LiteFold/GO huggingface dataset:
bacterial-type DNA replication (GO:0044787)
Namespace: biological_process
Definition: The DNA-dependent DNA replication, exemplified by prokaryotes, that occurs as part of the cell cycle. Prokaryotic DNA replication is bi-directional and originates at a single origin of replication on the circular genome.
Synonyms: bacterial-type cell cycle DNA replication
host-mediated perturbation of viral process (GO:0044788)
Namespace: biological_process
Definition: A process in which a host organism alters or subverts a biological process being mediated by a virus with which it is infected.
Synonyms: modulation by host of viral process
obsolete modulation by host of viral release from host cell (GO:0044789)
Namespace: biological_process
Definition: OBSOLETE. A process in which a host organism modulates the frequency, rate or extent of the release of a virus with which it is infected, from its cells.
Comment: This term was obsoleted because there is no evidence that it is a regulated process.
suppression of viral release by host (GO:0044790)
Namespace: biological_process
Definition: A process in which a host organism stops, prevents or reduces the frequency, rate or extent of the release of a virus with which it is infected, from its cells.
Synonyms: down regulation of release of virus from host; down regulation of viral exit; down regulation of viral release; down regulation of viral release from host cell; down regulation of viral shedding; down-regulation of release of virus from host; down-regulation of viral exit; down-regulation of viral release; down-regulation of viral release from host cell; down-regulation of viral shedding; downregulation of release of virus from host; downregulation of viral exit; downregulation of viral release; downregulation of viral release from host cell; downregulation of viral shedding; inhibition of release of virus from host; inhibition of viral exit; inhibition of viral release; inhibition of viral release from host cell; inhibition of viral shedding; negative regulation by host of viral release from host cell; negative regulation of release of virus from host; negative regulation of viral exit; negative regulation of viral release; negative regulation of viral release from host cell; negative regulation of viral shedding
obsolete positive regulation by host of viral release from host cell (GO:0044791)
Namespace: biological_process
Definition: OBSOLETE. A process in which a host organism activates or increases the frequency, rate or extent of the release of a virus with which it is infected, from its cells.
Comment: This term was obsoleted because there is no evidence that it is a regulated process.
host-mediated suppression of viral proces (GO:0044793)
Namespace: biological_process
Definition: A process in which a host organism interferes with, inhibits or disrupts a process being mediated by a virus with which it is infected.
Synonyms: negative regulation by host of viral process
host-mediated activation of viral process (GO:0044794)
Namespace: biological_process
Definition: A process in which a host organism initiates, promotes, or enhances the normal execution of a biological process being mediated by a virus with which it is infected.
Synonyms: positive regulation by host of viral process
trans-Golgi network to recycling endosome transport (GO:0044795)
Namespace: biological_process
Definition: The directed movement of substances, in membrane-bounded vesicles, from the trans-Golgi network to the recycling endosomes.
DNA polymerase processivity factor complex (GO:0044796)
Namespace: cellular_component
Definition: A protein complex which is capable of increasing the processivity of nucleotide polymerization by DNA polymerase as a part of DNA replication.
NarGHI complex (GO:0044799)
Namespace: cellular_component
Definition: A heterotrimeric protein complex with iron-sulfur and molybdenum cofactors that functions as a terminal reductase in electron transport pathways that operate during anaerobic nitrate respiration. In E. coli electrons are passed from the FdnGHI complex to the NarGHI complex via menoquinone and menaquinol. Within NarGHI, electrons are passed from the two heme molecules in the NarI subunit down a Fe-S cluster chain in the NarH and NarG subunits to the Molybdenum cofactor, Mo-bisMGD, in the NarG subunit.
Synonyms: cytoplasmic membrane-bound quinol-nitrate oxidoreductase; nitrate reductase A
obsolete multi-organism membrane fusion (GO:0044800)
Namespace: biological_process
Definition: OBSOLETE. The membrane organization process that joins two lipid bilayers to form a single membrane, involving more than one organism.
Comment: This term was obsoleted because it is not a biologically meaningful grouping class.
nucleophagy (GO:0044804)
Namespace: biological_process
Definition: A form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.
Synonyms: autophagy of nucleus; late nucleophagy; nucleus degradation
obsolete late nucleophagy (GO:0044805)
Namespace: biological_process
Definition: OBSOLETE. A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.
Comment: The reason for obsoletion is that this term was added in error (process no different from parent)
obsolete G-quadruplex DNA unwinding (GO:0044806)
Namespace: biological_process
Definition: OBSOLETE. The process by which G-quadruplex (also known as G4) DNA, which is a four-stranded DNA structure held together by guanine base pairing, is unwound or 'melted'.
Comment: The reason for obsoletion is that the term represents a molecular function.
macrophage migration inhibitory factor production (GO:0044807)
Namespace: biological_process
Definition: The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Synonyms: MIF production
chemokine (C-C motif) ligand 17 production (GO:0044809)
Namespace: biological_process
Definition: The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Synonyms: CCL17 production; TARC production; thymus and activation regulated chemokine production
obsolete fermentative hydrogen production (GO:0044812)
Namespace: biological_process
Definition: OBSOLETE. The fermentation of organic substances with a net release of hydrogen.
Synonyms: carbohydrate fermentation
Comment: The reason for obsoletion is that the term is not clearly defined and may be referring to synthetic processes.
pyruvate fermentation to butanoate (GO:0044813)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of pyruvate into butanoate. This pathway is found in strict anaerobes such as Clostridia species.
Synonyms: glycolytic fermentation via PFOR pathway; pyruvate fermentation via PFOR
obsolete pyruvate fermentation via PFL (GO:0044814)
Namespace: biological_process
Definition: OBSOLETE. The anaerobic metabolic process in which pyruvate is converted to acetyl-CoA and formate by the action of pyruvate formate lyase (PFL), typically occurring in facultative anaerobic bacteria during mixed-acid fermentation.
Comment: The reason for obsoletion is that this term represents a single enzymatic step (the conversion of pyruvate to acetyl-CoA and formate by pyruvate formate lyase) which is a molecular function, not a biological process.
obsolete DNA packaging complex (GO:0044815)
Namespace: cellular_component
Definition: OBSOLETE. A protein complex that plays a role in the process of DNA packaging.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
hydrogen generation via biophotolysis (GO:0044817)
Namespace: biological_process
Definition: The production of hydrogen which results from the dissociation by light of water into molecular hydrogen and oxygen. This process is observed in cyanobacteria and microalgae.
Synonyms: hydrogen biosynthesis via biophotolysis
mitotic G1/S transition checkpoint signaling (GO:0044819)
Namespace: biological_process
Definition: A cell cycle checkpoint that detects and negatively regulates progression from G1 to S phase as part of a mitotic cell cycle.
Synonyms: mitotic G1/S transition checkpoint
mitotic telomere tethering at nuclear periphery (GO:0044820)
Namespace: biological_process
Definition: The process in which a telomere is maintained in a specific location at the nuclear periphery, as part of a mitotic cell cycle.
meiotic telomere tethering at nuclear periphery (GO:0044821)
Namespace: biological_process
Definition: The process in which a telomere is maintained in a specific location at the nuclear periphery, as part of a meiotic cell cycle.
retroviral integrase activity (GO:0044823)
Namespace: molecular_function
Definition: Catalysis of the covalent insertion of double-stranded retroviral DNA into host DNA. Proceeds by an endonucleolytic cleavage at each 3'-OH extremity of the viral genome, named 3'-processing, followed by a strand transfer reaction leading to the insertion of the processed viral DNA into the target DNA by a trans-esterification mechanism.
retroviral 3' processing activity (GO:0044824)
Namespace: molecular_function
Definition: The catalysis of the removal of two di- or tri-nucleotides from each 3' end of double-stranded viral DNA, exposing recessed 3' hydroxyls.
Synonyms: 3' processing reaction; 3'-processing activity
Comment: This reaction may serve to remove heterogeneous extra bases from the viral DNA end, and to stabilize the integrase-DNA complex. The chemistry of cleavage is a simple hydrolysis by single-step transesterification.
obsolete retroviral strand transfer activity (GO:0044825)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the covalent insertion of processed 3'-viral DNA ends into host chromosomal DNA by a trans-esterification reaction.
Synonyms: strand transfer reaction
Comment: This term was obsoleted because it represents part of an activity.
viral genome integration into host DNA (GO:0044826)
Namespace: biological_process
Definition: The insertion into a host genome of viral DNA, usually by the action of an integrase enzyme. Once integrated, the provirus persists in the host cell and serves as a template for the transcription of viral genes and replication of the viral genome, leading to the production of new viruses.
Synonyms: viral genome integration
host-mediated perturbation of viral genome replication (GO:0044827)
Namespace: biological_process
Definition: A process in which a host organism alters or subverts viral genome replication.
Synonyms: modulation by host of viral genome replication; regulation by host of viral genome reproduction
host-mediated suppression of viral genome replication (GO:0044828)
Namespace: biological_process
Definition: A process in which a host organism interferes with, inhibits or disrupts viral genome replication.
Synonyms: negative regulation by host of viral genome replication
host-mediated activation of viral genome replication (GO:0044829)
Namespace: biological_process
Definition: A process in which a host organism initiates, promotes, or enhances the normal execution of viral genome replication.
Synonyms: positive regulation by host of viral genome replication
obsolete modulation by virus of host cytokine production (GO:0044831)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus modulates the frequency, rate or extent of cytokine production in its host organism.
Comment: This term was obsoleted because it is an unnecessary grouping term.
obsolete induction by virus of host cytokine production (GO:0044832)
Namespace: biological_process
Definition: OBSOLETE. The process in which a virus increases the frequency, rate or extent of cytokine production in its host organism.
Synonyms: positive regulation by virus of host cytokine production
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete modulation by virus of host protein transport (GO:0044833)
Namespace: biological_process
Definition: OBSOLETE. Any viral process that modulates the frequency, rate or extent of protein transport in its host organism.
Comment: This term was obsoleted because its definition was too vague.
retroviral intasome (GO:0044834)
Namespace: cellular_component
Definition: A tetramer of retroviral integrase subunits tightly associated with a pair of viral DNA ends. Functions to insert viral DNA into a host cell chromosome.
hydrogen generation via nitrogenase (GO:0044835)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of H2 (dihydrogen) which involve a nitrogenase activity as one of the steps. This process is observed in cyanobacteria.
obsolete D-xylose fermentation (GO:0044836)
Namespace: biological_process
Definition: OBSOLETE. The anaerobic enzymatic conversion of D-xylose to ethanol, yielding energy in the form of ATP.
Comment: The reason for obsoletion is that the term is not clearly different from its parent term xylose catabolic process to ethanol.
actomyosin contractile ring organization (GO:0044837)
Namespace: biological_process
Definition: A process which results in the assembly, arrangement of constituent parts, or disassembly of an actomyosin contractile ring.
Synonyms: cytokinesis, actomyosin contractile ring organization
cell quiescence (GO:0044838)
Namespace: biological_process
Definition: A specialized resting state that cells enter in response to cues from the cell's environment. Quiescence is characterized by the absence of cell growth and division, by a reprogramming of global gene expression, and by changes characteristic of the organism and specific cell type. Depending on external conditions, quiescence may persist until cell death or cells may resume cell growth and division. In some cell types or under certain conditions, cellular metabolism may proceed.
Synonyms: cell cycle quiescence; cellular quiescence; G0 phase; quiescence
Comment: Note that terminally differentiated cells in higher eukaryotes are typically quiescent but metabolically active. Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). Also, note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
cell cycle G2/M phase transition (GO:0044839)
Namespace: biological_process
Definition: The cell cycle process by which a cell in G2 phase commits to M phase.
gut granule (GO:0044840)
Namespace: cellular_component
Definition: A lysosome-related organelle contained within the intestinal cells of the nematode C. elegans. Gut granules are acidified, birefringent, autofluorescent, and contain the vacuolar H+-ATPase. They also serve as sites of cellular zinc storage.
gut granule membrane (GO:0044841)
Namespace: cellular_component
Definition: The membrane of a gut granule, a lysosome-related organelle contained within the intestinal cells of the nematode C. elegans.
gut granule lumen (GO:0044842)
Namespace: cellular_component
Definition: The lumen of a gut granule, a lysosome-related organelle contained within the intestinal cells of the nematode C. elegans.
obsolete chain elongation of O-linked mannose residue (GO:0044845)
Namespace: biological_process
Definition: OBSOLETE. Extension of the O-linked mannose residue of a mannoprotein by the stepwise addition of further mannose molecules.
Comment: The reason for obsoletion is that this term represents a molecular function
obsolete negative regulation by symbiont of indole acetic acid levels in host (GO:0044846)
Namespace: biological_process
Definition: OBSOLETE. Any process in which an organism reduces the indole acetic acid levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: negative regulation by symbiont of auxin levels in host; negative regulation by symbiont of IAA levels in host
Comment: This term was obsoleted because there is no evidence that this process exists.
iron acquisition from host (GO:0044847)
Namespace: biological_process
Definition: The process by which a symbiont acquires iron from its host, either from heme or other iron containing molecules such as transferrin and lactoferrin. Begins with either the secretion of symbiont gene products that bind iron- or heme-containing molecules (siderophores and hemophores) from the symbiont cell into the host, or by expression of receptors that bind iron- or heme-containing molecules on the symbiont cell surface. Ends when the iron-containing compound is transported into the symbiont cell.
Synonyms: acquisition by organism of nutrients from host via siderophores; acquisition by symbiont of nutrients from host via siderophores; heme acquisition; iron acquisition; iron acquisition by symbiont from host; iron acquisition by symbiont from host heme
biological phase (GO:0044848)
Namespace: biological_process
Definition: A distinct period or stage in a biological process or cycle.
Comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.
menstrual cycle (GO:0044850)
Namespace: biological_process
Definition: A type of ovulation cycle where the endometrium is shed if pregnancy does not occur.
hair cycle phase (GO:0044851)
Namespace: biological_process
Definition: The cyclical periods of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body.
Comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase. To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
obsolete nonrepetitive DNA condensation (GO:0044852)
Namespace: biological_process
Definition: OBSOLETE. The process in which chromatin structure of nonrepetitive regions of DNA is compacted prior to and during mitosis in eukaryotic cells.
Synonyms: nonrepetitive DNA packaging
Comment: This term was obsoleted because is is defined in a negative manner.
plasma membrane raft (GO:0044853)
Namespace: cellular_component
Definition: A membrane raft that is part of the plasma membrane.
plasma membrane raft assembly (GO:0044854)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a plasma membrane raft.
plasma membrane raft distribution (GO:0044855)
Namespace: biological_process
Definition: The process that establishes the spatial arrangement of membrane rafts within a plasma membrane.
plasma membrane raft localization (GO:0044856)
Namespace: biological_process
Definition: Any process in which plasma membrane rafts are transported to, or maintained in, a specific location.
plasma membrane raft organization (GO:0044857)
Namespace: biological_process
Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of plasma membrane rafts.
plasma membrane raft polarization (GO:0044858)
Namespace: biological_process
Definition: The clustering and aggregation of a plasma membrane into domains. This serves as a mechanism to compartmentalize cellular activities and to establish cell polarity.
Synonyms: plasma membrane polarization
protein insertion into plasma membrane raft (GO:0044859)
Namespace: biological_process
Definition: The process in which a protein is incorporated into a plasma membrane raft.
protein localization to plasma membrane raft (GO:0044860)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, a location within a plasma membrane raft.
protein transport into plasma membrane raft (GO:0044861)
Namespace: biological_process
Definition: The directed movement of a protein into a plasma membrane raft.
protein transport out of plasma membrane raft (GO:0044862)
Namespace: biological_process
Definition: The directed movement of a protein out of a plasma membrane raft.
obsolete modulation by virus of host cell division (GO:0044863)
Namespace: biological_process
Definition: OBSOLETE. Any process where an infecting virus modulates the frequency, rate or extent of the physical partitioning and separation of its host's cell into daughter cells.
Synonyms: regulation by virus of host cell division
Comment: This term was obsoleted because it is an unnecessary grouping term.
obsolete positive regulation by virus of host cell division (GO:0044864)
Namespace: biological_process
Definition: OBSOLETE. Any process where an infecting virus activates or increases the frequency, rate or extent of its host's cell division.
Comment: This term was obsoleted because it represents the same process as transformation of host cell by virus ; GO:0019087.
symbiont-mediated suppression of host cell division (GO:0044865)
Namespace: biological_process
Definition: A process in which a symbiont inhibits or disrupts the normal execution of cell division in the host cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: inhibition by virus of host cell division; negative regulation by virus of host cell division
modulation by host of viral exo-alpha-sialidase activity (GO:0044866)
Namespace: biological_process
Definition: The process in which a host organism effects a change in viral exo-alpha-sialidase activity, the catalysis of the hydrolysis of peptide bonds in a protein.
modulation by host of viral molecular function (GO:0044868)
Namespace: biological_process
Definition: A process in which a host organism modulates the frequency, rate or extent of any molecular function being mediated by a virus with which it is infected.
obsolete negative regulation by host of viral exo-alpha-sialidase activity (GO:0044869)
Namespace: biological_process
Definition: OBSOLETE. The process in which a host organism decreases viral exo-alpha-sialidase activity, the catalysis of the hydrolysis of peptide bonds in a protein.
Comment: This term was obsoleted because it represents a molecular function.
modulation by host of viral glycoprotein metabolic process (GO:0044870)
Namespace: biological_process
Definition: A process in which a host organism modulates the frequency, rate or extent of viral glycoprotein metabolic process.
negative regulation by host of viral glycoprotein metabolic process (GO:0044871)
Namespace: biological_process
Definition: A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral glycoprotein metabolic process.