LiteFold/GO huggingface dataset:
obsolete GSI anchor biosynthetic process (GO:0042082)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of a glycosylsphingolipidinositol (GSI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The sphingolipid group is linked, via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via a ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GSI anchors have variants on this canonical linkage.
Synonyms: GPI/GSI anchor biosynthesis; GPI/GSI anchor biosynthetic process; GSI anchor anabolism; GSI anchor biosynthesis; GSI anchor formation; GSI anchor synthesis
Comment: This term was obsoleted because it represents a molecular function.
5,10-methylenetetrahydrofolate-dependent methyltransferase activity (GO:0042083)
Namespace: molecular_function
Definition: Catalysis of the transfer of a methyl group to an acceptor molecule; dependent on the presence of 5,10-methylenetetrahydrofolate.
obsolete 5-methyltetrahydrofolate-dependent methyltransferase activity (GO:0042084)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the transfer of a methyl group to an acceptor molecule; dependent on the presence of 5-methyltetrahydrofolate.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
obsolete 5-methyltetrahydropteroyltri-L-glutamate-dependent methyltransferase activity (GO:0042085)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the transfer of a methyl group to an acceptor molecule; dependent on the presence of 5-methyltetrahydropteroyltri-L-glutamate.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
T-helper 1 type immune response (GO:0042088)
Namespace: biological_process
Definition: An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
Synonyms: Th1 immune response
type 2 immune response (GO:0042092)
Namespace: biological_process
Definition: An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects.
Synonyms: T-helper 2 type immune response; Th2 immune response
T-helper cell differentiation (GO:0042093)
Namespace: biological_process
Definition: The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell.
Synonyms: helper T cell differentiation; T-helper cell development
obsolete alpha-beta T cell receptor activity (GO:0042096)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: alpha-beta T cell receptor activity
Comment: This term was made obsolete because it describes a receptor type, and not an activity.
T cell proliferation (GO:0042098)
Namespace: biological_process
Definition: The expansion of a T cell population by cell division. Follows T cell activation.
Synonyms: T lymphocyte proliferation; T-cell proliferation; T-lymphocyte proliferation
obsolete gamma-delta T cell receptor activity (GO:0042099)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: gamma-delta T cell receptor activity
Comment: This term was made obsolete because it describes a receptor type, and not an activity.
B cell proliferation (GO:0042100)
Namespace: biological_process
Definition: The expansion of a B cell population by cell division. Follows B cell activation.
Synonyms: B lymphocyte proliferation; B-cell proliferation; B-lymphocyte proliferation
T cell receptor complex (GO:0042101)
Namespace: cellular_component
Definition: A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
Synonyms: T lymphocyte receptor complex; T-cell receptor complex; T-lymphocyte receptor complex; TCR; TCR complex
positive regulation of T cell homeostatic proliferation (GO:0042103)
Namespace: biological_process
Definition: Any process that activates or increases the rate or extent of resting T cell proliferation.
Synonyms: activation of T cell homeostatic proliferation; positive regulation of resting T cell proliferation; positive regulation of T lymphocyte homeostatic proliferation; positive regulation of T-cell homeostatic proliferation; positive regulation of T-lymphocyte homeostatic proliferation; stimulation of T cell homeostatic proliferation; up regulation of T cell homeostatic proliferation; up-regulation of T cell homeostatic proliferation; upregulation of T cell homeostatic proliferation
positive regulation of activated T cell proliferation (GO:0042104)
Namespace: biological_process
Definition: Any process that activates or increases the rate or extent of activated T cell proliferation.
Synonyms: activation of activated T cell proliferation; positive regulation of activated T lymphocyte proliferation; positive regulation of activated T-cell proliferation; positive regulation of activated T-lymphocyte proliferation; stimulation of activated T cell proliferation; up regulation of activated T cell proliferation; up-regulation of activated T cell proliferation; upregulation of activated T cell proliferation
alpha-beta T cell receptor complex (GO:0042105)
Namespace: cellular_component
Definition: A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
Synonyms: alpha-beta T lymphocyte receptor complex; alpha-beta T-cell receptor complex; alpha-beta T-lymphocyte receptor complex; alpha-beta TCR complex
gamma-delta T cell receptor complex (GO:0042106)
Namespace: cellular_component
Definition: A T cell receptor complex in which the TCR heterodimer comprises gamma and delta chains, associated with the CD3 complex; recognizes antigen directly, without a requirement for processing and presentation by an MHC protein.
Synonyms: gamma-delta T lymphocyte receptor complex; gamma-delta T-cell receptor complex; gamma-delta T-lymphocyte receptor complex; gamma-delta TCR complex
T cell activation (GO:0042110)
Namespace: biological_process
Definition: The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
Synonyms: T lymphocyte activation; T-cell activation; T-lymphocyte activation
B cell activation (GO:0042113)
Namespace: biological_process
Definition: The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
Synonyms: B lymphocyte activation; B-cell activation; B-lymphocyte activation
macrophage activation (GO:0042116)
Namespace: biological_process
Definition: A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
Synonyms: macrophage polarization
monocyte activation (GO:0042117)
Namespace: biological_process
Definition: The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
endothelial cell activation (GO:0042118)
Namespace: biological_process
Definition: The change in morphology and behavior of an endothelial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
neutrophil activation (GO:0042119)
Namespace: biological_process
Definition: The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
obsolete alginic acid metabolic process (GO:0042120)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
Synonyms: alginate metabolic process; alginate metabolism; alginic acid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
alginic acid catabolic process (GO:0042122)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
Synonyms: alginate catabolic process; alginate catabolism; alginic acid breakdown; alginic acid catabolism; alginic acid degradation
glucanosyltransferase activity (GO:0042123)
Namespace: molecular_function
Definition: Catalysis of the splitting and linkage of glucan molecules, resulting in glucan chain elongation.
1,3-beta-glucanosyltransferase activity (GO:0042124)
Namespace: molecular_function
Definition: Catalysis of the splitting and linkage of (1->3)-beta-D-glucan molecules, resulting in (1->3)-beta-D-glucan chain elongation.
obsolete protein galactosylation (GO:0042125)
Namespace: biological_process
Definition: OBSOLETE. The addition of a galactose molecule to a protein amino acid.
Synonyms: protein amino acid galactosylation
Comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
nitrate metabolic process (GO:0042126)
Namespace: biological_process
Definition: The chemical reactions and pathways involving nitrates, inorganic or organic salts and esters of nitric acid.
Synonyms: nitrate metabolism
regulation of cell population proliferation (GO:0042127)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of cell proliferation.
Synonyms: regulation of cell proliferation
regulation of T cell proliferation (GO:0042129)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of T cell proliferation.
Synonyms: regulation of T lymphocyte proliferation; regulation of T-cell proliferation; regulation of T-lymphocyte proliferation
negative regulation of T cell proliferation (GO:0042130)
Namespace: biological_process
Definition: Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
Synonyms: down regulation of T cell proliferation; down-regulation of T cell proliferation; downregulation of T cell proliferation; inhibition of T cell proliferation; negative regulation of T lymphocyte proliferation; negative regulation of T-cell proliferation; negative regulation of T-lymphocyte proliferation
fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)
Namespace: molecular_function
Definition: Catalysis of the reaction: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate.
Synonyms: D-fructose 1,6-diphosphatase activity; D-fructose-1,6-bisphosphate 1-phosphohydrolase activity; D-fructose-1,6-bisphosphate phosphatase activity; FBPase activity; fructose 1,6-bisphosphatase activity; fructose 1,6-bisphosphate phosphatase activity; fructose 1,6-diphosphatase activity; fructose 1,6-diphosphate phosphatase activity; fructose bisphosphate phosphatase activity; fructose diphosphatase activity; fructose diphosphate phosphatase activity; fructose-1,6-bisphosphatase activity; fructose-bisphosphatase activity; hexose bisphosphatase activity; hexose diphosphatase activity; hexosediphosphatase activity
obsolete neurotransmitter metabolic process (GO:0042133)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
Synonyms: neurotransmitter metabolism
Comment: The reason for obsoletion is that 'neurotransmitter' is unnecessary grouping in the metabolism branch of the ontology, and it creates true path violations.
rRNA primary transcript binding (GO:0042134)
Namespace: molecular_function
Definition: Binding to an unprocessed ribosomal RNA transcript.
Synonyms: pre-rRNA binding
obsolete neurotransmitter catabolic process (GO:0042135)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
Synonyms: neurotransmitter breakdown; neurotransmitter catabolism; neurotransmitter degradation
Comment: The reason for obsoletion is that 'neurotransmitter' is unnecessary grouping in the metabolism branch of the ontology, and it creates true path violations.
obsolete neurotransmitter biosynthetic process (GO:0042136)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
Synonyms: neurotransmitter anabolism; neurotransmitter biosynthesis; neurotransmitter biosynthesis and storage; neurotransmitter biosynthetic process and storage; neurotransmitter formation; neurotransmitter synthesis
Comment: The reason for obsoletion is that 'neurotransmitter' is unnecessary grouping in the metabolism branch of the ontology, and it creates true path violations.
obsolete sequestering of neurotransmitter (GO:0042137)
Namespace: biological_process
Definition: OBSOLETE. The process of binding or confining a neurotransmitter such that it is separated from other components of a biological system.
Synonyms: neurotransmitter biosynthesis and storage; neurotransmitter biosynthetic process and storage; neurotransmitter retention; neurotransmitter sequestration; neurotransmitter storage; retention of neurotransmitter; sequestration of neurotransmitter; storage of neurotransmitter
Comment: The reason for obsoletion is that this term represent a molecular function, not biological process.
meiotic DNA double-strand break formation (GO:0042138)
Namespace: biological_process
Definition: The cell cycle process in which double-strand breaks are generated at defined hotspots throughout the genome during meiosis I. This results in the initiation of meiotic recombination.
early meiotic recombination nodule assembly (GO:0042139)
Namespace: biological_process
Definition: During meiosis, the aggregation, arrangement and bonding together of strand exchange proteins (recombinases) to form small, electron dense structures in association with meiotic chromosomes during leptotene and zygotene.
late meiotic recombination nodule assembly (GO:0042140)
Namespace: biological_process
Definition: During meiosis, the aggregation, arrangement and bonding together of strand exchange proteins (recombinases) to form small, electron dense structures in association with meiotic chromosomes during pachytene. Involved in the catalysis crossing over.
obsolete mating pheromone exporter (GO:0042141)
Namespace: molecular_function
Definition: OBSOLETE. Exports diffusible peptide signals that are responsible for binding to other cells and triggering a series of responses to facilitate mating.
Synonyms: mating pheromone exporter
Comment: This term was made obsolete because it is too gene product specific.
obsolete heavy metal chelation (GO:0042142)
Namespace: biological_process
Definition: OBSOLETE. The strong but reversible binding of a heavy metal ion by a larger molecule such as protein.
Synonyms: heavy metal chelation
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
vacuole fusion, non-autophagic (GO:0042144)
Namespace: biological_process
Definition: The fusion of two vacuole membranes to form a single vacuole.
Synonyms: homotypic vacuole fusion; homotypic vacuole fusion (non-autophagic); homotypic vacuole fusion, non-autophagic; vacuole fusion (non-autophagic)
retrograde transport, endosome to Golgi (GO:0042147)
Namespace: biological_process
Definition: The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
Synonyms: retrograde (endosome to Golgi) transport
DNA strand invasion (GO:0042148)
Namespace: biological_process
Definition: The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules.
Synonyms: D-loop biosynthesis; D-loop formation; displacement loop biosynthesis; displacement loop formation; Rad51-mediated strand invasion; strand invasion
cellular response to glucose starvation (GO:0042149)
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 deprivation of glucose.
plasmid recombination (GO:0042150)
Namespace: biological_process
Definition: A process of DNA recombination occurring within a plasmid or between plasmids and other plasmids or DNA molecules.
nematocyst (GO:0042151)
Namespace: cellular_component
Definition: An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus.
Synonyms: cnidocyst
RNA-mediated DNA recombination (GO:0042152)
Namespace: biological_process
Definition: The reverse transcription of an RNA molecule followed by recombination between the resultant cDNA and its homologous chromosomal allele.
obsolete RPTP-like protein binding (GO:0042153)
Namespace: molecular_function
Definition: OBSOLETE. Binding to proteins with similar structure/function to receptor protein tyrosine phosphatases.
Synonyms: receptor protein tyrosine phosphatase-like protein binding; RPTP-like protein binding
Comment: This term was made obsolete because it represents binding to an individual protein.
obsolete zinc-mediated transcriptional activator activity (GO:0042156)
Namespace: molecular_function
Definition: OBSOLETE. Initiates or upregulates transcription in the presence of zinc.
Synonyms: zinc-mediated transcriptional activator activity
Comment: This term was obsoleted because it is defined as a Process term, i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
lipoprotein metabolic process (GO:0042157)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
Synonyms: lipoprotein metabolism
lipoprotein biosynthetic process (GO:0042158)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
Synonyms: lipoprotein anabolism; lipoprotein biosynthesis; lipoprotein formation; lipoprotein synthesis
lipoprotein oxidation (GO:0042161)
Namespace: biological_process
Definition: The modification of a lipoprotein by oxidation of one or more amino acids or the lipid group.
telomeric repeat DNA binding (GO:0042162)
Namespace: molecular_function
Definition: Any molecular function by which a gene product interacts selectively and non-covalently with a telomeric DNA repeat sequence.
Synonyms: telomere binding; telomeric repeat binding
interleukin-12 beta subunit binding (GO:0042163)
Namespace: molecular_function
Definition: Binding to the beta subunit of interleukin-12.
Synonyms: CLMFp40 binding; IL-12B binding; IL-12p40 binding; NKSFp40 binding
interleukin-12 alpha subunit binding (GO:0042164)
Namespace: molecular_function
Definition: Binding to the alpha subunit of interleukin-12.
Synonyms: CLMFp35 binding; IL-12A binding; IL-12p35 binding; NKSFp35 binding
obsolete neurotransmitter binding (GO:0042165)
Namespace: molecular_function
Definition: OBSOLETE. Binding to a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
Comment: The reason for obsoletion is that 'neurotransmitter' is unnecessary grouping in the metabolism branch of the ontology, and it creates true path violations.
acetylcholine binding (GO:0042166)
Namespace: molecular_function
Definition: Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.
heme catabolic process (GO:0042167)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
Synonyms: haem catabolic process; haem catabolism; heme breakdown; heme catabolism; heme degradation
heme metabolic process (GO:0042168)
Namespace: biological_process
Definition: The chemical reactions and pathways involving heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
Synonyms: haem metabolic process; haem metabolism; heme metabolism
SH2 domain binding (GO:0042169)
Namespace: molecular_function
Definition: Binding to a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
plastid membrane (GO:0042170)
Namespace: cellular_component
Definition: Any lipid bilayer that surrounds a plastid or is part of the plastid envelope. Primary plastids (in plants, green algae, red algae, and glaucophytes) are surrounded by two membranes; complex plastids derived from secondary endosymbiosis are surrounded by three or four membranes.