LiteFold/GO huggingface dataset:
obsolete NADH metabolic process (GO:0006734)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
Synonyms: NAD (reduced) metabolic process; NAD (reduced) metabolism; NADH metabolism; reduced NAD metabolic process; reduced NAD metabolism; reduced nicotinamide adenine dinucleotide metabolic process; reduced nicotinamide adenine dinucleotide metabolism
Comment: This term was obsoleted because it represents the same process as NAD+ metabolic process; GO:0019674.
NADH regeneration (GO:0006735)
Namespace: biological_process
Definition: A metabolic process that generates a pool of NADH by the reduction of NAD+.
Synonyms: NAD (reduced) regeneration; reduced NAD regeneration; reduced nicotinamide adenine dinucleotide regeneration
nicotinamide riboside catabolic process (GO:0006738)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of nicotinamide riboside, the product of the formation of a glycosidic bond between ribose and nicotinamide.
Synonyms: N-ribosylnicotinamide catabolic process; nicotinamide riboside breakdown; nicotinamide riboside catabolism; nicotinamide riboside degradation
NADPH regeneration (GO:0006740)
Namespace: biological_process
Definition: A metabolic process that generates a pool of NADPH by the reduction of NADP+.
Synonyms: NADP (reduced) regeneration; reduced NADP regeneration; reduced nicotinamide adenine dinucleotide phosphate regeneration
NADP+ biosynthetic process (GO:0006741)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide phosphate (NADP+), a coenzyme that interconverts with its reduced form, NADPH, in many redox and biosynthetic reactions.
Synonyms: NADP (oxidized) biosynthesis; NADP (oxidized) biosynthetic process; NADP (reduced) biosynthesis; NADP (reduced) biosynthetic process; NADP anabolism; NADP biosynthesis; NADP biosynthetic process; NADP formation; NADP synthesis; NADPH biosynthesis; NADPH biosynthetic process; nicotinamide adenine dinucleotide phosphate biosynthesis; nicotinamide adenine dinucleotide phosphate biosynthetic process; oxidized NADP biosynthesis; oxidized NADP biosynthetic process; oxidized nicotinamide adenine dinucleotide phosphate biosynthesis; oxidized nicotinamide adenine dinucleotide phosphate biosynthetic process; reduced NADP biosynthesis; reduced NADP biosynthetic process; reduced nicotinamide adenine dinucleotide phosphate biosynthesis; reduced nicotinamide adenine dinucleotide phosphate biosynthetic process
NADP+ catabolic process (GO:0006742)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide phosphate (NADP+), a coenzyme that interconverts with its reduced form, NADPH, in many redox and biosynthetic reactions.
Synonyms: NADP (oxidized) catabolic process; NADP (oxidized) catabolism; NADP (reduced) catabolic process; NADP (reduced) catabolism; NADP breakdown; NADP catabolic process; NADP catabolism; NADP degradation; NADPH catabolic process; NADPH catabolism; nicotinamide adenine dinucleotide phosphate catabolic process; nicotinamide adenine dinucleotide phosphate catabolism; oxidized NADP catabolic process; oxidized NADP catabolism; oxidized nicotinamide adenine dinucleotide phosphate catabolic process; oxidized nicotinamide adenine dinucleotide phosphate catabolism; reduced NADP catabolic process; reduced NADP catabolism; reduced nicotinamide adenine dinucleotide phosphate catabolic process; reduced nicotinamide adenine dinucleotide phosphate catabolism
FADH2 metabolic process (GO:0006746)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the reduced form of flavin adenine dinucleotide.
Synonyms: FADH2 metabolism; reduced flavin adenine dinucleotide metabolic process
FAD biosynthetic process (GO:0006747)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of FAD, the oxidized form of flavin-adenine dinucleotide.
Synonyms: FAD anabolism; FAD biosynthesis; FAD formation; FAD synthesis; oxidized flavin adenine dinucleotide biosynthesis; oxidized flavin adenine dinucleotide biosynthetic process; oxidized flavin-adenine dinucleotide biosynthesis; oxidized flavin-adenine dinucleotide biosynthetic process
glutathione metabolic process (GO:0006749)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
Synonyms: glutathione metabolism; oxidized glutathione reduction
glutathione biosynthetic process (GO:0006750)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
Synonyms: glutathione anabolism; glutathione biosynthesis; glutathione formation; glutathione synthesis
glutathione catabolic process (GO:0006751)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
Synonyms: glutathione breakdown; glutathione catabolism; glutathione degradation
nucleoside phosphate metabolic process (GO:0006753)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any phosphorylated nucleoside.
Synonyms: nucleoside phosphate metabolism
obsolete carbamoyl phosphate-ADP transphosphorylation (GO:0006755)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: carbamoyl phosphate-ADP transphosphorylation
Comment: This term was made obsolete because, according to PUMA2, this "pathway" is a single reaction, corresponding to 'carbamate kinase activity ; GO:0008804' (EC:2.7.2.2).
AMP phosphorylation (GO:0006756)
Namespace: biological_process
Definition: The process of introducing a phosphate group into AMP, adenosine monophosphate, to produce ADP. Addition of two phosphate groups produces ATP.
obsolete ATP generation from ADP (GO:0006757)
Namespace: biological_process
Definition: OBSOLETE. The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP.
Synonyms: ADP phosphorylation
Comment: The reason for obsoletion is that this term represents a single step MF.
folic acid-containing compound metabolic process (GO:0006760)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
Synonyms: folate and derivative metabolic process; folate and derivative metabolism; folate-containing compound metabolic process; folate-containing compound metabolism; folic acid and derivative metabolic process; folic acid and derivative metabolism; folic acid-containing compound metabolism; vitamin B9 and derivative metabolic process; vitamin B9 and derivative metabolism; vitamin M and derivative metabolic process; vitamin M and derivative metabolism
dihydrofolate biosynthetic process (GO:0006761)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dihydrofolate, the dihydroxylated derivative of folate.
Synonyms: 7,8-dihydrofolate biosynthesis; 7,8-dihydrofolate biosynthetic process; dihydrofolate anabolism; dihydrofolate biosynthesis; dihydrofolate formation; dihydrofolate synthesis
obsolete dihydrofolate reduction (GO:0006762)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: dihydrofolate reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
vitamin metabolic process (GO:0006766)
Namespace: biological_process
Definition: The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
Synonyms: vitamin metabolism
obsolete water-soluble vitamin metabolic process (GO:0006767)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water.
Synonyms: water-soluble vitamin metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
biotin metabolic process (GO:0006768)
Namespace: biological_process
Definition: The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
Synonyms: biotin metabolism; vitamin B7 metabolic process; vitamin B7 metabolism; vitamin H metabolic process; vitamin H metabolism
nicotinamide metabolic process (GO:0006769)
Namespace: biological_process
Definition: The chemical reactions and pathways involving nicotinamide, pyridine-3-carboxamide, the amide of nicotinic acid. It is a member of the B complex of vitamins and occurs widely in living organisms.
Synonyms: niacin metabolic process; niacin metabolism; nicotinamide metabolism; vitamin B3 metabolic process; vitamin B3 metabolism
riboflavin metabolic process (GO:0006771)
Namespace: biological_process
Definition: The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
Synonyms: riboflavin metabolism; vitamin B2 metabolic process; vitamin B2 metabolism; vitamin G metabolic process; vitamin G metabolism
obsolete vitamin B12 reduction (GO:0006774)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: vitamin B12 reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete fat-soluble vitamin metabolic process (GO:0006775)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water.
Synonyms: fat-soluble vitamin metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
vitamin A metabolic process (GO:0006776)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene.
Synonyms: vitamin A metabolism
Mo-molybdopterin cofactor biosynthetic process (GO:0006777)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
Synonyms: Mo-molybdopterin cofactor anabolism; Mo-molybdopterin cofactor biosynthesis; Mo-molybdopterin cofactor formation; Mo-molybdopterin cofactor synthesis; Moco biosynthesis; Moco biosynthetic process; molybdenum cofactor biosynthetic process
porphyrin-containing compound metabolic process (GO:0006778)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
Synonyms: porphyrin metabolic process; porphyrin metabolism
porphyrin-containing compound biosynthetic process (GO:0006779)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
Synonyms: porphyrin anabolism; porphyrin biosynthesis; porphyrin biosynthetic process; porphyrin formation; porphyrin synthesis
uroporphyrinogen III biosynthetic process (GO:0006780)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of uroporphyrinogen III.
Synonyms: uroporphyrinogen III anabolism; uroporphyrinogen III biosynthesis; uroporphyrinogen III formation; uroporphyrinogen III synthesis
succinyl-CoA pathway (GO:0006781)
Namespace: biological_process
Definition: The chemical reactions that utilize succinyl-CoA in the synthesis of protoporphyrin IX.
Synonyms: biosynthesis of protoporphyrin IX via succinyl CoA; biosynthesis of protoporphyrin IX via succinyl-CoA; biosynthetic process of protoporphyrin IX via succinyl CoA; biosynthetic process of protoporphyrin IX via succinyl-CoA; succinyl CoA pathway
protoporphyrinogen IX biosynthetic process (GO:0006782)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
Synonyms: protoporphyrinogen IX anabolism; protoporphyrinogen IX biosynthesis; protoporphyrinogen IX formation; protoporphyrinogen IX synthesis
heme biosynthetic process (GO:0006783)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
Synonyms: haem biosynthesis; haem biosynthetic process; heme anabolism; heme biosynthesis; heme formation; heme synthesis
heme A biosynthetic process (GO:0006784)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of heme A, a derivative of heme found in cytochrome aa3.
Synonyms: haem A biosynthesis; haem A biosynthetic process; heme A anabolism; heme A biosynthesis; heme A formation; heme A synthesis
heme B biosynthetic process (GO:0006785)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of heme B, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes.
Synonyms: haem B biosynthesis; haem B biosynthetic process; heme B anabolism; heme B biosynthesis; heme B formation; heme B synthesis; protoheme biosynthesis; protoheme biosynthetic process
heme C biosynthetic process (GO:0006786)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of heme c, a derivative of heme found in cytochromes c, b4, and f.
Synonyms: haem C biosynthesis; haem C biosynthetic process; heme C anabolism; heme C biosynthesis; heme C formation; heme C synthesis
heme oxidation (GO:0006788)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the loss of electrons from one or more atoms in heme.
Synonyms: haem oxidation
bilirubin conjugation (GO:0006789)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of bilirubin monoglucuronide or bilirubin diglucuronide, water-soluble derivatives of bilirubin.
sulfur compound metabolic process (GO:0006790)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
Synonyms: sulfur metabolism; sulphur metabolic process; sulphur metabolism
sulfur utilization (GO:0006791)
Namespace: biological_process
Definition: A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism.
Synonyms: sulphur utilization
regulation of sulfur utilization (GO:0006792)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of sulfur utilization.
Synonyms: regulation of sulphur utilization
phosphorus metabolic process (GO:0006793)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.
Synonyms: phosphorus metabolism
phosphorus utilization (GO:0006794)
Namespace: biological_process
Definition: A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary phosphorus source and then activates genes to scavenge the last traces of the primary phosphorus source and to transport and metabolize alternative phosphorus sources. The utilization process begins when the cell or organism detects phosphorus levels, includes the phosphorus-containing substances, and ends when phosphorus is incorporated into the cell or organism's metabolism.
regulation of phosphorus utilization (GO:0006795)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of phosphorus utilization.
phosphate-containing compound metabolic process (GO:0006796)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
Synonyms: phosphate metabolic process; phosphate metabolism
polyphosphate metabolic process (GO:0006797)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.
Synonyms: polyphosphate metabolism
polyphosphate biosynthetic process (GO:0006799)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a polyphosphate, the anion or salt of polyphosphoric acid.
Synonyms: polyphosphate anabolism; polyphosphate biosynthesis; polyphosphate formation; polyphosphate synthesis
obsolete oxygen and reactive oxygen species metabolic process (GO:0006800)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH).
Synonyms: oxygen and active oxygen species metabolism; oxygen and AOS metabolism; oxygen and reactive oxidative species metabolism; oxygen and reactive oxygen intermediate metabolism; oxygen and reactive oxygen species metabolic process; oxygen and reactive oxygen species metabolism; oxygen and ROI metabolism; oxygen and ROS metabolic process; oxygen and ROS metabolism
Comment: This term was made obsolete because, as part of the GO/ChEBI alignment effort, curators determined that oxygen and reactive oxygen species should not be grouped together.
superoxide metabolic process (GO:0006801)
Namespace: biological_process
Definition: The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
Synonyms: oxygen free radical metabolic process; oxygen free radical metabolism; superoxide free radical metabolic process; superoxide free radical metabolism; superoxide metabolism
obsolete catalase reaction (GO:0006802)
Namespace: biological_process
Definition: OBSOLETE. The processes involved in the induction or activation of catalase, an enzyme that catalyzes the conversion of H2O2 into H2O.
Synonyms: catalase reaction; hydroperoxidase reaction
Comment: This term was made obsolete because it represents a molecular function.
obsolete glutathione conjugation reaction (GO:0006803)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: glutathione conjugation reaction
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete peroxidase reaction (GO:0006804)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: peroxidase reaction
Comment: This term was made obsolete because it represents a molecular function.
xenobiotic metabolic process (GO:0006805)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
Synonyms: drug metabolic process; drug metabolism; xenobiotic metabolism
obsolete nitrogen compound metabolic process (GO:0006807)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
nitric oxide biosynthetic process (GO:0006809)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
Synonyms: nitric oxide anabolism; nitric oxide biosynthesis; nitric oxide formation; nitric oxide synthesis
monoatomic ion transport (GO:0006811)
Namespace: biological_process
Definition: The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
Synonyms: ion transport
monoatomic cation transport (GO:0006812)
Namespace: biological_process
Definition: The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom.
Synonyms: cation transport; di-, tri-valent inorganic cation transport; trivalent inorganic cation transport
potassium ion transport (GO:0006813)
Namespace: biological_process
Definition: The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Synonyms: cellular potassium ion transport; K+ conductance; low voltage-dependent potassium channel auxiliary protein activity; low voltage-gated potassium channel auxiliary protein activity; potassium conductance; potassium ion conductance; potassium transport; sodium/potassium transport
sodium ion transport (GO:0006814)
Namespace: biological_process
Definition: The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Synonyms: mitochondrial sodium/calcium ion exchange; sodium channel auxiliary protein activity; sodium transport; sodium/potassium transport; sodium:calcium exchange; sodium:solute transport
obsolete sodium/potassium transport (GO:0006815)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: sodium/potassium transport
Comment: This term was made obsolete because it is a composite term that represents two individual processes.