LiteFold/GO huggingface dataset:
obsolete mitochondrial genome maintenance (GO:0000002)
Namespace: biological_process
Definition: OBSOLETE. The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.
Comment: This term described phenotypic observations for multiple processes (including transport/lipid metabolism/ DNA metabolism/ fission/ fusion etc)
obsolete reproduction (GO:0000003)
Namespace: biological_process
Definition: OBSOLETE. The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
Synonyms: reproductive physiological process
Comment: The reason for obsoletion is that this term is equivalent to reproductive process.
high-affinity zinc transmembrane transporter activity (GO:0000006)
Namespace: molecular_function
Definition: Enables the transfer of zinc ions (Zn2+) from one side of a membrane to the other, probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.
Synonyms: high affinity zinc uptake transmembrane transporter activity; high-affinity zinc uptake transmembrane transporter activity
low-affinity zinc ion transmembrane transporter activity (GO:0000007)
Namespace: molecular_function
Definition: Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low-affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.
obsolete thioredoxin (GO:0000008)
Namespace: molecular_function
Definition: OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol.
Synonyms: thioredoxin
Comment: This term was made obsolete because it represents gene products.
alpha-1,6-mannosyltransferase activity (GO:0000009)
Namespace: molecular_function
Definition: Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->6) linkage.
Synonyms: 1,6-alpha-mannosyltransferase activity
heptaprenyl diphosphate synthase activity (GO:0000010)
Namespace: molecular_function
Definition: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate.
Synonyms: all-trans-heptaprenyl-diphosphate synthase activity; HepPP synthase activity; heptaprenyl pyrophosphate synthase activity; heptaprenyl pyrophosphate synthetase activity; trans-hexaprenyltranstransferase activity
vacuole inheritance (GO:0000011)
Namespace: biological_process
Definition: The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
single strand break repair (GO:0000012)
Namespace: biological_process
Definition: The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
single-stranded DNA endonuclease activity (GO:0000014)
Namespace: molecular_function
Definition: Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
Synonyms: single-stranded DNA endodeoxyribonuclease activity; single-stranded DNA specific endodeoxyribonuclease activity; ssDNA-specific endodeoxyribonuclease activity
phosphopyruvate hydratase complex (GO:0000015)
Namespace: cellular_component
Definition: A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.
Synonyms: enolase complex
lactase activity (GO:0000016)
Namespace: molecular_function
Definition: Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose.
Synonyms: lactose galactohydrolase activity
alpha-glucoside transport (GO:0000017)
Namespace: biological_process
Definition: The directed movement of alpha-glucosides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Alpha-glucosides are glycosides in which the sugar group is a glucose residue, and the anomeric carbon of the bond is in an alpha configuration.
regulation of DNA recombination (GO:0000018)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.
regulation of mitotic recombination (GO:0000019)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of DNA recombination during mitosis.
Synonyms: regulation of recombination within rDNA repeats
obsolete negative regulation of recombination within rDNA repeats (GO:0000020)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA.
Synonyms: negative regulation of recombination within rDNA repeats
Comment: This term was made obsolete because it describes a substrate-specific process.
mitotic spindle elongation (GO:0000022)
Namespace: biological_process
Definition: The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
Synonyms: microtubule sliding involved in mitotic spindle elongation; spindle elongation during mitosis
maltose metabolic process (GO:0000023)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.
Synonyms: malt sugar metabolic process; malt sugar metabolism; maltose metabolism
maltose biosynthetic process (GO:0000024)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose).
Synonyms: malt sugar biosynthesis; malt sugar biosynthetic process; maltose anabolism; maltose biosynthesis; maltose formation; maltose synthesis
maltose catabolic process (GO:0000025)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose).
Synonyms: malt sugar catabolic process; malt sugar catabolism; maltose breakdown; maltose degradation; maltose hydrolysis
alpha-1,2-mannosyltransferase activity (GO:0000026)
Namespace: molecular_function
Definition: Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->2) linkage.
ribosomal large subunit assembly (GO:0000027)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
Synonyms: 50S ribosomal subunit assembly; 60S ribosomal subunit assembly
ribosomal small subunit assembly (GO:0000028)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.
Synonyms: 30S ribosomal subunit assembly; 40S ribosomal subunit assembly
mannosyltransferase activity (GO:0000030)
Namespace: molecular_function
Definition: Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
mannosylphosphate transferase activity (GO:0000031)
Namespace: molecular_function
Definition: Catalysis of the reaction: GDP-alpha-D-mannose + n {[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]-alpha-D-Man-(1->6)}60-(Man9GlcNAc2-[protein] = phosphorylated {[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]-alpha-D-Man-(1->6)}60-(Man9GlcNAc2-[protein] + n GMP + n H+ or GDP-alpha-D-mannose + alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-3-O-(Ser/Thr)-[protein] = alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-6P-]-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-3-O-(Ser/Thr)-[protein] + GMP + H+.
cell wall mannoprotein biosynthetic process (GO:0000032)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of cell wall mannoproteins, any cell wall protein that contains covalently bound mannose residues.
Synonyms: cell wall mannoprotein anabolism; cell wall mannoprotein biosynthesis; cell wall mannoprotein formation; cell wall mannoprotein synthesis
alpha-1,3-mannosyltransferase activity (GO:0000033)
Namespace: molecular_function
Definition: Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->3) linkage.
acyl binding (GO:0000035)
Namespace: molecular_function
Definition: Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid.
Synonyms: acyl-CoA or acyl binding
acyl carrier activity (GO:0000036)
Namespace: molecular_function
Definition: Binding an acyl group and presenting it for processing or offloading to a cognate enzyme. Covalently binds the acyl group via a phosphopantetheine prosthetic group and mediates protein-protein interactions with the enzyme conferring specificity. The acyl carrier protein (ACP) presents substrates to enzymes involved in fatty acid biosynthesis or in polyketide secondary metabolite biosynthesis.
Synonyms: ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process
very long-chain fatty acid metabolic process (GO:0000038)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a very long-chain fatty acid. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons.
Synonyms: very long chain fatty acid metabolic process; very-long-chain fatty acid metabolic process; very-long-chain fatty acid metabolism
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
obsolete plasma membrane long-chain fatty acid transporter (GO:0000039)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: plasma membrane long-chain fatty acid transporter
Comment: This term was made obsolete because it describes a gene product and it contains component information.
transition metal ion transport (GO:0000041)
Namespace: biological_process
Definition: The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
Synonyms: transition metal transport
obsolete ascorbate stabilization (GO:0000044)
Namespace: biological_process
Definition: OBSOLETE. The reduction of the ascorbate free radical to a stable form.
Synonyms: ascorbate stabilization; vitamin C stabilization
Comment: This term was made obsolete because it is defined as a function term and is in the process ontology.
autophagosome assembly (GO:0000045)
Namespace: biological_process
Definition: The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
Synonyms: autophagic vacuole assembly; autophagic vacuole formation; autophagosome biosynthesis; autophagosome formation; PAS formation
obsolete Rieske iron-sulfur protein (GO:0000047)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: Rieske iron-sulfur protein; Rieske iron-sulphur protein
Comment: This term was made obsolete because it represents a gene product.
peptidyltransferase activity (GO:0000048)
Namespace: molecular_function
Definition: Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2). This reaction is catalyzed by a ribozyme.
tRNA binding (GO:0000049)
Namespace: molecular_function
Definition: Binding to a transfer RNA.
Synonyms: base pairing with tRNA
obsolete urea cycle intermediate metabolic process (GO:0000051)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving any of the intermediate compounds involved in the urea cycle, a cyclic metabolic pathway that converts waste nitrogen in the form of ammonium to urea.
Synonyms: urea cycle intermediate metabolic process; urea cycle intermediate metabolism
Comment: This term was made obsolete because it is a grouping term that is not useful, but has caused true path violations.
citrulline metabolic process (GO:0000052)
Namespace: biological_process
Definition: The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.
Synonyms: citrulline metabolism
obsolete argininosuccinate metabolic process (GO:0000053)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate.
Synonyms: argininosuccinate metabolism
Comment: This term was obsoleted because it represents a pathway intermediate.
ribosomal subunit export from nucleus (GO:0000054)
Namespace: biological_process
Definition: The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
Synonyms: ribosomal subunit export from cell nucleus; ribosomal subunit export out of nucleus; ribosomal subunit transport from nucleus to cytoplasm; ribosomal subunit-nucleus export; ribosome export from nucleus
ribosomal large subunit export from nucleus (GO:0000055)
Namespace: biological_process
Definition: The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
Synonyms: 50S ribosomal subunit export from nucleus; 60S ribosomal subunit export from nucleus; ribosomal large subunit export from cell nucleus; ribosomal large subunit export out of nucleus; ribosomal large subunit transport from nucleus to cytoplasm; ribosomal large subunit-nucleus export
ribosomal small subunit export from nucleus (GO:0000056)
Namespace: biological_process
Definition: The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm.
Synonyms: 30S ribosomal subunit export from nucleus; 40S ribosomal subunit export from nucleus; ribosomal small subunit export from cell nucleus; ribosomal small subunit export out of nucleus; ribosomal small subunit transport from nucleus to cytoplasm; ribosomal small subunit-nucleus export
obsolete protein import into nucleus, docking (GO:0000059)
Namespace: biological_process
Definition: OBSOLETE. A protein complex assembly process that contributes to protein import into the nucleus, and that results in the association of a cargo protein, a carrier protein such as an importin alpha/beta heterodimer, and a nucleoporin located at the periphery of the nuclear pore complex.
Synonyms: protein docking during protein import into nucleus; protein docking during protein transport from cytoplasm to nucleus; protein docking during protein-nucleus import; protein transport from cytoplasm to nucleus, docking; protein-nucleus import, docking
Comment: This term was made obsolete because the transient assembly is better captured as a protein-protein association, if at all.
obsolete protein import into nucleus, translocation (GO:0000060)
Namespace: biological_process
Definition: OBSOLETE. A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
Synonyms: protein import into cell nucleus, translocation; protein translocation during protein import into nucleus; protein translocation during protein transport from cytoplasm to nucleus; protein translocation during protein-nucleus import; protein transport from cytoplasm to nucleus, translocation; protein-nucleus import, translocation
Comment: This term has been obsoleted because it represents a substep of the parent (GO:0006606 protein import into nucleus), has been incorrectly used.
obsolete protein import into nucleus, substrate release (GO:0000061)
Namespace: biological_process
Definition: OBSOLETE. A protein complex disassembly process that contributes to protein import into the nucleus, and that results in the dissociation of the cargo protein and the carrier (such as an importin alpha/beta heterodimer) from each other and from the nuclear pore complex.
Synonyms: protein import into cell nucleus, substrate release; protein substrate release during protein import into nucleus; protein substrate release during protein transport from cytoplasm to nucleus; protein substrate release during protein-nucleus import; protein transport from cytoplasm to nucleus, substrate release; protein-nucleus import, substrate release
Comment: This term has been obsoleted because it represents a substep of the parent (GO:0006606 protein import into nucleus), has been incorrectly used.
fatty-acyl-CoA binding (GO:0000062)
Namespace: molecular_function
Definition: Binding to a fatty-acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
Synonyms: fatty-acyl binding; fatty-acyl-coenzyme A binding
L-ornithine transmembrane transporter activity (GO:0000064)
Namespace: molecular_function
Definition: Enables the transfer of L-ornithine from one side of a membrane to the other. L-ornithine is 2,5-diaminopentanoic acid.
Synonyms: histidine/arginine/lysine/ornithine porter activity; L-ornithine transporter activity
obsolete DNA replication and chromosome cycle (GO:0000067)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: DNA replication and chromosome cycle
Comment: This term was made obsolete because it has been superseded by more accurate terms to represent the biological processes occurring, and it is not clear that this term represents a useful entity.
mitotic sister chromatid segregation (GO:0000070)
Namespace: biological_process
Definition: The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
Synonyms: mitotic chromosome segregation; mitotic sister-chromatid adhesion release
obsolete M phase specific microtubule process (GO:0000072)
Namespace: biological_process
Definition: OBSOLETE. A microtubule-based process that occurs only during M phase of the cell cycle.
Synonyms: M phase specific microtubule process; M-phase specific microtubule process
Comment: This term was made obsolete because terms already exist for centrosome/spindle organization which would be more suitable for the existing annotations, and the phase could be captured as an annotation extension if necessary.
initial mitotic spindle pole body separation (GO:0000073)
Namespace: biological_process
Definition: The release of duplicated mitotic spindle pole bodies (SPBs) that begins with the nucleation of microtubules from each SPB within the nucleus, leading to V-shaped spindle microtubules. Interpolar microtubules that elongate from each pole are interconnected, forming overlapping microtubules. Capturing and antiparallel sliding apart of microtubules promotes the initial separation of the SPB.
cell cycle checkpoint signaling (GO:0000075)
Namespace: biological_process
Definition: A signaling process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction.
Synonyms: cell cycle checkpoint; G1/S checkpoint; G1/S transition checkpoint; G2/M checkpoint; G2/M transition checkpoint; signal transduction involved in cell cycle checkpoint; signal transduction involved in G2/M transition checkpoint
Comment: This term should not be used in direct manual annotation as it should always be possible to minimally designate mitotic or meiotic checkpoint, and usually to additionally specify the checkpoint (i.e mitotic spindle assembly checkpoint, mitotic DNA damage checkpoint etc). Note also that the effector processes are not part of the checkpoint but are positively regulated by the checkpoint signaling and should not be annotated here.
DNA replication checkpoint signaling (GO:0000076)
Namespace: biological_process
Definition: A signal transduction process that contributes to a DNA replication checkpoint, that prevents the initiation of nuclear division until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.
Synonyms: DNA replication checkpoint; signal transduction involved in DNA replication checkpoint
DNA damage checkpoint signaling (GO:0000077)
Namespace: biological_process
Definition: A signal transduction process that contributes to a DNA damage checkpoint.
Synonyms: DNA damage checkpoint; DNA damage response, signal transduction resulting in cell cycle arrest; signal transduction involved in DNA damage checkpoint
obsolete cytokinesis after mitosis checkpoint (GO:0000078)
Namespace: biological_process
Definition: OBSOLETE. A mitotic cell cycle checkpoint that detects whether chromosome segregation is complete and negatively regulates cytokinesis following mitosis.
Synonyms: cell morphogenesis checkpoint; cell shape checkpoint
Comment: The reason this term was made obsolete is that the two terms cytokinesis checkpoint (GO:0031565) and cytokinesis after mitosis (GO:0000078) were conflated in meaning.
regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
Synonyms: regulation of CDK activity; regulation of cyclin-dependent protein kinase activity
mitotic G1 phase (GO:0000080)
Namespace: biological_process
Definition: The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
Synonyms: G1 phase of mitotic cell cycle
Comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).