed mucilage expands through hydration and breaks the outer cell wall that encapsulates the whole seed upon imbibition. Mucilage, mainly composed of pectins, is formed during seed development and deposited into the apoplast underneath the outer wall of the seed coat.
Synonyms: mucilage release from seed coat; secretion of mucilage from seed coat
UDP-glucose:4-aminobenzoate acylglucosyltransferase activity (GO:0080002)
Namespace: molecular_function
Definition: Catalysis of the reaction: 4-aminobenzoate + UDP-alpha-D-glucose = 1-O-(4-aminobenzoyl)-beta-D-glucose + UDP.
Synonyms: UDP-glucose:p-aminobenzoate acylglucosyltransferase activity; UDP-glucose:p-aminobenzoate glucosyltransferase activity; UDP-glucose:pABA acylglucosyltransferase activity
thalianol metabolic process (GO:0080003)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the triterpene thalianol.
Synonyms: thalianol metabolism
photosystem stoichiometry adjustment (GO:0080005)
Namespace: biological_process
Definition: Adjustment of Photosystem I/Photosystem II ratio in response to light conditions. The function of photosystem stoichiometry adjustment is to compensate for any deficiency in energy conversion at either photosystem I or photosystem II by increasing the quantity the photosystem that will otherwise become the rate-limiting to overall photosynthesis.
internode patterning (GO:0080006)
Namespace: biological_process
Definition: Determines the spacing between two shoot nodes. A shoot node is the region of the shoot where the spikelet, flower, floret, branch, bud and/or leaves are attached.
S-nitrosoglutathione reductase (NADH) activity (GO:0080007)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-nitrosoglutathione + NADH + H+ = S-(hydroxysulfenamide)glutathione + NAD+.
Comment: S-(hydroxysulfenamide)glutathione (GSNHOH) is an unstable intermediate. At high GSH levels, it is decomposed to glutathione disulfide (GSSG) and hydroxylamine. At low GSH levels, GSNHOH spontaneously converts to glutathione sulfinamid (GSONH2), which can be hydrolyzed to glutathione sulfinic acid (GSOOH) and ammonia. {xref="PMID:30795534"}
Cul4-RING E3 ubiquitin ligase complex (GO:0080008)
Namespace: cellular_component
Definition: A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
obsolete mRNA methylation (GO:0080009)
Namespace: biological_process
Definition: OBSOLETE. The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete regulation of oxygen and reactive oxygen species metabolic process (GO:0080010)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH).
Synonyms: regulation of oxygen and reactive oxygen species metabolic process
Comment: This term was made obsolete because, as part of the GO/ChEBI alignment effort, curators determined that oxygen and reactive oxygen species should not be grouped together.
trihydroxyferuloyl spermidine O-methyltransferase activity (GO:0080012)
Namespace: molecular_function
Definition: Catalysis of the reaction: trihydroxyferuloyl spermidine + S-adenosyl-L-methionine = dihydroxyferuloyl-sinapoyl spermidine + S-adenosyl-L-homocysteine + H+.
Synonyms: N1,N5,N10-tris-(5-hydroxyferuloyl)spermidine O-methyltransferase activity
(E,E)-geranyllinalool synthase activity (GO:0080013)
Namespace: molecular_function
Definition: Catalysis of the reaction: (2E,6E,10E)-geranylgeranyl diphosphate + H2O = (6E,10E)-geranyllinalool + diphosphate.
thalianol hydroxylase activity (GO:0080014)
Namespace: molecular_function
Definition: Catalysis of the reaction: a thalianol = a thalian-diol. This reaction is the addition of a hydroxyl group to thalianol ((13R,14R,17E)-podioda-8,17,21-trien-3beta-ol) to create a thalian-diol ((13R,14R,17E)-podioda-8,17,21-trien-3beta,X-diol), where the hydroxyl group may be attached at one of several different available carbons in ring B or C of thalianol, indicated by the X.
Comment: In Field and Osbourn 2008 (PMID:18356490), thalianol is referred to as (3S,13S,3R)-malabarica-8,17,21-trien-3-ol and thalian-diol is referred to as (3S,13S,14R)-malabarica-8,17,21-trien-3,?-diol, but the error in this naming system was pointed out in Kolesnikova 2007 (PMID:17474751). The new names used in the definition have been approved by the authors (Field and Osbourn 2008).
sabinene synthase activity (GO:0080015)
Namespace: molecular_function
Definition: Catalysis of the reaction: (2E)-geranyl diphosphate = diphosphate + sabinene.
alpha-humulene synthase activity (GO:0080017)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = alpha-humulene + diphosphate.
anthocyanin 5-O-glucosyltransferase activity (GO:0080018)
Namespace: molecular_function
Definition: Catalysis of the reaction: an anthocyanin + UDP-D-glucose = an anthocyanin-5-O-glucoside + UDP.