LiteFold/GO huggingface dataset:
4-chlorobiphenyl metabolic process (GO:0018880)
Namespace: biological_process
Definition: The chemical reactions and pathways involving 4-chlorobiphenyl, a member of the polychlorinated biphenyl (PCB) group of compounds, a very stable group of synthetic organic compounds composed of a biphenyl nucleus with 1-10 chlorine substituents. 4-chlorobiphenyl has been used as a model substrate to investigate PCB degradation.
Synonyms: 4-chlorobiphenyl metabolism
obsolete ether metabolic process (GO:0018904)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving organic ethers, any anhydride of the general formula R1-O-R2, formed between two identical or nonidentical organic hydroxy compounds.
Synonyms: ether metabolism; organic ether metabolic process; organic ether metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete 1,4-dichlorobenzene metabolic process (GO:0018912)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving 1,4-dichlorobenzene (p-dichlorobenzene or paramoth), a derivative of benzene with two chlorine atoms attached at opposite positions on the ring. It forms white crystals at room temperature and is used as an insecticidal fumigant, particularly in mothballs.
Synonyms: 1,4-dichlorobenzene metabolism
Comment: The reason for obsoletion is that this term is an unnecessary grouping term. The chemical is not naturally made by any organism.
obsolete 2-nitropropane metabolic process (GO:0018938)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving 2-nitropropane, a clear, colorless liquid with a mild, fruity odor. 2-nitropropane is used principally as a solvent and chemical intermediate. As a solvent, it is used in inks, paints, adhesives, varnishes, polymers, and synthetic materials. It is a feedstock for the manufacture of 2-nitro-2-methyl-1-propanol and 2-amino-2-methyl-1-propanol.
Synonyms: 2-nitropropane metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
tri-n-butyltin metabolic process (GO:0018944)
Namespace: biological_process
Definition: The chemical reactions and pathways involving tri-n-butyltin, an organometallic compound composed of three butyl chains attached to a tin atom. Tri-n-butyltin is used as an antifouling agent in ship bottom paints and can be toxic to many marine organisms.
Synonyms: tri-n-butyltin metabolism
obsolete p-cymene metabolic process (GO:0018953)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving p-cymene, 1-methyl-4-isopropylbenzene, one of the alkyl-substituted aromatic hydrocarbons found in volatile oils from over 100 plants.
Synonyms: p-cymene metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
4-nitrophenol metabolic process (GO:0018960)
Namespace: biological_process
Definition: The chemical reactions and pathways involving 4-nitrophenol, a nitroaromatic compound which is used in the production of dyes, leather treatment agents, fungicides and as an intermediate in the production of the insecticide parathion.
Synonyms: 4-nitrophenol metabolism; p-nitrophenol metabolic process; p-nitrophenol metabolism
phthalate metabolic process (GO:0018963)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phthalate, the anion of phthalic acid. Phthalic acid diesters are used industrially in the production of a variety of household and consumer goods including plastic polymers, lubricating oils, and carriers for perfumes in cosmetics, while phthalic acid itself is used industrially as a plasticizer. Terephthalate is used in the synthesis of polyethylene terephthalate (polyethene terephthlate, abbreviated PET or PETE), a plastic polymer with many commercial uses.
Synonyms: phthalate metabolism; phthalic acid metabolic process; phthalic acid metabolism
obsolete 2,4,6-trinitrotoluene metabolic process (GO:0018974)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving 2,4,6-trinitrotoluene, 1-methyl-2,4,6-trinitrobenzene, a highly explosive pale yellow crystalline solid. It is prepared from toluene treated with concentrated sulfuric and nitric acids and is used in shells, bombs, and blasting explosives.
Synonyms: 2,4,6-trinitrotoluene metabolism; TNT metabolic process; TNT metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane metabolic process (GO:0018977)
Namespace: biological_process
Definition: The chemical reactions and pathways involving 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane (DDT), a chlorinated broad spectrum contact insecticide.
Synonyms: 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane metabolism; DDT metabolic process; DDT metabolism
obsolete molting cycle, protein-based cuticle (GO:0018988)
Namespace: biological_process
Definition: OBSOLETE. The periodic shedding of part or all of a protein-based cuticle, which is then replaced by a new protein-based cuticle. A cuticle is the outer layer of an animal which acts to prevent water loss.
Synonyms: protein-based cuticle molting cycle
Comment: This term was made obsolete because 'protein-based cuticle' is an unnecessary grouping term.
obsolete multipartite viral genome (GO:0019020)
Namespace: cellular_component
Definition: OBSOLETE. A segmented viral genome consisting of more than three sub-genomic nucleic acids but each nucleic acid is packaged into a different virion.
Comment: This term was obsoleted because it does not represent a GO cellular component.
obsolete provirus (GO:0019038)
Namespace: cellular_component
Definition: OBSOLETE. The name given to a viral genome after it has been integrated into the host genome; particularly applies to retroviruses and is a required part of the retroviral replication cycle.
Comment: This term was obsoleted because it does not represent a GO cellular component.
latent virus replication (GO:0019045)
Namespace: biological_process
Definition: Any process required for latent viral replication in a cell.
obsolete virus-mediated perturbation of host defense response (GO:0019049)
Namespace: biological_process
Definition: OBSOLETE. A process in which a virus interferes with the ability of the host to mount a defense in response to its presence. Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: evasion of host defenses by virus; mitigation of host antiviral defense response; mitigation of host defenses by virus; perturbation of host defense response by virus; regulation by virus of antiviral response; regulation of defense response to virus by virus; viral host defence evasion; viral host defense evasion; viral regulation of antiviral response
Comment: This term was obsoleted because it represents the same process as symbiont-mediated perturbation of host defense response ; GO:0052031.
obsolete modulation by virus of host transcription (GO:0019056)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus modulates the frequency, rate or extent of its host's transcription.
Synonyms: modification of host transcription; modulation by virus of host transcription; perturbation of host cell transcription
Comment: This term was obsoleted because it represents the same process as symbiont-mediated perturbation of host transcription ; GO:0052026.
uncoating of virus (GO:0019061)
Namespace: biological_process
Definition: The process by which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
Synonyms: viral uncoating
obsolete translocation of virus into host cell (GO:0019066)
Namespace: biological_process
Definition: OBSOLETE. The translocation of an entire virus particle across the host cell plasma membrane.
Synonyms: translocation of virus into host cell; viral translocation
Comment: This term was made obsolete because it is ambiguous, and more specific terms have been created.
viral capsid assembly (GO:0019069)
Namespace: biological_process
Definition: The assembly of a virus capsid from its protein subunits.
virus maturation (GO:0019075)
Namespace: biological_process
Definition: The refolding and structural rearrangements of virion parts to transition from the intermediate virion to the more mature virion. Maturation usually involves proteolysis events and changes in the folding of the virion proteins. Can occur inside the host cell or after release.
Synonyms: bacteriophage maturation; viral maturation
viral release from host cell (GO:0019076)
Namespace: biological_process
Definition: The dissemination of mature viral particles from a host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
Synonyms: release of virus from host; viral exit; viral release; viral shedding; virus exit from host cell
obsolete N-palmitoyltransferase activity (GO:0019105)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the transfer of a palmitoyl group to a nitrogen atom on the acceptor molecule.
Comment: This term has been obsoleted because it represents an unnecessary grouping class and is not consistent with the ontology structure.
obsolete phenanthrol sulfotransferase activity (GO:0019111)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: phenanthrol + X-SO3(-) = HX + phenanthrylsulfate.
Synonyms: phenanthrol sulphotransferase activity
Comment: This term was obsoleted because it is not known to be catalyzed by any gene product.
limonene monooxygenase activity (GO:0019113)
Namespace: molecular_function
Definition: Catalysis of a monooxygenase reaction in which oxygen is incorporated into limonene.
obsolete peptidyl-leucine racemization (GO:0019129)
Namespace: biological_process
Definition: OBSOLETE. The racemization of peptidyl-leucine.
Comment: This term was obsoleted because it represents a molecular function.
deoxynucleoside kinase activity (GO:0019136)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + 2'-deoxynucleoside = ADP + 2'-deoxynucleoside 5'-phosphate.
Synonyms: ATP:deoxynucleoside 5'-phosphotransferase activity; D. melanogaster deoxynucleoside kinase activity; Dm-dNK; ms-dNK; Ms-dNK activity; multifunctional deoxynucleoside kinase activity; multispecific deoxynucleoside kinase activity; multisubstrate deoxyribonucleoside kinase activity
aminobutyraldehyde dehydrogenase (NAD+) activity (GO:0019145)
Namespace: molecular_function
Definition: Catalysis of the reaction: 4-aminobutanal + NAD+ + H2O = 4-aminobutanoate + NADH + 2 H+.
Synonyms: 4-aminobutanal dehydrogenase activity; 4-aminobutanal:NAD+ 1-oxidoreductase activity; 4-aminobutyraldehyde dehydrogenase activity; ABAL dehydrogenase activity; gamma-aminobutyraldehyde dehydroganase activity
arabinose-5-phosphate isomerase activity (GO:0019146)
Namespace: molecular_function
Definition: Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H+.
Synonyms: arabinose phosphate isomerase activity; D-arabinose-5-phosphate aldose-ketose-isomerase activity; D-arabinose-5-phosphate ketol-isomerase activity; phosphoarabinoisomerase activity
D-cysteine desulfhydrase activity (GO:0019148)
Namespace: molecular_function
Definition: Catalysis of the reaction: D-cysteine + H2O = hydrogen sulfide + pyruvate + NH4+ + H+.
Synonyms: D-cysteine lyase activity; D-cysteine sulfide-lyase (deaminating); D-cysteine sulfide-lyase (deaminating; pyruvate-forming)
obsolete tetrahydrothiophene 1-oxide reductase activity (GO:0019174)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: tetrahydrothiophene 1-oxide + reduced acceptor = tetrahydrothiophene + acceptor.
Comment: The reason for obsoletion is that is not known to be catalyzed by any gene product. Source reference MetaCyc has no annotations.
obsolete acyl-CoA N-acyltransferase activity (GO:0019186)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the transfer of an acyl group from acyl-CoA to a nitrogen atom on an acceptor molecule.
Comment: The reason for obsoletion is that more specific terms were created.
nucleobase-containing compound kinase activity (GO:0019205)
Namespace: molecular_function
Definition: Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
Synonyms: nucleobase, nucleoside, nucleotide kinase activity
cytokine-mediated signaling pathway (GO:0019221)
Namespace: biological_process
Definition: The series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription.
Synonyms: cytokine and chemokine mediated signaling pathway; cytokine mediated signalling pathway
perception of rate of movement (GO:0019232)
Namespace: biological_process
Definition: The series of events by which an organism senses the speed and direction of movement of the body and its parts.
Synonyms: kinesthesia
deaminase activity (GO:0019239)
Namespace: molecular_function
Definition: Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH4+/NH2R).
methylglyoxal biosynthetic process (GO:0019242)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.
Synonyms: methylglyoxal anabolism; methylglyoxal biosynthesis; methylglyoxal formation; methylglyoxal synthesis
anaerobic cobalamin biosynthetic process (GO:0019251)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the absence of oxygen.
Synonyms: anaerobic cobalamin anabolism; anaerobic cobalamin biosynthesis; anaerobic cobalamin formation; anaerobic cobalamin synthesis; anaerobic vitamin B12 biosynthesis; anaerobic vitamin B12 biosynthetic process; cobalamin biosynthesis, anaerobic; cobalamin biosynthetic process, anaerobic; vitamin B12 biosynthesis, anaerobic; vitamin B12 biosynthetic process, anaerobic
4-nitrotoluene catabolic process (GO:0019258)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of 4-nitrotoluene, 1-methyl-4-nitrobenzene.
Synonyms: 4-nitrotoluene breakdown; 4-nitrotoluene catabolism; 4-nitrotoluene degradation; 4NT catabolic process; 4NT catabolism
obsolete L-asparagine biosynthetic process from oxaloacetate (GO:0019266)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine from other compounds, including oxaloacetate.
Synonyms: asparagine anabolism from oxaloacetate; asparagine formation from oxaloacetate; asparagine synthesis from oxaloacetate
Comment: This term was obsoleted because it represents a specific pathway and is out of scope for GO.
obsolete L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate (GO:0019292)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of L-tyrosine from other compounds, including chorismate, via the intermediate 4-hydroxyphenylpyruvate.
Synonyms: L-tyrosine anabolism from chorismate via 4-hydroxyphenylpyruvate; L-tyrosine biosynthetic process from chorismate via p-hydroxyphenylpyruvate; L-tyrosine formation from chorismate via 4-hydroxyphenylpyruvate; L-tyrosine synthesis from chorismate via 4-hydroxyphenylpyruvate; tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate
Comment: The reason for obsoletion is that this term represents a GO-CAM model.
pentose catabolic process (GO:0019323)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
Synonyms: pentose breakdown; pentose catabolism; pentose degradation
L-lyxose metabolic process (GO:0019324)
Namespace: biological_process
Definition: The chemical reactions and pathways involving L-lyxose, the L-enantiomer of aldopentose lyxo-pentose, the C-2 epimer of xylose.
Synonyms: L-lyxose metabolism
pentachlorophenol catabolic process (GO:0019338)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of pentachlorophenol, a chlorinated insecticide and fungicide used primarily to protect timber from fungal rot and wood boring insects. Pentachlorophenol is significantly toxic to mammals, plants, and many microorganisms.
Synonyms: pentachlorophenol breakdown; pentachlorophenol catabolism; pentachlorophenol degradation
trypanothione biosynthetic process (GO:0019342)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of trypanothione (N1,N6,-bis(glutathionyl)spermidine) in two steps from glutathione and spermidine via an N1- or N8-glutathionylspermidine intermediate. Trypanothione appears to be an essential redox intermediate in intracellular thiol redox regulation. It also plays a role in protecting against oxidative stress.
Synonyms: trypanothione anabolism; trypanothione biosynthesis; trypanothione formation; trypanothione synthesis
obsolete L-cysteine biosynthetic process via L-cystathionine (GO:0019343)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate L-cystathionine.
Synonyms: cysteine anabolism via cystathionine; cysteine formation via cystathionine; cysteine synthesis via cystathionine
Comment: This term was obsoleted because it is too specific and is outside the scope of GO.
L-cysteine biosynthetic process (GO:0019344)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid.
Synonyms: cysteine anabolism; cysteine biosynthesis; cysteine formation; cysteine synthesis
obsolete L-cysteine biosynthetic process via S-sulfo-L-cysteine (GO:0019345)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate S-sulfo-L-cysteine.
Synonyms: cysteine anabolism via S-sulfo-L-cysteine; cysteine biosynthesis via S-sulpho-L-cysteine; cysteine biosynthetic process via S-sulpho-L-cysteine; cysteine formation via S-sulfo-L-cysteine; cysteine synthesis via S-sulfo-L-cysteine
Comment: This term was obsoleted because it is too specific and is outside the scope of GO.
GDP-alpha-D-mannosylchitobiosyldiphosphodolichol biosynthetic process (GO:0019347)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of GDP-alpha-D-mannosylchitobiosyldiphosphodolichol, a substance composed of mannosylchitobiosyldiphosphodolichol in glycosidic linkage with guanosine diphosphate.
Synonyms: GDP-alpha-D-mannosylchitobiosyldiphosphodolichol anabolism; GDP-alpha-D-mannosylchitobiosyldiphosphodolichol biosynthesis; GDP-alpha-D-mannosylchitobiosyldiphosphodolichol formation; GDP-alpha-D-mannosylchitobiosyldiphosphodolichol synthesis
obsolete ribitol metabolic process (GO:0019349)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving ribitol, a pentitol derived formally by reduction of the -CHO group of either D- or L-ribose. It occurs free in some plants and is a component of riboflavin.
Synonyms: ribitol metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete dethiobiotin biosynthetic process (GO:0019351)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of dethiobiotin, a derivative of biotin in which the sulfur atom has been replaced by two hydrogen atoms.
Synonyms: desthiobiotin biosynthesis; desthiobiotin biosynthetic process; dethiobiotin anabolism; dethiobiotin biosynthesis; dethiobiotin formation; dethiobiotin synthesis
Comment: This term was obsoleted because it represents an intermediate in biotin biosynthetic process ;  GO:0009102.
protoporphyrinogen IX biosynthetic process from glutamate (GO:0019353)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glutamate.
Synonyms: protoporphyrinogen IX anabolism from glutamate; protoporphyrinogen IX formation from glutamate; protoporphyrinogen IX synthesis from glutamate
nicotinamide nucleotide biosynthetic process (GO:0019359)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.
Synonyms: nicotinamide nucleotide anabolism; nicotinamide nucleotide biosynthesis; nicotinamide nucleotide formation; nicotinamide nucleotide synthesis
pyridine nucleotide salvage (GO:0019365)
Namespace: biological_process
Definition: Any process that generates a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base, from derivatives of them without de novo synthesis.
Synonyms: pyridine nucleotide cycling
arachidonate metabolic process (GO:0019369)
Namespace: biological_process
Definition: The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
Synonyms: arachidonic acid metabolic process; arachidonic acid metabolism
galactolipid catabolic process (GO:0019376)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine.
Synonyms: galactolipid breakdown; galactolipid catabolism; galactolipid degradation
glycolipid catabolic process (GO:0019377)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
Synonyms: glycolipid breakdown; glycolipid catabolism; glycolipid degradation
cyclohexanol oxidation (GO:0019399)
Namespace: biological_process
Definition: The cyclohexanol metabolic process in which cyclohexanol is converted to adipate.
galactitol catabolic process (GO:0019404)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of galactitol, the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose.
Synonyms: galactitol breakdown; galactitol catabolism; galactitol degradation
aerobic respiration, using carbon monoxide as electron donor (GO:0019410)
Namespace: biological_process
Definition: The metabolic process in which carbon monoxide (CO) is oxidized to carbon dioxide (CO2) to generate energy. Conservation of energy in this process likely uses sodium ion gradients for ATP synthesis and is coupled to quantitative sulfide methylation.
aerobic respiration, using sulfur or sulfate as electron donor (GO:0019414)
Namespace: biological_process
Definition: An aerobic respiration process in which a sulfur-containing molecule (hydrogen sulfide, sulfur, sulfite, thiosulfate, and various polythionates) is oxidized.
Synonyms: aerobic respiration, using sulphur or sulphate as electron donor
thiosulfate oxidation (GO:0019416)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the conversion of thiosulfate to tetrathionate, using cytochrome c as an electron acceptor.
Synonyms: polythionate oxidation