LiteFold/GO huggingface dataset:
creatinine catabolic process (GO:0006602)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of creatinine, 2-amino-1,5-dihydro-1-methyl-4H-imidazol-4-one, an end product of creatine metabolism and a normal constituent of urine.
Synonyms: creatinine breakdown; creatinine catabolism; creatinine degradation
phosphocreatine metabolic process (GO:0006603)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phosphocreatine, a phosphagen of creatine present in high concentration in striated muscle which is synthesized and broken down by creatine phosphokinase to buffer ATP concentration. It acts as an immediate energy reserve for muscle.
Synonyms: phosphocreatine metabolism
obsolete phosphoarginine metabolic process (GO:0006604)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving phosphoarginine, a phosphagen of L-arginine with phosphoric acid containing the phosphoamide bond. It is a source of energy in the contraction of muscle in invertebrates, corresponding to phosphocreatine in the muscles of vertebrates.
Synonyms: phosphoarginine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
protein targeting (GO:0006605)
Namespace: biological_process
Definition: The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
Synonyms: nascent polypeptide association; protein sorting along secretory pathway
protein import into nucleus (GO:0006606)
Namespace: biological_process
Definition: The directed movement of a protein from the cytoplasm to the nucleus.
Synonyms: establishment of protein localization to nucleus; protein import into cell nucleus; protein nucleus import; protein transport from cytoplasm to nucleus
NLS-bearing protein import into nucleus (GO:0006607)
Namespace: biological_process
Definition: The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear envelope.
Synonyms: NLS-bearing substrate import into cell nucleus; NLS-bearing substrate import into nucleus; NLS-bearing substrate transport from cytoplasm to nucleus; NLS-bearing substrate-nucleus import
obsolete snRNP protein import into nucleus (GO:0006608)
Namespace: biological_process
Definition: OBSOLETE. The directed movement of a small nuclear ribonucleoprotein from the cytoplasm into the nucleus, across the nuclear membrane.
Synonyms: snRNP protein import into cell nucleus; snRNP protein transport from cytoplasm to nucleus; snRNP protein-nucleus import
Comment: The reason for obsoletion is that all proteins are imported into the nucleus via the same mechanism, so the import of individual proteins should be captured with extensions or by GO-CAM models.
obsolete mRNA-binding (hnRNP) protein import into nucleus (GO:0006609)
Namespace: biological_process
Definition: OBSOLETE. The directed movement of a heterogeneous nuclear ribonucleoprotein from the cytoplasm into the nucleus, across the nuclear membrane.
Synonyms: mRNA-binding (hnRNP) protein import into cell nucleus; mRNA-binding (hnRNP) protein transport from cytoplasm to nucleus; mRNA-binding (hnRNP) protein-nucleus import
Comment: The reason for obsoletion is that all proteins are imported into the nucleus via the same mechanism, so the import of individual proteins should be captured with extensions or by GO-CAM models.
ribosomal protein import into nucleus (GO:0006610)
Namespace: biological_process
Definition: The directed movement of a ribosomal protein from the cytoplasm into the nucleus, across the nuclear membrane. At least some ribosomal proteins, including rpl12, uses the importin 11 pathway as a major route into the nucleus.
Synonyms: ribosomal protein import into cell nucleus; ribosomal protein transport from cytoplasm to nucleus; ribosomal protein-nucleus import
Comment: Ribosomal protein rpl12 uses a different import pathway, which is why it has a separate GO term.
protein export from nucleus (GO:0006611)
Namespace: biological_process
Definition: The directed movement of a protein from the nucleus into the cytoplasm.
Synonyms: copper-induced protein export from nucleus; protein export from cell nucleus; protein export out of nucleus; protein transport from nucleus to cytoplasm; protein-nucleus export
protein targeting to membrane (GO:0006612)
Namespace: biological_process
Definition: The process of directing proteins towards a membrane, usually using signals contained within the protein.
Synonyms: protein membrane targeting; protein-membrane targeting
cotranslational protein targeting to membrane (GO:0006613)
Namespace: biological_process
Definition: The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner, as does the import of some proteins into mitochondria.
Synonyms: cotranslational membrane targeting; cotranslational protein membrane targeting; cotranslational protein-membrane targeting
SRP-dependent cotranslational protein targeting to membrane (GO:0006614)
Namespace: biological_process
Definition: The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
Synonyms: ER translocation; SRP-dependent cotranslational membrane targeting; SRP-dependent cotranslational protein-membrane targeting
SRP-dependent cotranslational protein targeting to membrane, docking (GO:0006615)
Namespace: biological_process
Definition: The process in which an SRP-bound ribosome forms a complex with the SRP receptor in the ER membrane, allowing the ribosome to bind to the membrane, during cotranslational membrane targeting.
Synonyms: protein docking during SRP-dependent cotranslational protein targeting to membrane; SRP-dependent cotranslational membrane targeting, docking; SRP-dependent cotranslational protein-membrane targeting, docking
SRP-dependent cotranslational protein targeting to membrane, translocation (GO:0006616)
Namespace: biological_process
Definition: The process during cotranslational membrane targeting wherein proteins move across a membrane. SRP and its receptor initiate the transfer of the nascent chain across the endoplasmic reticulum (ER) membrane; they then dissociate from the chain, which is transferred to a set of transmembrane proteins, collectively called the translocon. Once the nascent chain translocon complex is assembled, the elongating chain passes directly from the large ribosomal subunit into the centers of the translocon, a protein-lined channel within the membrane. The growing chain is never exposed to the cytosol and does not fold until it reaches the ER lumen.
Synonyms: ER translocation; SRP-dependent cotranslational membrane targeting, translocation; SRP-dependent cotranslational protein-membrane targeting, translocation; translocation during SRP-dependent cotranslational protein targeting to membrane
SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)
Namespace: biological_process
Definition: The process in which SRP binds to the signal peptide in a nascent protein, causing protein elongation to pause, during cotranslational membrane targeting.
Synonyms: signal sequence recognition during SRP-dependent cotranslational protein targeting to membrane; SRP-dependent cotranslational membrane targeting, signal sequence recognition; SRP-dependent cotranslational protein-membrane targeting, signal sequence recognition
obsolete SRP-dependent cotranslational protein targeting to membrane, signal sequence processing (GO:0006618)
Namespace: biological_process
Definition: OBSOLETE. The removal of the signal peptide from a nascent protein during cotranslational membrane targeting.
Synonyms: signal sequence processing during SRP-dependent cotranslational protein targeting to membrane; SRP-dependent cotranslational membrane targeting, signal sequence processing; SRP-dependent cotranslational protein-membrane targeting, signal sequence processing
Comment: This term was obsoleted because it reprenset a molecular function, signal peptidase activity ; GO:0009003.
obsolete SRP-independent cotranslational protein-membrane targeting (GO:0006619)
Namespace: biological_process
Definition: OBSOLETE. The targeting of proteins to a membrane that occurs during translation and is independent of SRP and signal recognition.
Synonyms: ER translocation; SRP-independent cotranslational membrane targeting; SRP-independent cotranslational protein-membrane targeting
Comment: This term was made obsolete because there is no evidence for the existence of this process.
post-translational protein targeting to endoplasmic reticulum membrane (GO:0006620)
Namespace: biological_process
Definition: The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.
Synonyms: posttranslational endoplasmic reticulum membrane targeting; posttranslational endoplasmic reticulum protein-membrane targeting; posttranslational protein endoplasmic reticulum membrane targeting; posttranslational protein targeting to endoplasmic reticulum membrane; posttranslational protein targeting to ER membrane; SRP-independent endoplasmic reticulum protein-membrane targeting
protein retention in ER lumen (GO:0006621)
Namespace: biological_process
Definition: The retention in the endoplasmic reticulum (ER) lumen of soluble resident proteins. Sorting receptors retrieve proteins with ER localization signals, such as KDEL and HDEL sequences or some transmembrane domains, that have escaped to the cis-Golgi network and return them to the ER. Abnormally folded proteins and unassembled subunits are also selectively retained in the ER.
Synonyms: maintenance of protein location in ER lumen
protein targeting to lysosome (GO:0006622)
Namespace: biological_process
Definition: The process of directing proteins towards the lysosome using signals contained within the protein.
Synonyms: protein-lysosome targeting
protein targeting to vacuole (GO:0006623)
Namespace: biological_process
Definition: The process of directing proteins towards the vacuole, usually using signals contained within the protein.
Synonyms: protein vacuolar targeting; protein-vacuolar targeting; protein-vacuole targeting; vacuolar protein sorting
vacuolar protein processing (GO:0006624)
Namespace: biological_process
Definition: Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes.
Synonyms: vacuolar protein maturation; vacuolar proteolysis
protein targeting to peroxisome (GO:0006625)
Namespace: biological_process
Definition: The process of directing proteins towards the peroxisome, usually using signals contained within the protein.
Synonyms: protein-peroxisome targeting
obsolete protein targeting to mitochondrion (GO:0006626)
Namespace: biological_process
Definition: OBSOLETE. The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
Synonyms: mitochondrial protein import; mitochondrial translocation; protein import into mitochondrion; protein targeting to mitochondria; protein-mitochondrial targeting
Comment: The reason for obsoletion is that this term was added in error.
obsolete protein processing involved in protein targeting to mitochondrion (GO:0006627)
Namespace: biological_process
Definition: OBSOLETE. The cleavage of peptide bonds in proteins, usually near the N terminus, contributing to the process of import into the mitochondrion. Several different peptidases mediate cleavage of proteins destined for different mitochondrial compartments.
Synonyms: mitochondrial processing; mitochondrial protein processing during import
Comment: The reason for obsoletion is that this term was added in error.
obsolete mitochondrial translocation (GO:0006628)
Namespace: biological_process
Definition: OBSOLETE. The translocation of proteins across the mitochondrial membrane. In the presence of a translocating chain, the outer membrane import machinery (MOM complex) and the inner membrane import machinery (MIM complex) form translocation contact sites as a part of the membrane preprotein import machinery.
Synonyms: mitochondrial translocation
Comment: This term was made obsolete because its definition was equivalent to that of the biological process term 'mitochondrial matrix protein import ; GO:0030150' while the mitochondrial translocation has a broader meaning; this led to mis-annotation.
lipid metabolic process (GO:0006629)
Namespace: biological_process
Definition: The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
Synonyms: lipid metabolism
obsolete lipid binding (GO:0006630)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: lipid binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
fatty acid metabolic process (GO:0006631)
Namespace: biological_process
Definition: The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
Synonyms: fatty acid metabolism
fatty acid biosynthetic process (GO:0006633)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
Synonyms: fatty acid anabolism; fatty acid biosynthesis; fatty acid formation; fatty acid synthesis
hexadecanal biosynthetic process (GO:0006634)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of hexadecanal, the C16 straight chain aldehyde.
Synonyms: hexadecanal anabolism; hexadecanal biosynthesis; hexadecanal formation; hexadecanal synthesis; palmitaldehyde biosynthesis; palmitaldehyde biosynthetic process
fatty acid beta-oxidation (GO:0006635)
Namespace: biological_process
Definition: A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
unsaturated fatty acid biosynthetic process (GO:0006636)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms.
Synonyms: fatty acid desaturation; polyunsaturated fatty acid biosynthesis; unsaturated fatty acid anabolism; unsaturated fatty acid biosynthesis; unsaturated fatty acid formation; unsaturated fatty acid synthesis
acyl-CoA metabolic process (GO:0006637)
Namespace: biological_process
Definition: The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.
Synonyms: acyl-CoA metabolism
neutral lipid metabolic process (GO:0006638)
Namespace: biological_process
Definition: The chemical reactions and pathways involving neutral lipids, lipids only soluble in solvents of very low polarity.
Synonyms: neutral lipid metabolism
acylglycerol metabolic process (GO:0006639)
Namespace: biological_process
Definition: The chemical reactions and pathways involving acylglycerol, any mono-, di- or triester of glycerol with (one or more) fatty acids.
Synonyms: acylglycerol metabolism; glyceride metabolic process; glyceride metabolism
monoacylglycerol biosynthetic process (GO:0006640)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of monoacylglycerol, any ester of glycerol in which any one of its hydroxyl groups has been acylated with a fatty acid, the other being non-esterified.
Synonyms: monoacylglycerol anabolism; monoacylglycerol biosynthesis; monoacylglycerol formation; monoacylglycerol synthesis; monoglyceride biosynthesis; monoglyceride biosynthetic process
triglyceride metabolic process (GO:0006641)
Namespace: biological_process
Definition: The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
Synonyms: triacylglycerol metabolic process; triacylglycerol metabolism; triglyceride metabolism
triglyceride mobilization (GO:0006642)
Namespace: biological_process
Definition: The release of triglycerides, any triester of glycerol, from storage within cells or tissues, making them available for metabolism.
Synonyms: triacylglycerol mobilization
obsolete membrane lipid metabolic process (GO:0006643)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane.
Synonyms: membrane lipid metabolism
Comment: The reason for obsoletion is that this term groups lipids by their localization rather than by their metabolic function, which is problematic since most lipids can function in multiple locations.
phospholipid metabolic process (GO:0006644)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
Synonyms: phospholipid metabolism
phosphatidylethanolamine biosynthetic process (GO:0006646)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
Synonyms: phosphatidylethanolamine anabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine formation; phosphatidylethanolamine synthesis
phosphatidyl-N-monomethylethanolamine biosynthetic process (GO:0006647)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phosphatidyl-N-monomethylethanolamine (PMME), a derivative of phosphatidylethanolamine with a methylated amine group.
Synonyms: phosphatidyl-N-monomethylethanolamine anabolism; phosphatidyl-N-monomethylethanolamine biosynthesis; phosphatidyl-N-monomethylethanolamine formation; phosphatidyl-N-monomethylethanolamine synthesis; PMME biosynthesis; PMME biosynthetic process
dihydrosphingosine-1-P pathway (GO:0006648)
Namespace: biological_process
Definition: A phosphatidylethanolamine biosynthetic process that proceeds via the enzymatic action of dihydrosphingosine phosphate lyase.
phospholipid transfer to membrane (GO:0006649)
Namespace: biological_process
Definition: The transfer of a phospholipid from its site of synthesis to the plasma membrane.
glycerophospholipid metabolic process (GO:0006650)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
Synonyms: alpha-glycerophosphate pathway; glycerophospholipid metabolism; phosphoglyceride metabolic process; phosphoglyceride metabolism
diacylglycerol biosynthetic process (GO:0006651)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group.
Synonyms: diacylglycerol anabolism; diacylglycerol biosynthesis; diacylglycerol formation; diacylglycerol synthesis; diglyceride biosynthesis
phosphatidylglycerol biosynthetic process (GO:0006655)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidylglycerols, any of a class of phospholipids in which the phosphatidyl group is esterified to the hydroxyl group of glycerol.
Synonyms: phosphatidylglycerol anabolism; phosphatidylglycerol biosynthesis; phosphatidylglycerol formation; phosphatidylglycerol synthesis
phosphatidylcholine biosynthetic process (GO:0006656)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
Synonyms: phosphatidylcholine anabolism; phosphatidylcholine biosynthesis; phosphatidylcholine formation; phosphatidylcholine synthesis
CDP-choline pathway (GO:0006657)
Namespace: biological_process
Definition: The phosphatidylcholine biosynthetic process that begins with the phosphorylation of choline and ends with the combination of CDP-choline with diacylglycerol to form phosphatidylcholine.
Synonyms: Kennedy pathway; phosphatidylcholine biosynthesis from choline
phosphatidylserine metabolic process (GO:0006658)
Namespace: biological_process
Definition: The chemical reactions and pathways involving phosphatidylserines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of L-serine. They are important constituents of cell membranes.
Synonyms: phosphatidylserine metabolism
phosphatidylserine catabolic process (GO:0006660)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of phosphatidylserines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of L-serine.
Synonyms: phosphatidylserine breakdown; phosphatidylserine catabolism; phosphatidylserine degradation
phosphatidylinositol biosynthetic process (GO:0006661)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
Synonyms: phosphatidylinositol anabolism; phosphatidylinositol biosynthesis; phosphatidylinositol formation; phosphatidylinositol synthesis; phosphoinositide biosynthesis; phosphoinositide biosynthetic process; PtdIns biosynthesis; PtdIns biosynthetic process
obsolete glycerol ether metabolic process (GO:0006662)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
Synonyms: glycerol ether metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.