LiteFold/GO huggingface dataset:
phagocytosis, engulfment (GO:0006911)
Namespace: biological_process
Definition: The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
Synonyms: phagosome biosynthesis; phagosome formation
obsolete phagosome formation (GO:0006912)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: phagosome formation
Comment: This term was made obsolete because of the ambiguity in its meaning.
nucleocytoplasmic transport (GO:0006913)
Namespace: biological_process
Definition: The directed movement of molecules between the nucleus and the cytoplasm.
Synonyms: nucleocytoplasmic shuttling
Comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
autophagy (GO:0006914)
Namespace: biological_process
Definition: The cellular catabolic process in which cells digest cellular materials, such as organelles and other macromolecular constituents, or non-self materials such as intracellular pathogens. Autophagy serves to provide essential nutrients under conditions of cellular stress; or can remodel intracellular structures during cell differentiation.
obsolete induction of apoptosis by p53 (GO:0006918)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: induction of apoptosis by p53
Comment: This term was made obsolete because more accurate terms were created.
obsolete activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)
Namespace: biological_process
Definition: OBSOLETE. Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
Synonyms: activation of caspase activity; activation of metacaspase activity; caspase activation
Comment: This term should be used when the annotation refers to a process that occurs in a context of apoptotic cell death. To annotate gene products involved in activation of cysteine-type endopeptidases in other cellular process (e.g., cell cycle arrest) that do not necessarily develop into an apoptotic process, please use the more general parent term GO:0097202. Examples of 'activation of cysteine-type endopeptidase activity involved in apoptotic process' are cytochrome c and Apaf1. When cytochrome c is released from mitochondria and forms a complex with Apaf1, they form a scaffolding platform in which the pro-caspase 9 is bound (the 'apoptosome'). The caspase is then cleaved and activated. Cytochrome c and Apaf1 are therefore involved in the conversion of the zymogen procaspase 9 to the active form of the caspase.\nThe reason for obsoletion is that this term represents a GO-CAM model.
obsolete commitment to apoptosis (GO:0006920)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: commitment to apoptosis
Comment: This term was made obsolete because more accurate terms were created.
cellular component disassembly involved in execution phase of apoptosis (GO:0006921)
Namespace: biological_process
Definition: The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
Synonyms: cellular component disassembly involved in apoptosis; cellular component disassembly involved in apoptotic process; disassembly of cell structures
obsolete cleavage of lamin involved in execution phase of apoptosis (GO:0006922)
Namespace: biological_process
Definition: OBSOLETE. The proteolytic degradation of lamins during apoptosis, leading to the irreversible breakdown of the nuclear lamina.
Synonyms: cleavage of lamin; cleavage of lamin involved in execution phase of apoptosis
Comment: This term was obsoleted because it refers to targets of effector proteins (caspases); the 'cleavage' process referred to in the term name is in fact the same molecular function represented by GO:0097200 'cysteine-type endopeptidase activity involved in execution phase of apoptosis'.
obsolete cleavage of cytoskeletal proteins involved in execution phase of apoptosis (GO:0006923)
Namespace: biological_process
Definition: OBSOLETE. The proteolytic degradation of cytoskeletal proteins that contributes to apoptosis, leading to the collapse of cytoskeletal structures.
Synonyms: apoptotic cleavage of cytoskeletal proteins; cleavage of cytoskeletal proteins involved in apoptosis; cleavage of cytoskeletal proteins involved in execution phase of apoptosis
Comment: This term was obsoleted because it refers to targets of effector proteins (caspases); the 'cleavage' process referred to in the term name is in fact the same molecular function represented by GO:0097200 'cysteine-type endopeptidase activity involved in execution phase of apoptosis'.
activation-induced cell death of T cells (GO:0006924)
Namespace: biological_process
Definition: A T cell apoptotic process that occurs towards the end of the expansion phase following the initial activation of mature T cells by antigen and is triggered by T cell receptor stimulation and signals transmitted via various surface-expressed members of the TNF receptor family such as Fas ligand, Fas, and TNF and the p55 and p75 TNF receptors.
Synonyms: activated T cell apoptosis; activation-induced cell death of T lymphocytes; activation-induced cell death of T-cells; activation-induced cell death of T-lymphocytes; AICD; antigen-driven apoptosis
inflammatory cell apoptotic process (GO:0006925)
Namespace: biological_process
Definition: Any apoptotic process in an inflammatory cell, any cell participating in the inflammatory response to a foreign substance e.g. neutrophil, macrophage.
Synonyms: apoptosis of inflammatory cells; inflammatory cell apoptosis; inflammatory cell programmed cell death by apoptosis; killing of inflammatory cells; programmed cell death of inflammatory cells by apoptosis; programmed cell death, inflammatory cells
obsolete virus-infected cell apoptotic process (GO:0006926)
Namespace: biological_process
Definition: OBSOLETE. Any apoptotic process in a cell infected with a virus.
Synonyms: apoptosis of virus-infected cells; killing virus-infected cells; programmed cell death of virus-infected cells by apoptosis; programmed cell death, virus-infected cells; virus-infected cell apoptosis; virus-infected cell apoptotic process; virus-infected cell programmed cell death by apoptosis
Comment: This term was made obsolete because the meaning of the term is ambiguous, as it's possibly conflating at least two scenarios: 1) the organism apoptoses its own cell because it detects it is infected with a virus; 2) the virus induces apoptosis so the cell is lysed and the virus disseminated. Please consider using viral process terms to annotate viral proteins. As for the cellular apoptotic process, this likely occurs via the same mechanisms described by existing apoptotic process terms, so please consider using those to annotate cellular proteins.
obsolete transformed cell apoptotic process (GO:0006927)
Namespace: biological_process
Definition: OBSOLETE. Any apoptotic process in a transformed cell, a cell that has undergone changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm.
Synonyms: apoptosis of transformed cells; killing transformed cells; programmed cell death of transformed cells by apoptosis; programmed cell death, transformed cells; transformed cell apoptosis; transformed cell programmed cell death by apoptosis
Comment: This term was made obsolete because it does not refer to a normal process.
substrate-dependent cell migration, cell extension (GO:0006930)
Namespace: biological_process
Definition: The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
Synonyms: substrate-bound cell migration, cell extension
substrate-dependent cell migration, cell attachment to substrate (GO:0006931)
Namespace: biological_process
Definition: The formation of adhesions that stabilize protrusions at the leading edge of a migrating cell; involves integrin activation, clustering, and the recruitment of structural and signaling components to nascent adhesions.
Synonyms: substrate-bound cell migration, cell attachment to substrate
substrate-dependent cell migration, cell contraction (GO:0006932)
Namespace: biological_process
Definition: The translocation of the cell body forward during cell migration, mediated by tractional force on its substrate and tension in the cortical cytoskeleton. Adhesions transmit propulsive forces and serve as traction points over which the cell moves.
Synonyms: substrate-bound cell migration, cell contraction
substrate-bound cell migration, adhesion receptor recycling (GO:0006934)
Namespace: biological_process
Definition: The directed movement of accumulated adhesion components such as integrins from the rear of a migrating cell toward the cell front, where they are available to form new protrusions and adhesions.
chemotaxis (GO:0006935)
Namespace: biological_process
Definition: The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
Synonyms: taxis in response to chemical stimulus
muscle contraction (GO:0006936)
Namespace: biological_process
Definition: A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
regulation of muscle contraction (GO:0006937)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of muscle contraction.
smooth muscle contraction (GO:0006939)
Namespace: biological_process
Definition: A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
Synonyms: visceral muscle contraction
regulation of smooth muscle contraction (GO:0006940)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of smooth muscle contraction.
striated muscle contraction (GO:0006941)
Namespace: biological_process
Definition: A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope.
Synonyms: sarcomeric muscle contraction
obsolete nuclear fusion during karyogamy (GO:0006945)
Namespace: biological_process
Definition: OBSOLETE. The fusion of two haploid nuclei to form a single diploid nucleus, as seen in the yeast mating process.
Synonyms: nuclear fusion during karyogamy
Comment: This term was made obsolete because it is redundant outside the context of Saccharomyces biology.
obsolete induction by virus of host cell-cell fusion (GO:0006948)
Namespace: biological_process
Definition: OBSOLETE. The process of syncytia-forming cell-cell fusion, caused by a virus.
Synonyms: induction by virus of cell-cell fusion in host; viral-induced cell-cell fusion; viral-induced host cell-cell fusion; viral-induced membrane fusion
Comment: This term was obsoleted because it represents the same process as positive regulation of syncytium formation by virus ; GO:0060141.
obsolete syncytium formation (GO:0006949)
Namespace: biological_process
Definition: OBSOLETE. The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
response to stress (GO:0006950)
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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Synonyms: response to abiotic stress; response to biotic stress
defense response (GO:0006952)
Namespace: biological_process
Definition: Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
Synonyms: antimicrobial peptide activity; defence response; defense/immunity protein activity; physiological defense response
acute-phase response (GO:0006953)
Namespace: biological_process
Definition: An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
inflammatory response (GO:0006954)
Namespace: biological_process
Definition: The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
Synonyms: inflammation
immune response (GO:0006955)
Namespace: biological_process
Definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
complement activation (GO:0006956)
Namespace: biological_process
Definition: Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
Synonyms: complement activity; complement cascade; complement response
complement activation, alternative pathway (GO:0006957)
Namespace: biological_process
Definition: Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
Synonyms: complement cascade, alternative pathway
complement activation, classical pathway (GO:0006958)
Namespace: biological_process
Definition: Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
Synonyms: complement cascade, classical pathway
humoral immune response (GO:0006959)
Namespace: biological_process
Definition: An immune response mediated through a body fluid.
male-specific antibacterial humoral response (GO:0006962)
Namespace: biological_process
Definition: An immune response against bacteria, specific to males and mediated through a body fluid.
positive regulation of antibacterial peptide biosynthetic process (GO:0006963)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate, or extent of antibacterial peptide biosynthesis.
Synonyms: activation of antibacterial peptide biosynthetic process; antibacterial peptide induction; antibacterial polypeptide induction; stimulation of antibacterial peptide biosynthetic process; up regulation of antibacterial peptide biosynthetic process; up-regulation of antibacterial peptide biosynthetic process; upregulation of antibacterial peptide biosynthetic process
positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria (GO:0006964)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate, or extent of biosynthesis of antibacterial peptides active against Gram-negative bacteria.
Synonyms: activation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria; anti-Gram-negative bacterial peptide induction; anti-Gram-negative bacterial polypeptide induction; stimulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria; up regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria; up-regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria; upregulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria
positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate, or extent of biosynthesis of antibacterial peptides active against Gram-positive bacteria.
Synonyms: activation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria; anti-Gram-positive bacterial peptide induction; anti-Gram-positive bacterial polypeptide induction; stimulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria; up regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria; up-regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria; upregulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria
positive regulation of antifungal peptide biosynthetic process (GO:0006967)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate, or extent of antifungal peptide biosynthesis.
Synonyms: activation of antifungal peptide biosynthetic process; antifungal peptide induction; antifungal polypeptide induction; stimulation of antifungal peptide biosynthetic process; up regulation of antifungal peptide biosynthetic process; up-regulation of antifungal peptide biosynthetic process; upregulation of antifungal peptide biosynthetic process
cellular defense response (GO:0006968)
Namespace: biological_process
Definition: A defense response that is mediated by cells.
Synonyms: cellular defence response; intracellular defence response; intracellular defense response
obsolete melanotic tumor response (GO:0006969)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: melanotic mass response; melanotic tumor response
Comment: This term was made obsolete because it was undefined and represented an abnormal process.
response to osmotic stress (GO:0006970)
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 stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
Synonyms: osmotic response; osmotic stress response
hypotonic response (GO:0006971)
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 detection of, or exposure to, a hypotonic environment, i.e. an environment with a lower concentration of solutes than the organism or cell.
Synonyms: hypo-osmotic response
hyperosmotic response (GO:0006972)
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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
Synonyms: HOG response; hypertonic response; response to hypertonicity
intracellular accumulation of glycerol (GO:0006973)
Namespace: biological_process
Definition: The accumulation of glycerol within a cell, for example by increased glycerol biosynthesis combined with decreased permeability of the cell membrane to glycerol, in response to the detection of a hyperosmotic environment.
DNA damage response (GO:0006974)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
Synonyms: cellular DNA damage response; cellular response to DNA damage stimulus; response to DNA damage stimulus; response to genotoxic stress
obsolete DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)
Namespace: biological_process
Definition: OBSOLETE. A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
Synonyms: positive regulation of cell cycle arrest by p53-mediated DNA damage response
Comment: The reason for obsoletion is that this term is about down stream effects, not the signaling pathway itself.
obsolete DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)
Namespace: biological_process
Definition: OBSOLETE. A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
Comment: The reason for obsoletion is that this term is about down stream effects, not the signaling pathway itself.
response to oxidative stress (GO:0006979)
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
obsolete activation of SoxR protein (GO:0006981)
Namespace: biological_process
Definition: OBSOLETE. The conversion of the SoxR transcription factor to its active (oxidized) form.
Comment: This term was made obsolete because it was too specific with respect to a single gene product.