LiteFold/GO huggingface dataset:
methanogenesis, from acetate (GO:0019385)
Namespace: biological_process
Definition: The formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other components, including acetate.
Synonyms: methane biosynthesis from acetate; methane biosynthetic process from acetate
methanogenesis, from carbon dioxide (GO:0019386)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
Synonyms: methane biosynthesis from carbon dioxide; methane biosynthetic process from carbon dioxide
methanogenesis, from methanol (GO:0019387)
Namespace: biological_process
Definition: The formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other components, including methanol.
Synonyms: methane biosynthesis from methanol; methane biosynthetic process from methanol
galactose catabolic process (GO:0019388)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of galactose, the aldohexose galacto-hexose.
Synonyms: galactose breakdown; galactose catabolism; galactose degradation
obsolete glucuronoside metabolic process (GO:0019389)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving glucuronosides, any compound formed by combination in glycosidic linkage of a hydroxy compound with the anomeric carbon atom of a glucuronate.
Synonyms: glucuronide metabolic process; glucuronide metabolism; glucuronoside metabolism
Comment: The reason for obsoletion is that this term is an unnecessary grouping term.
obsolete glucuronoside biosynthetic process (GO:0019390)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of glucuronosides, compound composed of a hydroxy compound linked to a glucuronate residue.
Synonyms: glucuronide biosynthesis; glucuronide biosynthetic process; glucuronoside anabolism; glucuronoside biosynthesis; glucuronoside formation; glucuronoside synthesis
Comment: The reason for obsoletion is that this term represents a molecular function.
glucuronoside catabolic process (GO:0019391)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glucuronosides, compound composed of a hydroxy compound linked to a glucuronate residue.
Synonyms: glucuronide catabolic process; glucuronide catabolism; glucuronoside breakdown; glucuronoside catabolism; glucuronoside degradation
Comment: Note that this term was reinstated from obsolete.
obsolete glucarate metabolic process (GO:0019392)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving glucarate, the dianion of glucaric acid, an aldaric acid derived from either glucose or gulose. There are two enantiomers L- and D-glucarate.
Synonyms: glucarate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
glucarate biosynthetic process (GO:0019393)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of glucarate, the anion of glucaric acid.
Synonyms: glucarate anabolism; glucarate biosynthesis; glucarate formation; glucarate synthesis
obsolete glucarate catabolic process (GO:0019394)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glucarate, the anion of glucaric acid.
Comment: The reason for obsoletion is that this term is redundant with its more specific child term GO:0042838 'D-glucarate catabolic process'. The existing annotations are specific for D-glucarate.
fatty acid oxidation (GO:0019395)
Namespace: biological_process
Definition: The removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydrogen.
gallate catabolic process (GO:0019396)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of gallate, the anion of gallic acid (3,4,5-trihydroxybenzoic acid).
Synonyms: gallate breakdown; gallate catabolism; gallate degradation; gallate metabolic process; gallate metabolism; gallic acid catabolic process; gallic acid catabolism; gallic acid metabolic process; gallic acid metabolism
gallate catabolic process via 2-pyrone-4,6-dicarboxylate (GO:0019397)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of gallate, the anion of gallic acid, via the intermediate 2-pyrone-4,6-dicarboxylate.
Synonyms: gallate breakdown via 2-pyrone-4,6-dicarboxylate; gallate degradation via 2-pyrone-4,6-dicarboxylate; gallic acid catabolic process via 2-pyrone-4,6-dicarboxylate; gallic acid catabolism via 2-pyrone-4,6-dicarboxylate
gallate catabolic process via gallate dioxygenase activity (GO:0019398)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of gallate, the anion of gallic acid, where the first step is the conversion of gallate to (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate catalyzed by gallate dioxygenase.
Synonyms: gallate breakdown via 4-carboxy-2-hydroxhexa-2,3-dienedioate; gallate catabolic process via 4-carboxy-2-hydroxhexa-2,3-dienedioate; gallate degradation via 4-carboxy-2-hydroxhexa-2,3-dienedioate; gallic acid catabolic process via 4-carboxy-2-hydroxhexa-2,3-dienedioate; gallic acid catabolism via 4-carboxy-2-hydroxhexa-2,3-dienedioate
obsolete alditol metabolic process (GO:0019400)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving alditols, any polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group.
Synonyms: alditol metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
alditol biosynthetic process (GO:0019401)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of alditols, any polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group.
Synonyms: alditol anabolism; alditol biosynthesis; alditol formation; alditol synthesis
galactitol metabolic process (GO:0019402)
Namespace: biological_process
Definition: The chemical reactions and pathways involving galactitol, the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose.
Synonyms: galactitol metabolism
galactitol biosynthetic process (GO:0019403)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of galactitol, the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose.
Synonyms: galactitol anabolism; galactitol biosynthesis; galactitol formation; galactitol synthesis
alditol catabolic process (GO:0019405)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of alditols, any polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group.
Synonyms: alditol breakdown; alditol catabolism; alditol degradation
hexitol biosynthetic process (GO:0019406)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of hexitols, any alditol with a chain of six carbon atoms in the molecule.
Synonyms: hexitol anabolism; hexitol biosynthesis; hexitol formation; hexitol synthesis
hexitol catabolic process (GO:0019407)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of hexitols, any alditol with a chain of six carbon atoms in the molecule.
Synonyms: hexitol breakdown; hexitol catabolism; hexitol degradation
obsolete dolichol biosynthetic process (GO:0019408)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of dolichols, any 2,3-dihydropolyprenol derived from four or more linked isoprene units.
Synonyms: dolichol anabolism; dolichol biosynthesis; dolichol formation; dolichol synthesis
Comment: This term was obsoleted because it represents an intermediate step in dolichyl monophosphate biosynthetic process ; GO:0043048.
aerobic respiration, using ammonia as electron donor (GO:0019409)
Namespace: biological_process
Definition: The metabolic process in which ammonia (NH4+) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite.
Synonyms: aerobic ammonia oxidation to nitrite via hydrazine; nitrification
aerobic respiration, using ferrous ions as electron donor (GO:0019411)
Namespace: biological_process
Definition: The metabolic process in which ferrous ions (Fe2+) are oxidized to ferric ions (Fe3+) to generate energy, coupled to the reduction of carbon dioxide.
aerobic respiration, using hydrogen as electron donor (GO:0019412)
Namespace: biological_process
Definition: The oxidation of hydrogen (H2) to water (H2O), using oxygen (O2) as the electron acceptor. A hydrogenase enzyme binds H2 and the hydrogen atoms are passed through an electron transfer chain to O2 to form water.
Synonyms: hydrogen oxidation
acetate biosynthetic process (GO:0019413)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid.
Synonyms: acetate anabolism; acetate biosynthesis; acetate formation; acetate synthesis
acetate biosynthetic process from carbon monoxide (GO:0019415)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide.
Synonyms: acetate anabolism from carbon monoxide; acetate formation from carbon monoxide; acetate synthesis from carbon monoxide; carbon monoxide dehydrogenase pathway
sulfur oxidation (GO:0019417)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur.
Synonyms: sulphur oxidation
sulfide oxidation (GO:0019418)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the conversion of sulfide to elemental sulfur in a higher oxidation state, or to sulfite or sulfate.
Synonyms: sulphide oxidation
obsolete sulfate reduction (GO:0019419)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the reduction of sulfate to another sulfur-containing ion or compound such as hydrogen sulfide, adenosine-phosphosulfate (APS) or thiosulfate.
Synonyms: assimilatory sulfate reduction; assimilatory sulphate reduction; sulfate reduction, APS pathway; sulphate reduction; sulphate reduction, APS pathway
Comment: This term was obsoleted because it has the same meaning as sulfate assimilation ; GO:0000103.
dissimilatory sulfate reduction (GO:0019420)
Namespace: biological_process
Definition: The reduction of sulfate to hydrogen sulfide, which acts as a terminal electron acceptor. Sulfate is activated to adenosine-phosphosulfate (APS) which is then reduced to sulfite, which is in turn reduced to hydrogen sulfide.
Synonyms: dissimilatory sulphate reduction
disproportionation of elemental sulfur (GO:0019422)
Namespace: biological_process
Definition: The process in which sulfur compounds with an intermediate oxidation state serve as both electron donors and electron acceptors in an energy-generating redox process.
Synonyms: disproportionation of elemental sulphur
sulfur oxidation, ferric ion-dependent (GO:0019423)
Namespace: biological_process
Definition: A sulfur oxidation process that proceeds via the reaction catalyzed by sulfur:ferric ion oxidoreductase, and requires the presence of ferric ion (Fe3+).
Synonyms: sulphur oxidation, ferric ion-dependent
obsolete bisulfite reduction (GO:0019426)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the reduction of sulfate to thiosulfate via bisulfite.
Synonyms: bisulphite reduction
Comment: This term was obsoleted because it was solely defined by a MetaCyc pathway that is now deprecated.
obsolete acetyl-CoA biosynthetic process from acetate (GO:0019427)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate.
Synonyms: acetate utilization; acetyl-CoA anabolism from acetate; acetyl-CoA formation from acetate; acetyl-CoA synthesis from acetate
Comment: The reason for obsoletion is that this term represents a GO-CAM.
allantoin biosynthetic process (GO:0019428)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
Synonyms: allantoin anabolism; allantoin biosynthesis; allantoin formation; allantoin synthesis
fluorene catabolic process (GO:0019429)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of fluorene, a tricyclic polycyclic aromatic hydrocarbon containing a five-membered ring. It is a major component of fossil fuels and their derivatives and is also a by-product of coal-conversion and energy-related industries. It is commonly found in vehicle exhaust emissions, crude oils, motor oils, coal and oil combustion products, waste incineration, and industrial effluents.
Synonyms: fluorene breakdown; fluorene catabolism; fluorene degradation; fluorene metabolic process; fluorene metabolism
removal of superoxide radicals (GO:0019430)
Namespace: biological_process
Definition: Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
Synonyms: cellular detoxification of superoxide radicals; removal of O2-; removal of oxygen free radicals
obsolete acetyl-CoA biosynthetic process from ethanol (GO:0019431)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from ethanol via acetaldehyde.
Synonyms: acetyl-CoA anabolism from ethanol; acetyl-CoA formation from ethanol; acetyl-CoA synthesis from ethanol
Comment: The reason for obsoletion is that this term represents a GO-CAM.
triglyceride biosynthetic process (GO:0019432)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol.
Synonyms: triacylglycerol biosynthesis; triacylglycerol biosynthetic process; triglyceride anabolism; triglyceride biosynthesis; triglyceride formation; triglyceride synthesis
triglyceride catabolic process (GO:0019433)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
Synonyms: triacylglycerol catabolic process; triacylglycerol catabolism; triglyceride breakdown; triglyceride catabolism; triglyceride degradation
obsolete sophorosyloxydocosanoate metabolic process (GO:0019434)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving sophorosyloxydocosanoate, 13-sophorosyloxydocosanoate 6',6''-diacetate, an aromatic hydrocarbon.
Synonyms: sophorosyloxydocosanoate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
sophorosyloxydocosanoate biosynthetic process (GO:0019435)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of sophorosyloxydocosanoate, 13-sophorosyloxydocosanoate 6',6''-diacetate.
Synonyms: sophorosyloxydocosanoate anabolism; sophorosyloxydocosanoate biosynthesis; sophorosyloxydocosanoate formation; sophorosyloxydocosanoate synthesis
sophorosyloxydocosanoate catabolic process (GO:0019436)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of sophorosyloxydocosanoate, 13-sophorosyloxydocosanoate 6',6''-diacetate.
Synonyms: sophorosyloxydocosanoate breakdown; sophorosyloxydocosanoate catabolism; sophorosyloxydocosanoate degradation
obsolete aromatic compound biosynthetic process (GO:0019438)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
obsolete aromatic compound catabolic process (GO:0019439)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
obsolete L-tryptophan catabolic process to indole-3-acetate (GO:0019440)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including indole-3-acetate.
Synonyms: tryptophan breakdown to indole-3-acetate; tryptophan catabolic process to IAA; tryptophan catabolic process to indole-3-acetate; tryptophan catabolic process to indoleacetic acid; tryptophan catabolism to indoleacetic acid; tryptophan degradation to indole-3-acetate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-tryptophan catabolic process to L-kynurenine (GO:0019441)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including L-kynurenine.
Synonyms: tryptophan breakdown to kynurenine; tryptophan catabolic process to kynurenine; tryptophan degradation to kynurenine
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-tryptophan catabolic process to acetyl-CoA (GO:0019442)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including acetyl-CoA.
Synonyms: tryptophan breakdown to acetyl-CoA; tryptophan catabolic process to acetyl-CoA; tryptophan degradation to acetyl-CoA
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete tryptophan catabolic process, using tryptophanase (GO:0019443)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of tryptophan, catalyzed by the enzyme tryptophanase (EC:4.1.99.1).
Synonyms: tryptophan breakdown, using tryptophanase; tryptophan catabolic process, using tryptophanase; tryptophan degradation, using tryptophanase
Comment: This term was made obsolete because it refers to a one-step pathway.
obsolete L-tryptophan catabolic process to catechol (GO:0019444)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including catechol.
Synonyms: tryptophan breakdown to catechol; tryptophan catabolic process to catechol; tryptophan degradation to catechol
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-tyrosine catabolic process to fumarate (GO:0019445)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tyrosine into other compounds, including fumarate.
Synonyms: tyrosine breakdown to fumarate; tyrosine degradation to fumarate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete tyrosine catabolic process to phosphoenolpyruvate (GO:0019446)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of tyrosine into other compounds, including phosphoenolpyruvate.
Synonyms: tyrosine breakdown to phosphoenolpyruvate; tyrosine degradation to phosphoenolpyruvate
Comment: The reason for obsoletion is that there is no evidence that this is a real process.
obsolete D-cysteine catabolic process (GO:0019447)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-cysteine, (S)-2-amino-3-mercaptopropanoic acid, which occurs naturally in firefly luciferin.
Synonyms: D-cysteine breakdown; D-cysteine catabolism; D-cysteine degradation
Comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-cysteine.
L-cysteine catabolic process (GO:0019448)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-cysteine.
Synonyms: L-cysteine breakdown; L-cysteine catabolism; L-cysteine degradation
obsolete L-cysteine catabolic process to hypotaurine (GO:0019449)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including hypotaurine.
Synonyms: L-cysteine breakdown to hypotaurine; L-cysteine degradation to hypotaurine
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-cysteine catabolic process to pyruvate (GO:0019450)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including pyruvate.
Synonyms: L-cysteine breakdown to pyruvate; L-cysteine degradation to pyruvate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-cysteine catabolic process to pyruvate, using cysteine dioxygenase (GO:0019451)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown into pyruvate of L-cystine, catalyzed by the enzyme cysteine dioxygenase (EC:1.13.11.20).
Synonyms: L-cysteine breakdown to pyruvate, using cysteine dioxygenase; L-cysteine degradation to pyruvate, using cysteine dioxygenase
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete taurine biosynthetic process from L-cysteine (GO:0019452)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of taurine (2-aminoethanesulfonic acid) from L-cysteine.
Synonyms: L-cysteine breakdown to taurine; L-cysteine degradation to taurine
Comment: This term was obsoleted because it is too specific and is outside the scope of GO.
obsolete L-cysteine catabolic process via cystine (GO:0019453)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine, via the intermediate cystine.
Synonyms: L-cysteine breakdown via cystine; L-cysteine degradation via cystine
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-cysteine catabolic process via cystine, using glutathione-cystine transhydrogenase (GO:0019454)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme glutathione-cystine transhydrogenase.
Synonyms: L-cysteine breakdown via cystine, using glutathione-cystine transhydrogenase; L-cysteine degradation via cystine, using glutathione-cystine transhydrogenase
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.