LiteFold/GO huggingface dataset:
peptidyl-tyrosine sulfation (GO:0006478)
Namespace: biological_process
Definition: The sulfation of peptidyl-tyrosine residues to form peptidyl-O4'-sulfo-L-tyrosine.
Synonyms: peptidyl-tyrosine sulphation
obsolete GPI anchor release (GO:0006507)
Namespace: biological_process
Definition: OBSOLETE. The GPI anchor metabolic process that results in enzymatic cleavage of the anchor, releasing an anchored protein from the membrane.
Comment: The reason for obsoletion is that this term represents a molecular function.
protein quality control for misfolded or incompletely synthesized proteins (GO:0006515)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
Synonyms: degradation of misfolded or incompletely synthesized proteins; misfolded or incompletely synthesized protein breakdown; misfolded or incompletely synthesized protein catabolic process; misfolded or incompletely synthesized protein catabolism; misfolded or incompletely synthesized protein degradation; protein quality control (PQC); protein quality control by the ubiquitin-proteasome system
regulation of amino acid metabolic process (GO:0006521)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.
Synonyms: regulation of amino acid metabolism
obsolete alanine metabolic process (GO:0006522)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
Synonyms: alanine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
L-asparagine catabolic process (GO:0006530)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-asparagine.
Synonyms: asparagine breakdown; asparagine catabolism; asparagine degradation
L-aspartate catabolic process (GO:0006533)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-aspartate.
Synonyms: aspartate breakdown; aspartate catabolism; aspartate degradation
obsolete proline biosynthetic process (GO:0006561)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
Synonyms: proline anabolism; proline biosynthesis; proline formation; proline synthesis
Comment: This term was obsoleted because it represents the same process as L-proline biosynthetic process ; GO:0055129.
L-serine biosynthetic process (GO:0006564)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-serine.
Synonyms: L-serine anabolism; L-serine biosynthesis; L-serine formation; L-serine synthesis
amino-acid betaine biosynthetic process (GO:0006578)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of any betaine, the N-trimethyl derivative of an amino acid.
Synonyms: betaine anabolism; betaine biosynthesis; betaine biosynthetic process; betaine formation; betaine synthesis
polyamine catabolic process (GO:0006598)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of polyamines, any organic compound containing two or more amino groups.
Synonyms: polyamine breakdown; polyamine catabolism; polyamine degradation
1,2-diacyl-sn-glycero-3-phosphocholine metabolic process (GO:0006653)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any 1,2-diacyl-sn-glycero-3-phosphocholine, the compounds most commonly designated lecithin.
Synonyms: 1,2-diacyl-sn-glycero-3-phosphocholine metabolism; lecithin metabolic process
phosphatidic acid biosynthetic process (GO:0006654)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
Synonyms: phosphatidic acid anabolism; phosphatidic acid biosynthesis; phosphatidic acid formation; phosphatidic acid synthesis
phosphatidylserine biosynthetic process (GO:0006659)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidylserines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of L-serine.
Synonyms: phosphatidylserine anabolism; phosphatidylserine biosynthesis; phosphatidylserine formation; phosphatidylserine synthesis
sphingosine metabolic process (GO:0006670)
Namespace: biological_process
Definition: The chemical reactions and pathways involving sphingosine (sphing-4-enine), trans-D-erytho-2-amino-octadec-4-ene-1,3-diol, a long chain amino diol sphingoid base that occurs in most sphingolipids in animal tissues.
Synonyms: (4E)-sphing-4-enine metabolic process; (4E)-sphing-4-enine metabolism; sphing-4-enine metabolic process; sphing-4-enine metabolism; sphingosine metabolism
phytosphingosine metabolic process (GO:0006671)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phytosphingosine, (2S,3S,4R)-2-aminooctadecane-1,3,4-triol, a constituent of many plant sphingolipids.
Synonyms: phytosphingosine metabolism
ceramide metabolic process (GO:0006672)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ceramides, any N-acylated sphingoid.
Synonyms: ceramide metabolism
galactosylceramide biosynthetic process (GO:0006682)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of galactosylceramides, any composed of a ceramide backbone covalently linked to a galactose. The galactose can be sulfated or further elongated with one more monosaccharide often a sialic acid.
Synonyms: gala-series glycosphingolipid biosynthesis; galactosylceramide anabolism; galactosylceramide biosynthesis; galactosylceramide formation; galactosylceramide synthesis
C21-steroid hormone biosynthetic process (GO:0006700)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones.
Synonyms: C21-steroid hormone anabolism; C21-steroid hormone biosynthesis; C21-steroid hormone formation; C21-steroid hormone synthesis
triterpenoid metabolic process (GO:0006722)
Namespace: biological_process
Definition: The chemical reactions and pathways involving triterpenoid compounds, terpenoids with six isoprene units.
Synonyms: triterpene metabolic process; triterpene metabolism; triterpenoid metabolism
obsolete cellular aromatic compound metabolic process (GO:0006725)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
NADP+ metabolic process (GO:0006739)
Namespace: biological_process
Definition: The chemical reactions and pathways involving nicotinamide adenine dinucleotide phosphate (NADP+), a coenzyme that interconverts with its reduced form, NADPH, in many redox and biosynthetic reactions.
Synonyms: NAD phosphorylation and dephosphorylation; NADP (oxidized) metabolic process; NADP (oxidized) metabolism; NADP (reduced) metabolic process; NADP (reduced) metabolism; NADP metabolic process; NADP metabolism; NADPH metabolic process; NADPH metabolism; nicotinamide adenine dinucleotide phosphate metabolic process; nicotinamide adenine dinucleotide phosphate metabolism; oxidized NADP metabolic process; oxidized NADP metabolism; oxidized nicotinamide adenine dinucleotide phosphate metabolic process; oxidized nicotinamide adenine dinucleotide phosphate metabolism; reduced NADP metabolic process; reduced NADP metabolism; reduced nicotinamide adenine dinucleotide phosphate metabolic process; reduced nicotinamide adenine dinucleotide phosphate metabolism
ubiquinone metabolic process (GO:0006743)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ubiquinone, a lipid-soluble electron-transporting coenzyme.
Synonyms: coenzyme Q metabolic process; coenzyme Q metabolism; ubiquinone metabolism
ubiquinone biosynthetic process (GO:0006744)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
Synonyms: coenzyme Q biosynthesis; coenzyme Q biosynthetic process; coenzyme Q10 biosynthesis; coenzyme Q10 biosynthetic process; coenzyme Q6 biosynthesis; coenzyme Q6 biosynthetic process; coenzyme Q8 biosynthesis; coenzyme Q8 biosynthetic process; coenzyme Q9 biosynthesis; coenzyme Q9 biosynthetic process; ubiquinone anabolism; ubiquinone biosynthesis; ubiquinone formation; ubiquinone synthesis
obsolete lipoamide metabolic process (GO:0006748)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group.
Synonyms: lipoamide metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
ATP biosynthetic process (GO:0006754)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
Synonyms: ATP anabolism; ATP biosynthesis; ATP formation; ATP regeneration; ATP synthesis
thiamine metabolic process (GO:0006772)
Namespace: biological_process
Definition: The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
Synonyms: thiamin metabolic process; thiamin metabolism; thiamine metabolism; vitamin B1 metabolic process; vitamin B1 metabolism
porphyrin-containing compound catabolic process (GO:0006787)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown 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 breakdown; porphyrin catabolic process; porphyrin catabolism; porphyrin degradation
polyphosphate catabolic process (GO:0006798)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid.
Synonyms: polyphosphate breakdown; polyphosphate catabolism; polyphosphate degradation
obsolete insecticide resistance (GO:0006806)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: insecticide resistance
Comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
regulation of nitrogen utilization (GO:0006808)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of nitrogen utilization.
transport (GO:0006810)
Namespace: biological_process
Definition: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
Synonyms: single-organism transport
Comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
copper ion transport (GO:0006825)
Namespace: biological_process
Definition: The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
mitochondrial citrate transmembrane transport (GO:0006843)
Namespace: biological_process
Definition: The directed movement of citrate, 2-hydroxy-1,2,3-propanetricarboxylate, into or out of a mitochondrial matrix.
Synonyms: mitochondrial citrate transport
obsolete mitochondrial aspartate/glutamate transport (GO:0006845)
Namespace: biological_process
Definition: OBSOLETE. The directed movement of aspartate and glutamate into, out of or within a mitochondrion.
Synonyms: mitochondrial aspartate/glutamate transport
Comment: This term was made obsolete because it represents a function rather than a process.
acetate transport (GO:0006846)
Namespace: biological_process
Definition: The directed movement of acetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
plasma membrane acetate transport (GO:0006847)
Namespace: biological_process
Definition: The directed movement of acetate across a plasma membrane.
pyruvate transport (GO:0006848)
Namespace: biological_process
Definition: The directed movement of pyruvate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
amino acid transport (GO:0006865)
Namespace: biological_process
Definition: The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890)
Namespace: biological_process
Definition: The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
Synonyms: cis-Golgi to rough endoplasmic reticulum transport; cis-Golgi to rough endoplasmic reticulum vesicle-mediated transport; cis-Golgi to rough ER transport; cis-Golgi to rough ER vesicle-mediated transport; retrograde (Golgi to ER) transport; retrograde transport, Golgi to endoplasmic reticulum; retrograde transport, Golgi to ER; retrograde vesicle-mediated transport, Golgi to ER
post-Golgi vesicle-mediated transport (GO:0006892)
Namespace: biological_process
Definition: The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles.
Synonyms: post-Golgi transport
obsolete vesicle transport (GO:0006905)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: vesicle transport
Comment: This term was made obsolete because the meaning of the term is ambiguous.
apoptotic process (GO:0006915)
Namespace: biological_process
Definition: A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
Synonyms: activation of apoptosis; apoptosis; apoptosis activator activity; apoptosis signaling; apoptotic cell death; apoptotic program; apoptotic programmed cell death; caspase-dependent programmed cell death; cell suicide; cellular suicide; commitment to apoptosis; induction of apoptosis; induction of apoptosis by p53; programmed cell death by apoptosis; signaling (initiator) caspase activity; type I programmed cell death
obsolete movement of cell or subcellular component (GO:0006928)
Namespace: biological_process
Definition: OBSOLETE. The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
Synonyms: cell movement; cellular component motion; cellular component movement
Comment: This term was obsoleted because it mixes cellular and subcellular processes.
substrate-dependent cell migration (GO:0006929)
Namespace: biological_process
Definition: The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate.
Synonyms: substrate-bound cell migration
negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)
Namespace: biological_process
Definition: The disassembly of adhesions at the front and rear of a migrating cell. At the leading edge, adhesion disassembly accompanies the formation of new protrusions; at the cell rear, it promotes tail retraction.
Synonyms: substrate-bound cell migration, cell release from substrate
regulation of striated muscle contraction (GO:0006942)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of striated muscle contraction.
obsolete chemi-mechanical coupling (GO:0006943)
Namespace: biological_process
Definition: OBSOLETE. The conversion of chemical energy into mechanical work (as in the contraction of a muscle).
Synonyms: chemi-mechanical coupling; mechanochemical coupling
Comment: This term was made obsolete because its meaning is vague, and it does not fit with other terms in GO.
response to lipid hydroperoxide (GO:0006982)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid hydroperoxide stimulus. Lipid hydroperoxide is the highly reactive primary oxygenated products of polyunsaturated fatty acids.
Synonyms: response to LHPO
obsolete telomere binding (GO:0007003)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: telomere binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
obsolete regulation of cytoskeleton (GO:0007011)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton.
Synonyms: regulation of cytoskeleton
Comment: This term was made obsolete because cytoskeleton is neither a process nor a trait, so the term made no sense.
tubulin complex assembly (GO:0007021)
Namespace: biological_process
Definition: The aggregation and bonding together of alpha- and beta-tubulin to form a tubulin heterodimer.
Synonyms: tubulin assembly; tubulin folding; tubulin-specific chaperone activity
Golgi organization (GO:0007030)
Namespace: biological_process
Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
Synonyms: Golgi apparatus organization; Golgi organisation; Golgi organization and biogenesis
vacuolar transport (GO:0007034)
Namespace: biological_process
Definition: The directed movement of substances into, out of or within a vacuole.
spindle assembly involved in male meiosis I (GO:0007054)
Namespace: biological_process
Definition: The formation of the spindle during meiosis I of a meiotic cell cycle in males. An example of this is found in Drosophila melanogaster.
Synonyms: male meiosis I spindle assembly
sister chromatid cohesion (GO:0007062)
Namespace: biological_process
Definition: The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
Synonyms: cohesion-mediated DNA tethering
obsolete negative regulation of transcription from RNA polymerase III promoter during mitotic cell cycle (GO:0007071)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle.
Synonyms: down regulation of transcription from RNA polymerase III promoter during mitosis; down-regulation of transcription from RNA polymerase III promoter during mitosis; downregulation of transcription from RNA polymerase III promoter during mitosis; inhibition of transcription from RNA polymerase III promoter during mitosis; mitotic repression of transcription from Pol III promoter; negative regulation of transcription from Pol III promoter during mitosis; negative regulation of transcription from RNA polymerase III promoter, mitotic
Comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
lamin depolymerization (GO:0007078)
Namespace: biological_process
Definition: The cell cycle process in which lamin is depolymerized.
obsolete mitotic sister-chromatid adhesion release (GO:0007081)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: mitotic sister-chromatid adhesion release
Comment: This term was made obsolete because the term name is ambiguous and appears to encompass two processes.
obsolete cytokinesis, completion of separation (GO:0007109)
Namespace: biological_process
Definition: OBSOLETE. The process of finishing cell separation, which results in two physically separated cells.
Synonyms: completion of separation involved in cytokinesis; cytokinesis, completion of separation
Comment: This term was obsoleted because it was vaguely defined and had very likely been used in error. Consider the child terms of cytokinesis related to ring positioning, assembly, ring constriction etc. which would be more appropriate.
budding cell bud growth (GO:0007117)
Namespace: biological_process
Definition: The process in which the bud portion of a cell that reproduces by budding irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
Synonyms: bud growth
budding cell apical bud growth (GO:0007118)
Namespace: biological_process
Definition: Growth at the tip of a bud, in a cell that reproduces by budding.
Synonyms: apical bud growth
male meiotic nuclear division (GO:0007140)
Namespace: biological_process
Definition: A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
Synonyms: male meiosis; male nuclear division
obsolete colony morphology (GO:0007149)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: colony morphology
Comment: This term was made obsolete because it describes a phenotype rather than a biological goal.
negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.
Synonyms: down regulation of epidermal growth factor receptor activity; down-regulation of epidermal growth factor receptor activity; downregulation of epidermal growth factor receptor activity; EGF receptor downregulation; inhibition of epidermal growth factor receptor activity; negative regulation of EGF receptor activity; negative regulation of EGFR activity; negative regulation of epidermal growth factor receptor activity