LiteFold/GO huggingface dataset:
obsolete rhamnogalacturonan I backbone metabolic process (GO:0010399)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving the alternating alpha-(1->2)-linked rhamnose and alpha-(1->2)-linked B-galacturonic acid residues of the rhamnogalacturonan I backbone.
Synonyms: rhamnogalacturonan I backbone metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete rhamnogalacturonan II side chain metabolic process (GO:0010419)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving the side chains of pectic rhamnogalacturonan II. A number of structurally distinct di- and oligosaccharides can be attached to the C-3 and C-2 of the backbone, respectively.
Synonyms: rhamnogalacturonan II side chain metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
fatty acid omega-oxidation (GO:0010430)
Namespace: biological_process
Definition: A fatty acid oxidation process in which the methyl group at the end of the fatty acid molecule (the omega carbon) is first oxidized to a hydroxyl group, then to an oxo group, and finally to a carboxyl group. The long chain dicarboxylates derived from omega-oxidation then enter the beta-oxidation pathway for further degradation.
seed maturation (GO:0010431)
Namespace: biological_process
Definition: A process in seed development that occurs after embryogenesis by which a quiescent state is established in a seed. Seed maturation is characterized by storage compound accumulation, acquisition of desiccation tolerance, growth arrest and the entry into a dormancy period of variable length that is broken upon germination.
response to alkaline pH (GO:0010446)
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 pH stimulus with pH > 7. pH is a measure of the acidity or basicity of an aqueous solution.
Synonyms: response to alkalinity; response to basic pH
vegetative meristem growth (GO:0010448)
Namespace: biological_process
Definition: The increase in size or mass of a vegetative meristem, a population of undifferentiated cells in a plant shoot which maintains a continuous balance between the production of stem cells and the incorporation of their derivatives into lateral organ primordia.
cell proliferation in dorsal spinal cord (GO:0010456)
Namespace: biological_process
Definition: The multiplication or reproduction of cells, resulting in the expansion of the dorsal spinal cord cell population.
chlororespiration (GO:0010478)
Namespace: biological_process
Definition: A respiratory electron flow (from NAD(P)H to plastoquinone (PQ) and O2) involving both a nonphotochemical reduction and re-oxidation of PQ pool.
maintenance of shoot apical meristem identity (GO:0010492)
Namespace: biological_process
Definition: The process in which an organism retains a population of shoot apical meristem cells, preventing the commitment of all stem cell progeny to a differentiated cell fate.
siRNA-mediated long-distance post-transcriptional gene silencing (GO:0010495)
Namespace: biological_process
Definition: An siRNA-mediated posttranscriptional gene silencing pathway in which small interfering RNAs (siRNAs) direct the cleavage of target mRNAs, and in which the silencing signal originates in one tissue and occurs in a different tissue.
Synonyms: long-distance posttranscriptional gene silencing; long-distance propagation of posttranscriptional gene silencing; siRNA-mediated long-distance posttranscriptional gene silencing
intercellular transport (GO:0010496)
Namespace: biological_process
Definition: The movement of substances between cells.
Synonyms: single organism intercellular transport; single-organism intercellular transport
obsolete negative regulation of phospholipase activity (GO:0010519)
Namespace: biological_process
Definition: OBSOLETE. Any process that decreases the frequency, rate or extent of phospholipase activity, the hydrolysis of a phospholipid.
Comment: This term was obsoleted because it represents a molecular function.
regulation of filamentous growth (GO:0010570)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the process in which a multicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape.
positive regulation of nuclear cell cycle DNA replication (GO:0010571)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of the DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.
Synonyms: positive regulation of DNA replication during S phase; positive regulation of DNA replication involved in S phase; positive regulation of DNA replication involved in S-phase
pollen exine formation (GO:0010584)
Namespace: biological_process
Definition: The formation of the pollen exine. The reticulate pollen wall pattern consists of two layers, exine and intine.
positive regulation of endothelial cell migration (GO:0010595)
Namespace: biological_process
Definition: Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
regulation of cytoplasmic mRNA processing body assembly (GO:0010603)
Namespace: biological_process
Definition: Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
negative regulation of cytoplasmic mRNA processing body assembly (GO:0010607)
Namespace: biological_process
Definition: Any process that decreases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
post-transcriptional regulation of gene expression (GO:0010608)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
Synonyms: posttranscriptional regulation of gene expression
specification of ovule identity (GO:0010622)
Namespace: biological_process
Definition: The regionalization process in which the identity of an ovule is specified. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
regulation of epithelial cell migration (GO:0010632)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of epithelial cell migration.
regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
Synonyms: regulation of platelet-derived growth factor receptor signalling pathway
negative regulation of cell communication by chemical coupling (GO:0010653)
Namespace: biological_process
Definition: Any process that decreases the frequency, rate or extent of cell communication via chemical coupling. Cell communication by chemical coupling is the process that mediates signaling interactions between one cell and another cell by the transfer of small, water-soluble molecules or metabolites between their adjacent cytoplasms via intercellular protein channels.
muscle cell apoptotic process (GO:0010657)
Namespace: biological_process
Definition: A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle.
Synonyms: muscle cell apoptosis
cardiac muscle cell apoptotic process (GO:0010659)
Namespace: biological_process
Definition: A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
Synonyms: cardiac muscle cell apoptosis
obsolete negative regulation of oxygen and reactive oxygen species metabolic process (GO:0010671)
Namespace: biological_process
Definition: OBSOLETE. Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH).
Synonyms: negative regulation of oxygen and reactive oxygen species metabolic process
Comment: This term was made obsolete because, as part of the GO/ChEBI alignment effort, curators determined that oxygen and reactive oxygen species should not be grouped together.
obsolete negative regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle (GO:0010674)
Namespace: biological_process
Definition: OBSOLETE. Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as part of the meiotic cell cycle.
Synonyms: activation of meiosis by negative regulation of transcription from RNA polymerase II promoter; negative regulation of transcription from RNA polymerase II promoter, meiotic; positive regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter; stimulation of meiosis by negative regulation of transcription from RNA polymerase II promoter; up regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter; up-regulation of meiosis by negative regulation of transcription from RNA polymerase II promoter; upregulation of meiosis by negative regulation of transcription from RNA polymerase II promoter
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete negative regulation of alkaline phosphatase activity (GO:0010693)
Namespace: biological_process
Definition: OBSOLETE. Any process that decreases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
Comment: This term was obsoleted because it represents a molecular function. Consider molecular function regulator activity ; GO:0098772 or a child.
positive regulation of alkaline phosphatase activity (GO:0010694)
Namespace: biological_process
Definition: Any process that increases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
obsolete regulation of histolysis (GO:0010702)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the rate, frequency or extent of the breakdown of tissues; usually, if not always, accompanied by cell death.
Comment: This term was made obsolete because it refers to a phenotype. When death of a cell or tissue is a result of a true biological process, this should be captured using 'programmed cell death' or one of its descendants.
regulation of collagen metabolic process (GO:0010712)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
Synonyms: regulation of collagen metabolism
regulation of epithelial to mesenchymal transition (GO:0010717)
Namespace: biological_process
Definition: Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
obsolete positive regulation of transcription from RNA polymerase II promoter in response to iron (GO:0010723)
Namespace: biological_process
Definition: OBSOLETE. Any process that increases the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus.
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete positive regulation of hydrogen peroxide metabolic process (GO:0010726)
Namespace: biological_process
Definition: OBSOLETE. Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.
Synonyms: positive regulation of hydrogen peroxide metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete regulation of protein kinase A signaling (GO:0010738)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
Synonyms: regulation of PKA signaling cascade; regulation of protein kinase A signaling cascade; regulation of protein kinase A signalling cascade
Comment: This term was obsoleted because it does not represent the regulation of a specific pathway. Consider regulation of cAMP/PKA signal transduction ; GO:0141161 or  regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway ; GO:0106070.
macrophage derived foam cell differentiation (GO:0010742)
Namespace: biological_process
Definition: The process in which a monocyte acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
negative regulation of nitric oxide mediated signal transduction (GO:0010751)
Namespace: biological_process
Definition: Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO).
Synonyms: negative regulation of nitric oxide-mediated signal transduction
obsolete positive regulation of cGMP-mediated signaling (GO:0010753)
Namespace: biological_process
Definition: OBSOLETE. Any process that increases the rate, frequency or extent of cGMP-mediated signaling.
Synonyms: positive regulation of cGMP-mediated signalling
Comment: This term was obsoleted because it does not represents the regulation of a specific pathway; many pathways use cGMP as a second messenger.
negative regulation of plasminogen activation (GO:0010757)
Namespace: biological_process
Definition: Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
Synonyms: inhibition of plasminogen activation
obsolete regulation of cell morphogenesis involved in differentiation (GO:0010769)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
Comment: This term is equivalent to regulation of cell morphogenesis.
proboscis morphogenesis, labial disc-derived (GO:0010782)
Namespace: biological_process
Definition: The process in which the anatomical structures of the proboscis that are derived from the labial disc are generated and organized.
meiosis I sister chromatid cohesion (GO:0010789)
Namespace: biological_process
Definition: The cell cycle process in which sister chromatids of a replicated chromosome are joined along the entire length of the chromosome during meiosis I.
Synonyms: meiotic sister chromatid cohesion involved in meiosis I
DNA double-strand break processing involved in repair via synthesis-dependent strand annealing (GO:0010791)
Namespace: biological_process
Definition: The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang that results in the repair of a double strand break via synthesis-dependent strand annealing.
regulation of dolichyl monophosphate biosynthetic process (GO:0010794)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of dolichol biosynthesis. Dolichol biosynthesis consists of the chemical reactions and pathways resulting in the formation of dolichols, any 2,3-dihydropolyprenol derived from four or more linked isoprene units.
Synonyms: regulation of dolichol biosynthetic process
negative regulation of peptidyl-threonine phosphorylation (GO:0010801)
Namespace: biological_process
Definition: Any process that decreases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)
Namespace: biological_process
Definition: Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
Synonyms: regulation of TNF signaling; regulation of TNF-mediated signaling pathway; regulation of tumor necrosis factor-mediated signalling pathway
negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)
Namespace: biological_process
Definition: Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
Synonyms: negative regulation of TNF signaling; negative regulation of TNF-mediated signaling pathway; negative regulation of tumor necrosis factor-mediated signalling pathway
negative regulation of cell-substrate adhesion (GO:0010812)
Namespace: biological_process
Definition: Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
regulation of myotube differentiation (GO:0010830)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
negative regulation of protein ADP-ribosylation (GO:0010836)
Namespace: biological_process
Definition: Any process that decreases the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids.
Synonyms: negative regulation of protein amino acid ADP-ribosylation
adenylate cyclase regulator activity (GO:0010854)
Namespace: molecular_function
Definition: Binds to and modulates the activity of adenylate cyclase.
adenylate cyclase inhibitor activity (GO:0010855)
Namespace: molecular_function
Definition: Binds to and decreases the activity of adenylate cyclase.
adenylate cyclase activator activity (GO:0010856)
Namespace: molecular_function
Definition: Binds to and increases the activity of adenylate cyclase.
obsolete calcium-dependent protein kinase activity (GO:0010857)
Namespace: molecular_function
Definition: OBSOLETE. Calcium-dependent catalysis of the reaction: a protein + ATP = a phosphoprotein + ADP.
Comment: This term was obsoleted because it is an unnecessary grouping class. All calcium-dependent protein kinases are serine/threonine protein kinases.
obsolete positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)
Namespace: biological_process
Definition: OBSOLETE. Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
Comment: This term was obsoleted because it represents a molecular function.
obsolete negative regulation of receptor biosynthetic process (GO:0010871)
Namespace: biological_process
Definition: OBSOLETE. Any process that decreases the frequency or rate of receptor biosynthesis. Receptor biosynthesis is the collection of chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
lipid transport involved in lipid storage (GO:0010877)
Namespace: biological_process
Definition: The directed movement of lipids into cells that is part of their accumulation and maintenance.
cholesterol storage (GO:0010878)
Namespace: biological_process
Definition: The accumulation and maintenance in cells or tissues of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
Synonyms: cholesterol sequestration; sequestration of cholesterol
negative regulation of cholesterol storage (GO:0010887)
Namespace: biological_process
Definition: Any process that decreases the rate or extent of cholesterol storage. Cholesterol storage is the accumulation and maintenance in cells or tissues of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
Synonyms: negative regulation of cholesterol sequestration
negative regulation of ergosterol biosynthetic process (GO:0010895)
Namespace: biological_process
Definition: Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ergosterol.
positive regulation of triglyceride catabolic process (GO:0010898)
Namespace: biological_process
Definition: Any process that increases the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of triglyceride.
Synonyms: positive regulation of triacylglycerol catabolic process
positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)
Namespace: biological_process
Definition: Any process that increases the rate, frequency or extent of very-low-density lipoprotein particle remodeling. Very-low-density lipoprotein particle remodeling is the acquisition, loss or modification of a protein or lipid within a very-low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase or lipoprotein lipase and the subsequent loss of free fatty acid.
Synonyms: positive regulation of very-low-density lipoprotein particle remodelling; positive regulation of VLDL remodeling; positive regulation of VLDL remodelling