LiteFold/GO huggingface dataset:
obsolete endogenous drug catabolic process (GO:0042739)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a drug that has originated internally within the cell or organism.
Synonyms: endogenous drug breakdown; endogenous drug catabolism; endogenous drug degradation
Comment: The reason for obsoletion is that there is no evidence that this process exists as a drug is by definition exogenous.
exogenous antibiotic catabolic process (GO:0042740)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of an antibiotic that has originated externally to the cell or organism.
Synonyms: exogenous antibiotic breakdown; exogenous antibiotic catabolism; exogenous antibiotic degradation
hydrogen peroxide metabolic process (GO:0042743)
Namespace: biological_process
Definition: The chemical reactions and pathways involving hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.
Synonyms: H2O2 metabolic process; hydrogen peroxide metabolism
hydrogen peroxide catabolic process (GO:0042744)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
Synonyms: detoxification of H2O2; detoxification of hydrogen peroxide; H2O2 catabolic process; H2O2 scavenging; hydrogen peroxide breakdown; hydrogen peroxide catabolism; hydrogen peroxide degradation; hydrogen peroxide removal; hydrogen peroxide scavenging
circadian sleep/wake cycle (GO:0042745)
Namespace: biological_process
Definition: The cycle from wakefulness through an orderly succession of sleep states and stages that occurs on an approximately 24 hour rhythm.
circadian sleep/wake cycle, wakefulness (GO:0042746)
Namespace: biological_process
Definition: The part of the circadian sleep/wake cycle where the organism is not asleep.
circadian sleep/wake cycle, REM sleep (GO:0042747)
Namespace: biological_process
Definition: A stage in the circadian sleep cycle during which dreams occur and the body undergoes marked changes including rapid eye movement, loss of reflexes, and increased pulse rate and brain activity.
circadian sleep/wake cycle, non-REM sleep (GO:0042748)
Namespace: biological_process
Definition: All sleep stages in the circadian sleep/wake cycle other than REM sleep. These stages are characterized by a slowing of brain waves and other physiological functions.
regulation of circadian sleep/wake cycle (GO:0042749)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the circadian sleep/wake cycle.
hibernation (GO:0042750)
Namespace: biological_process
Definition: Any process in which an organism enters and maintains a period of dormancy in which to pass the winter. It is characterized by narcosis and by sharp reduction in body temperature and metabolic activity and by a depression of vital signs.
estivation (GO:0042751)
Namespace: biological_process
Definition: Any process in which an organism enters and maintains a period of dormancy, similar to hibernation, but that occurs during the summer. It insulates against heat to prevent the harmful effects of the season.
Synonyms: aestivation
positive regulation of circadian rhythm (GO:0042753)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
Synonyms: activation of circadian rhythm; stimulation of circadian rhythm; up regulation of circadian rhythm; up-regulation of circadian rhythm; upregulation of circadian rhythm
negative regulation of circadian rhythm (GO:0042754)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior.
Synonyms: down regulation of circadian rhythm; down-regulation of circadian rhythm; downregulation of circadian rhythm; inhibition of circadian rhythm
eating behavior (GO:0042755)
Namespace: biological_process
Definition: The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
Synonyms: eating behaviour
drinking behavior (GO:0042756)
Namespace: biological_process
Definition: The specific behavior of an organism relating to the intake of liquids, especially water.
Synonyms: drinking behaviour
giant axon (GO:0042757)
Namespace: cellular_component
Definition: Extremely large, unmyelinated axon found in invertebrates. Has high conduction speeds and is usually involved in panic or escape responses.
long-chain fatty acid catabolic process (GO:0042758)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.
Synonyms: long-chain fatty acid breakdown; long-chain fatty acid catabolism; long-chain fatty acid degradation
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
long-chain fatty acid biosynthetic process (GO:0042759)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons.
Synonyms: long-chain fatty acid anabolism; long-chain fatty acid biosynthesis; long-chain fatty acid formation; long-chain fatty acid synthesis
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
very long-chain fatty acid catabolic process (GO:0042760)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a very long-chain fatty acid. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons.
Synonyms: very-long-chain fatty acid breakdown; very-long-chain fatty acid catabolic process; very-long-chain fatty acid catabolism; very-long-chain fatty acid degradation
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
very long-chain fatty acid biosynthetic process (GO:0042761)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a very long-chain fatty acid. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons.
Synonyms: very-long-chain fatty acid anabolism; very-long-chain fatty acid biosynthesis; very-long-chain fatty acid biosynthetic process; very-long-chain fatty acid formation; very-long-chain fatty acid synthesis
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
regulation of sulfur metabolic process (GO:0042762)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur.
Synonyms: regulation of sulfur metabolism; regulation of sulphur metabolic process; regulation of sulphur metabolism
intracellular immature spore (GO:0042763)
Namespace: cellular_component
Definition: A cell or part of the cell that constitutes an early developmental stage of a spore, a small reproductive body that is highly resistant to desiccation and heat and is capable of growing into a new organism, produced especially by certain bacteria, fungi, algae, and nonflowering plants.
Synonyms: forespore
ascospore-type prospore (GO:0042764)
Namespace: cellular_component
Definition: An immature spore undergoing development. The spore usually consists of nucleic acid, prospore membrane(s) that encase the nucleic acid, and ultimately a cell wall that covers the membrane(s). This type of spore is observed in ascospore-forming fungi.
GPI-anchor transamidase complex (GO:0042765)
Namespace: cellular_component
Definition: An enzyme complex which in humans and yeast consists of at least five proteins; for example, the complex contains GAA1, GPI8, PIG-S, PIG-U, and PIG-T in human, and Gaa1p, Gab1p, Gpi8p, Gpi16p, and Gpi17p in yeast. Catalyzes the posttranslational attachment of the carboxy-terminus of a precursor protein to a GPI-anchor.
Synonyms: GPIT complex
Comment: Note that this term should not be confused with 'glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex ; GO:0000506', which represents a distinct complex with a different catalytic activity.
obsolete nucleosome mobilization (GO:0042766)
Namespace: biological_process
Definition: OBSOLETE. The movement of nucleosomes along a DNA fragment.
Synonyms: nucleosome sliding
Comment: This term was obsoleted because it represents a molecular function.
ecdysteroid 22-hydroxylase activity (GO:0042767)
Namespace: molecular_function
Definition: Catalysis of the reaction: 3-dehydro-2,22-dideoxyecdysone + 2 reduced [adrenodoxin] + O2 + 2 H+ = 3-dehydro-2-deoxyecdysone + 2 oxidized [adrenodoxin] + H2O. Other substrates include 3-dehydro-2,22,25-deoxyecdysone and 2,22-dideoxyecdysone.
Synonyms: 3-dehydro-2,22-dideoxyecdysone 22-hydroxylase activity
ecdysteroid 2-hydroxylase activity (GO:0042768)
Namespace: molecular_function
Definition: Catalysis of the hydroxylation of an ecdysteroid at carbon position 2.
Comment: Note that in the ecdysteroidogenic pathway, this activity catalyzes the conversion of 2-deoxyecdysone to ecdysone. It can also catalyze the conversion of 2,22-dideoxyecdysone (ketotriol) to 22-deoxyecdysone.
obsolete DNA damage response, detection of DNA damage (GO:0042769)
Namespace: biological_process
Definition: OBSOLETE. The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
Synonyms: detection of DNA damage during DNA damage response; DNA damage response, perception of DNA damage
Comment: This term has been obsoleted because it represents a molecular function.
signal transduction in response to DNA damage (GO:0042770)
Namespace: biological_process
Definition: A cascade of processes induced by the detection of DNA damage within a cell.
Synonyms: DNA damage induced protein phosphorylation; DNA damage response, signal transduction; response to DNA damage stimulus by intracellular signaling cascade
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)
Namespace: biological_process
Definition: The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
Synonyms: DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis
DNA damage response, signal transduction resulting in transcription (GO:0042772)
Namespace: biological_process
Definition: A cascade of processes initiated in response to the detection of DNA damage, and resulting in the induction of transcription.
ATP synthesis coupled electron transport (GO:0042773)
Namespace: biological_process
Definition: The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.
plasma membrane ATP synthesis coupled electron transport (GO:0042774)
Namespace: biological_process
Definition: The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP in the plasma membrane.
mitochondrial ATP synthesis coupled electron transport (GO:0042775)
Namespace: biological_process
Definition: The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP, as it occurs in the mitochondrial inner membrane or chloroplast thylakoid membrane.
Synonyms: mitochondrial electron transport; organelle ATP synthesis coupled electron transport
proton motive force-driven plasma membrane ATP synthesis (GO:0042777)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ATP driven by transport of protons across a plasma membrane to generate an electrochemical gradient (proton-motive force).
Synonyms: ATP synthesis coupled proton transport; plasma membrane ATP synthesis coupled proton transport
tRNA end turnover (GO:0042778)
Namespace: biological_process
Definition: The process in which the 3'-terminal CCA of a tRNA is removed and restored. This often happens to uncharged tRNA.
obsolete tRNA 3'-trailer cleavage (GO:0042779)
Namespace: biological_process
Definition: OBSOLETE. Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both.
Synonyms: removal of tRNA 3'-trailer sequence; tRNA 3'-end cleavage
Comment: The reason for obsoletion is that the term represents a molecular function.
3'-tRNA processing endoribonuclease activity (GO:0042781)
Namespace: molecular_function
Definition: Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
Synonyms: 3 tRNase activity; 3' tRNA processing endoribonuclease activity; 3' tRNase activity; ribonuclease Z activity; RNase Z activity; tRNA 3 endonuclease activity; tRNA 3' endonuclease activity; tRNAse Z
symbiont-mediated evasion of host immune response (GO:0042783)
Namespace: biological_process
Definition: A process by which an organism 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.
Synonyms: active evasion of host immune response; active evasion of immune response of other organism involved in symbiotic interaction; active immune evasion; evasion by virus of host immune response; evasion of host immune response; evasion or tolerance of host immune response; immune evasion; mitigation by virus of host immune response; mitigation of host immune response; mitigation of host immune response by virus; passive evasion of host immune response; passive evasion of immune response of other organism involved in symbiotic interaction; passive immune evasion; suppression by virus of host immune response
symbiont-mediated suppression of host complement activation (GO:0042784)
Namespace: biological_process
Definition: A process by which a symbiont inhibits or disrupts the normal execution of the activation of complement in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: active evasion of host immune response via regulation of host complement system; active evasion of immune response of other organism via regulation of complement system of other organism involved in symbiotic interaction; active immune evasion via modulation of host complement system; active immune evasion via regulation of host complement system; evasion of host immune response via modulation of host complement system; evasion of host immune response via regulation of host complement system; suppression of complement activation by another organism
obsolete evasion of host immune response via modulation of host cytokine network (GO:0042785)
Namespace: biological_process
Definition: OBSOLETE. Any mechanism of active immune avoidance which works by regulating host cytokine networks, e.g. by secreting proteins that mimic cytokine receptors that act to sequester host cytokines and inhibit action. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: active evasion of host immune response via regulation of host cytokine network; active evasion of immune response of other organism via regulation of cytokine network of other organism involved in symbiotic interaction; active immune evasion via modulation of host cytokine network; active immune evasion via regulation of host cytokine network; evasion of host immune response via regulation of host cytokine network
Comment: This term was obsoleted because it was poorly defined and used inconsistently.
obsolete polysomal ribosome (GO:0042788)
Namespace: cellular_component
Definition: OBSOLETE. A ribosome bound to mRNA that forms part of a polysome.
Synonyms: active ribosome
Comment: The reason for obsoletion is that the term is out of scope for GO.
mRNA transcription by RNA polymerase II (GO:0042789)
Namespace: biological_process
Definition: The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
Synonyms: mRNA transcription from Pol II promoter; mRNA transcription from RNA polymerase II promoter
nucleolar large rRNA transcription by RNA polymerase I (GO:0042790)
Namespace: biological_process
Definition: The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I.
Synonyms: transcription of nuclear large rRNA transcript from RNA polymerase I promoter; transcription of nuclear rRNA large Pol I transcript; transcription of nucleolar large rRNA by RNA polymerase I
5S class rRNA transcription by RNA polymerase III (GO:0042791)
Namespace: biological_process
Definition: The synthesis of 5S ribosomal RNA (rRNA), or an equivalent rRNA, from a DNA template by RNA polymerase III (Pol III), originating at a type 1 RNA polymerase III promoter.
Synonyms: 5S class rRNA transcription from RNA polymerase III type 1 promoter; 5S rRNA transcription
obsolete mitochondrial rRNA transcription (GO:0042792)
Namespace: biological_process
Definition: OBSOLETE. The synthesis of ribosomal RNA (rRNA) from a mitochondrial DNA template.
Synonyms: rRNA transcription from mitochondrial promoter
Comment: This term was obsoleted because it is the same as its parent, 'mitochondrial transcription', since there is no specific pathway or factors for rRNA transcription.
plastid transcription (GO:0042793)
Namespace: biological_process
Definition: The synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase.
Synonyms: transcription from plastid promoter
plastid rRNA transcription (GO:0042794)
Namespace: biological_process
Definition: The synthesis of ribosomal RNA (rRNA) from a plastid DNA template, usually by a specific plastid RNA polymerase.
Synonyms: rRNA transcription from plastid promoter
snRNA transcription by RNA polymerase II (GO:0042795)
Namespace: biological_process
Definition: The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
Synonyms: snRNA transcription from Pol II promoter; snRNA transcription from RNA polymerase II promoter
snRNA transcription by RNA polymerase III (GO:0042796)
Namespace: biological_process
Definition: The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter.
Synonyms: snRNA transcription from Pol III promoter; snRNA transcription from RNA polymerase III promoter
tRNA transcription by RNA polymerase III (GO:0042797)
Namespace: biological_process
Definition: The synthesis of transfer RNA (tRNA) from a DNA template by RNA polymerase III (Pol III), originating at a Pol III promoter.
Synonyms: tRNA transcription from Pol III promoter; tRNA transcription from RNA polymerase III promoter
obsolete protein neddylation during NEDD8 class-dependent protein catabolic process (GO:0042798)
Namespace: biological_process
Definition: OBSOLETE. Covalent attachment of the ubiquitin-like protein NEDD8 (or equivalent protein) to another protein, as a part of NEDD8-dependant protein catabolism.
Synonyms: protein neddylation during NEDD8 class-dependent protein breakdown; protein neddylation during NEDD8 class-dependent protein catabolic process; protein neddylation during NEDD8 class-dependent protein catabolism; protein neddylation during NEDD8 class-dependent protein degradation; protein neddylation during RUB1-dependent protein catabolic process; protein neddylation during RUB1-dependent protein catabolism
Comment: This term was made obsolete because NEDD8-class tags do not target proteins for proteolytic destruction.
histone H4K20 methyltransferase activity (GO:0042799)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group to the lysine residue at position 20 of the histone H4 protein.
Synonyms: histone H4 lysine 20-specific methyltransferase activity; histone H4K20 methylase activity; histone H4K20 methylation; histone lysine N-methyltransferase activity (H4-K20 specific); histone methylase activity (H4-K20 specific); histone methyltransferase activity (H4-K20 specific); histone-H4K20 methyltransferase activity
Comment: Note that the residue position corresponds to the canonical human H4 histone (UniProtKB:P02309); this residue is conserved across all eukaryotes. Note that the initiation methionine is cleaved, so the first residue is S1.
histone H3K4 methyltransferase activity (GO:0042800)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of up to three methyl groups to the lysine residue at position 4 of the histone H3 protein.
Synonyms: histone H3 lysine 4-specific methyltransferase activity; histone H3K4 methylase activity; histone lysine N-methyltransferase activity (H3-K4 specific); histone methylase activity (H3-K4 specific); histone methyltransferase activity (H3-K4 specific); histone-H3K4 methyltransferase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
obsolete polo kinase kinase activity (GO:0042801)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the addition of a phosphate group onto a serine or threonine residue in any member of the polo kinase class of proteins.
Comment: This term was made obsolete because it represents a gene product and also refers to a non-existent activity (polo kinase).
identical protein binding (GO:0042802)
Namespace: molecular_function
Definition: Binding to an identical protein or proteins.
Synonyms: isoform-specific homophilic binding; protein homopolymerization
protein homodimerization activity (GO:0042803)
Namespace: molecular_function
Definition: Binding to an identical protein to form a homodimer.
Synonyms: dimerization activity
obsolete protein homooligomerization activity (GO:0042804)
Namespace: molecular_function
Definition: OBSOLETE. Interacting selectively with identical proteins to form a homooligomer.
Synonyms: oligomerization activity; protein homooligomerization activity
Comment: This term was made obsolete because it represents a biological process.
actinin binding (GO:0042805)
Namespace: molecular_function
Definition: Binding to actinin, any member of a family of proteins that crosslink F-actin.
Synonyms: beta-actinin binding; capZ binding
fucose binding (GO:0042806)
Namespace: molecular_function
Definition: Binding to fucose, the pentose 6-deoxygalactose.