LiteFold/GO huggingface dataset:
cytoskeleton (GO:0005856)
Namespace: cellular_component
Definition: A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
axonemal dynein complex (GO:0005858)
Namespace: cellular_component
Definition: A dynein complex found in eukaryotic cilia and flagella; the motor domain heads interact with adjacent microtubules to generate a sliding force which is converted to a bending motion.
Synonyms: axonemal dynein heavy chain; axonemal dynein intermediate chain; axonemal dynein intermediate light chain; axonemal dynein light chain
muscle thin filament tropomyosin (GO:0005862)
Namespace: cellular_component
Definition: A form of the tropomyosin dimer found associated with actin and the troponin complex in muscle thin filaments.
spindle microtubule (GO:0005876)
Namespace: cellular_component
Definition: Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
axonemal microtubule (GO:0005879)
Namespace: cellular_component
Definition: A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules.
neurofilament (GO:0005883)
Namespace: cellular_component
Definition: A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter.
Synonyms: type IV intermediate filament
potassium:proton exchanging ATPase complex (GO:0005889)
Namespace: cellular_component
Definition: A protein complex that possesses hydrogen:potassium-exchanging ATPase activity; characterized in animal cells, where it maintains ionic gradients of K+ at the expense of ATP hydrolysis; The complex contains two obligatory subunits, the catalytic alpha subunit and a glycosylated beta subunit; two additional subunits, gamma and channel-inducing factor (CHIF), may also be present.
Synonyms: hydrogen/potassium-exchanging ATPase complex; hydrogen:potassium-exchanging ATPase complex; proton pump
microvillus (GO:0005902)
Namespace: cellular_component
Definition: Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
Synonyms: microvilli
Comment: Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.
adherens junction (GO:0005912)
Namespace: cellular_component
Definition: A cell-cell junction composed of the epithelial cadherin-catenin complex. The epithelial cadherins, or E-cadherins, of each interacting cell extend through the plasma membrane into the extracellular space and bind to each other. The E-cadherins bind to catenins on the cytoplasmic side of the membrane, where the E-cadherin-catenin complex binds to cytoskeletal components and regulatory and signaling molecules.
Synonyms: cell-cell adherens junction
smooth septate junction (GO:0005920)
Namespace: cellular_component
Definition: A septate junction that lacks the regular arrays of electron-dense septae found in pleated septate junctions.
Synonyms: zonula continua
cellular bud (GO:0005933)
Namespace: cellular_component
Definition: A protuberance from a cell of an organism that reproduces by budding, which will grow larger and become a separate daughter cell after nuclear division, cytokinesis, and cell wall formation (when appropriate). The daughter cell may completely separate from the mother cell, or the mother and daughter cells may remain associated.
phosphatidylinositol 3-kinase complex, class IB (GO:0005944)
Namespace: cellular_component
Definition: A class I phosphatidylinositol 3-kinase complex that possesses 1-phosphatidylinositol-4-phosphate 3-kinase activity; comprises a catalytic class IB phosphoinositide 3-kinase (PI3K) subunit and an associated regulatory subunit that is larger than, and unrelated to, the p85 proteins present in class IA complexes. Class IB PI3Ks are stimulated by G-proteins and do not interact with the SH2-domain containing adaptors that bind to Class IA PI3Ks.
Synonyms: 1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex; 1-phosphatidylinositol-4-phosphate kinase, class IB complex; class IB PI3K complex; phosphoinositide 3-kinase complex, class IB
serine-pyruvate aminotransferase complex (GO:0005969)
Namespace: cellular_component
Definition: A protein homodimeric complex that catalyzes the formation of hydroxypyruvate and alanine from serine and pyruvate.
Synonyms: serine-pyruvate aminotransferase, type 1 complex; serine-pyruvate aminotransferase, type 2B complex
trehalose biosynthetic process (GO:0005992)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.
Synonyms: mycose biosynthesis; mycose biosynthetic process; mykose biosynthesis; mykose biosynthetic process; trehalose anabolism; trehalose biosynthesis; trehalose formation; trehalose synthesis
monosaccharide metabolic process (GO:0005996)
Namespace: biological_process
Definition: The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
Synonyms: monosaccharide metabolism
obsolete deoxyribose 1,5-bisphosphate biosynthetic process (GO:0006017)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of deoxyribose 1,5-bisphosphate, the diphosphorylated sugar 1,5-diphospho-2-deoxyribose.
Synonyms: deoxyribose 1,5-bisphosphate anabolism; deoxyribose 1,5-bisphosphate biosynthesis; deoxyribose 1,5-bisphosphate formation; deoxyribose 1,5-bisphosphate synthesis
Comment: This term was obsoleted because it is an unnecessary grouping term.
inositol metabolic process (GO:0006020)
Namespace: biological_process
Definition: The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
Synonyms: inositol metabolism; myo-inositol metabolic process; myo-inositol metabolism; vitamin Bh metabolic process; vitamin Bh metabolism
chitin metabolic process (GO:0006030)
Namespace: biological_process
Definition: The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
Synonyms: beta-1,4-linked N-acetylglucosamine metabolic process; beta-1,4-linked N-acetylglucosamine metabolism; chitin metabolism
chitin localization (GO:0006033)
Namespace: biological_process
Definition: A process in which chitin is transported to, or maintained in, a specific location.
Synonyms: chitin localisation; establishment and maintenance of chitin localization
obsolete cuticle chitin metabolic process (GO:0006034)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving cuticle chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues, found in cuticles.
Synonyms: cuticle chitin metabolism
Comment: The reason for obsoletion is that this^Cerm is mixing biological process and cellular component.
N-acetylglucosamine biosynthetic process (GO:0006045)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
Synonyms: N-acetylglucosamine anabolism; N-acetylglucosamine biosynthesis; N-acetylglucosamine formation; N-acetylglucosamine synthesis
ethanol catabolic process (GO:0006068)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.
Synonyms: ethanol breakdown; ethanol catabolism; ethanol degradation
obsolete ethanol oxidation (GO:0006069)
Namespace: biological_process
Definition: OBSOLETE. An ethanol metabolic process in which ethanol is converted to acetyl-CoA via acetaldehyde and acetate.
Comment: The reason for obsoletion is that this term represents a molecular function.
regulation of carbohydrate metabolic process (GO:0006109)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
Synonyms: regulation of carbohydrate metabolism
energy reserve metabolic process (GO:0006112)
Namespace: biological_process
Definition: The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
Synonyms: energy reserve metabolism
obsolete oxidized glutathione reduction (GO:0006128)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: oxidized glutathione reduction
Comment: This term was made obsolete because the term string represents a molecular function and not a biological pathway.
obsolete 5,10-methylenetetrahydrofolate oxidation (GO:0006133)
Namespace: biological_process
Definition: OBSOLETE. This term was not defined before being made obsolete.
Synonyms: 5,10-methylenetetrahydrofolate oxidation
Comment: This term was made obsolete because it is defined as a function term and is in the process ontology.
regulation of purine nucleobase metabolic process (GO:0006141)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines.
Synonyms: regulation of purine base metabolic process; regulation of purine base metabolism
obsolete purine nucleosidase reaction (GO:0006153)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: purine nucleosidase reaction
Comment: This term was made obsolete because it represents a molecular function.
AMP biosynthetic process (GO:0006167)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
Synonyms: AMP anabolism; AMP biosynthesis; AMP formation; AMP synthesis
cAMP biosynthetic process (GO:0006171)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
Synonyms: 3',5' cAMP biosynthesis; 3',5' cAMP biosynthetic process; 3',5'-cAMP biosynthesis; 3',5'-cAMP biosynthetic process; adenosine 3',5'-cyclophosphate biosynthesis; adenosine 3',5'-cyclophosphate biosynthetic process; cAMP anabolism; cAMP biosynthesis; cAMP formation; cAMP synthesis; cyclic AMP biosynthesis; cyclic AMP biosynthetic process
guanosine salvage (GO:0006179)
Namespace: biological_process
Definition: Any process that generates guanosine, guanine riboside, from derivatives of it without de novo synthesis.
Synonyms: guanine, xanthine and their nucleoside salvage
dGMP biosynthetic process (GO:0006181)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate).
Synonyms: dGMP anabolism; dGMP biosynthesis; dGMP formation; dGMP synthesis
obsolete GTP catabolic process (GO:0006184)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of GTP, guanosine triphosphate.
Synonyms: GTP breakdown; GTP catabolism; GTP degradation; GTP hydrolysis
Comment: The reason for making this term obsolete is that it gets misused in cases where phosphates are simply being removed from a small molecule. We found no cases where these molecules genuinely underwent catabolism.
obsolete ADP reduction (GO:0006199)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: ADP reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete uridine kinase reaction (GO:0006224)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: uridine kinase reaction
Comment: This term was made obsolete because it represents a molecular function.
dUMP biosynthetic process (GO:0006226)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
Synonyms: dUMP anabolism; dUMP biosynthesis; dUMP formation; dUMP synthesis
CTP catabolic process (GO:0006254)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of CTP, cytidine 5'-triphosphate.
Synonyms: CTP breakdown; CTP catabolism; CTP degradation; CTP hydrolysis
dUDP catabolic process (GO:0006257)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of dUDP, deoxyuridine (5'-)diphosphate.
Synonyms: dUDP breakdown; dUDP catabolism; dUDP degradation
pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO:0006267)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form the nuclear pre-replicative complex, a protein-DNA complex that forms at the eukaryotic DNA replication origin and is required for replication initiation.
Synonyms: nuclear pre-replicative complex assembly; pre-RC complex assembly; pre-replicative complex assembly; pre-replicative complex formation
obsolete DNA unwinding involved in DNA replication (GO:0006268)
Namespace: biological_process
Definition: OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
Synonyms: DNA unwinding during replication; DNA unwinding factor
Comment: Note that this term refers to a geometric change in DNA conformation, and should not be confused with 'DNA topological change ; GO:0006265'.\nThe reason for obsoletion is that the term represents a molecular function.
leading strand elongation (GO:0006272)
Namespace: biological_process
Definition: The process in which an existing DNA strand is extended continuously in a 5' to 3' direction by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. Leading strand elongation proceeds in the same direction as the replication fork.
obsolete base-excision repair, base-free sugar-phosphate removal (GO:0006286)
Namespace: biological_process
Definition: OBSOLETE. Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme.
Comment: This term was obsoleted because it represents a molecular function.
base-excision repair, gap-filling (GO:0006287)
Namespace: biological_process
Definition: Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.
nucleotide-excision repair, preincision complex assembly (GO:0006294)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
Synonyms: nucleotide-excision repair, preincision complex formation
double-strand break repair via nonhomologous end joining (GO:0006303)
Namespace: biological_process
Definition: The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
Synonyms: NHEJ
DNA modification (GO:0006304)
Namespace: biological_process
Definition: The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
chromatin organization (GO:0006325)
Namespace: biological_process
Definition: The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA.
Synonyms: chromatin assembly; chromatin assembly or disassembly; chromatin assembly/disassembly; chromatin maintenance; chromatin modification; chromatin organisation; DNA replication-independent chromatin assembly; DNA replication-independent chromatin organization; DNA replication-independent nucleosome organisation; DNA replication-independent nuclesome assembly; establishment of chromatin architecture; establishment or maintenance of chromatin architecture; transcription-coupled nucleosome assembly
nucleosome assembly (GO:0006334)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
Synonyms: histone chaperone; nucleosome modeling
obsolete positive regulation of transcription of homeotic gene (trithorax group) (GO:0006339)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the trithorax group.
Synonyms: positive regulation of transcription of homeotic gene (trithorax group)
Comment: This term was made obsolete because it relates to a specific gene family rather than a process.
regulation of DNA-templated transcription (GO:0006355)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
Synonyms: regulation of cellular transcription, DNA-dependent; regulation of gene-specific transcription; regulation of transcription, DNA-dependent; regulation of transcription, DNA-templated; transcriptional control
regulation of transcription by RNA polymerase II (GO:0006357)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
Synonyms: global transcription regulation from Pol II promoter; regulation of gene-specific transcription from RNA polymerase II promoter; regulation of global transcription from Pol II promoter; regulation of transcription from Pol II promoter; regulation of transcription from RNA polymerase II promoter; regulation of transcription from RNA polymerase II promoter, global
transcription by RNA polymerase III (GO:0006383)
Namespace: biological_process
Definition: The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
Synonyms: RNA polymerase III transcription factor activity; transcription from a RNA polymerase III hybrid type promoter; transcription from Pol III promoter; transcription from RNA polymerase III promoter; transcription from RNA polymerase III type 2 promoter; transcription from RNA polymerase III type 3 promoter; U2 snRNA transcription (S. cerevisiae); U6 snRNA transcription (mammalian)
termination of mitochondrial transcription (GO:0006393)
Namespace: biological_process
Definition: A transcription termination process that completes the production of a primary mitochondrial transcript.
Synonyms: mitochondrial transcription termination; RNA transcription termination from mitochondrial promoter
mRNA 3'-end processing by stem-loop binding and cleavage (GO:0006398)
Namespace: biological_process
Definition: Any mRNA 3'-end processing that involves the binding to and cleavage of a stem-loop structure. For example, histone mRNAs contain a highly conserved stem-loop sequence at the 3' end of the mRNA with a 6 base pairs (bp) stem and a 4-nt loop. The mRNA is cleaved between these two elements, after the fourth or fifth nucleotide, which is typically an adenosine.
Synonyms: histone mRNA 3' end processing
RNA localization (GO:0006403)
Namespace: biological_process
Definition: A process in which RNA is transported to, or maintained in, a specific location.
Synonyms: establishment and maintenance of RNA localization; RNA localisation
arginyl-tRNA aminoacylation (GO:0006420)
Namespace: biological_process
Definition: The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
aspartyl-tRNA aminoacylation (GO:0006422)
Namespace: biological_process
Definition: The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA.
lysyl-tRNA aminoacylation (GO:0006430)
Namespace: biological_process
Definition: The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA.
threonyl-tRNA aminoacylation (GO:0006435)
Namespace: biological_process
Definition: The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA.
tyrosyl-tRNA aminoacylation (GO:0006437)
Namespace: biological_process
Definition: The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
regulation of translational elongation (GO:0006448)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate, extent or accuracy of translational elongation.
obsolete peptidyl-prolyl isomerase B reaction (GO:0006460)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: peptidyl-prolyl isomerase B reaction
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
steroid hormone receptor complex assembly (GO:0006463)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a steroid hormone receptor complex, an intracellular receptor that binds steroid hormones. The complex is often a dimer, and forms after the steroid has bound the receptor.
protein dephosphorylation (GO:0006470)
Namespace: biological_process
Definition: The process of removing one or more phosphoric residues from a protein.
Synonyms: protein amino acid dephosphorylation