LiteFold/GO huggingface dataset:
obsolete dissemination or transmission of symbiont from host (GO:0044007)
Namespace: biological_process
Definition: OBSOLETE. The movement of an organism from a host to another host or from a host to another place in the environment. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: dissemination or transmission of organism from host
Comment: This term was obsoleted because it did not represent a specific process, but represented the life cycle of a symbiont.
obsolete viral transmission by vector (GO:0044009)
Namespace: biological_process
Definition: OBSOLETE. The transfer of virions by means of an organism (often an insect or other animal) in order to create new infection.
Comment: This term was obsoleted because it did not represent a specific process, but represented the life cycle of a virus.
single-species biofilm formation (GO:0044010)
Namespace: biological_process
Definition: A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
Synonyms: auto-aggregation; bfp-dependent aggregation; bundle-forming fimbriae-dependent aggregation; bundle-forming pili-dependent aggregation; tfp-dependent aggregation; type IV pili-dependent aggregation
histone H2AK9 acetyltransferase activity (GO:0044012)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine (position 9) = CoA + histone H2A N6-acetyl-L-lysine (position 9).
Synonyms: histone acetylase activity (H2A-K9 specific); histone acetyltransferase activity (H2A-K9 specific); histone H2A-K9 acetyltransferase activity; histone lysine N-acetyltransferase activity (H2A-K9 specific)
Comment: Note that the residue position corresponds to the canonical human H2A2A histone (UniProtKB:Q6FI13); this residue is conserved across all eukaryotes. Corresponds to H2AK7 in yeast and in flies. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H2B acetyltransferase activity (GO:0044013)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine = CoA + histone H2B N6-acetyl-L-lysine.
Synonyms: H2B histone acetylase activity; H2B histone acetyltransferase activity; H2B histone lysine N-acetyltransferase activity
histone H2BK5 acetyltransferase activity (GO:0044014)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine (position 5) = CoA + histone H2B N6-acetyl-L-lysine (position 5).
Synonyms: histone acetylase activity (H2B-K5 specific); histone acetyltransferase activity (H2B-K5 specific); histone lysine N-acetyltransferase activity (H2B-K5 specific)
Comment: Note that the residue position corresponds to the canonical human H2B histone (UniProtKB:P62807); the N-terminus of histone H2B is divergent across eukaryotes; make sure that the paper clearly references the human protein for the position of this modification to use this term. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H2BK12 acetyltransferase activity (GO:0044015)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine (position 12) = CoA + histone H2B N6-acetyl-L-lysine (position 12).
Synonyms: histone acetylase activity (H2B-K12 specific); histone acetyltransferase activity (H2B-K12 specific); histone H2B-K12 acetyltransferase activity; histone lysine N-acetyltransferase activity (H2B-K12 specific)
Comment: Note that the residue position corresponds to the canonical human H2B histone (UniProtKB:P62807); the N-terminus of histone H2B is divergent across eukaryotes; make sure that the paper clearly references the human protein for the position of this modification to use this term. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K4 acetyltransferase activity (GO:0044016)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 4) = CoA + histone H3 N6-acetyl-L-lysine (position 4).
Synonyms: histone acetylase activity (H3-K4 specific); histone acetyltransferase activity (H3-K4 specific); histone H3-K4 acetyltransferase activity; histone lysine N-acetyltransferase activity (H3-K4 specific)
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K27 acetyltransferase activity (GO:0044017)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 27) = CoA + histone H3 N6-acetyl-L-lysine (position 27).
Synonyms: histone acetylase activity (H3-K27 specific); histone acetyltransferase activity (H3-K27 specific); histone H3-K27 acetyltransferase activity; histone lysine N-acetyltransferase activity (H3-K27 specific)
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K36 acetyltransferase activity (GO:0044018)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 36) = CoA + histone H3 N6-acetyl-L-lysine (position 36).
Synonyms: histone acetylase activity (H3-K36 specific); histone acetyltransferase activity (H3-K36 specific); histone H3-K36 acetyltransferase activity; histone lysine N-acetyltransferase activity (H3-K36 specific)
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
obsolete histone H3K72 acetyltransferase activity (GO:0044019)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 72) = CoA + histone H3 N6-acetyl-L-lysine (position 72).
Synonyms: histone acetylase activity (H3-K72 specific); histone acetyltransferase activity (H3-K72 specific); histone H3-K72 acetyltransferase activity; histone lysine N-acetyltransferase activity (H3-K72 specific)
Comment: This term was obsoleted because there is no evidence that this activity exists.
histone H4R3 methyltransferase activity (GO:0044020)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H4, producing histone H4R3me.
Synonyms: histone H4KR3 methylation; histone H4R3 arginine methylase activity; histone methylase activity (H4-R3 specific); histone methyltransferase activity (H4-R3 specific); histone-arginine N-methyltransferase activity (H4-R3 specific)
Comment: Note that the residue position corresponds to the canonical human H4 histone (UniProtKB:P02309); this residue is conserved across all eukaryotes. Note that the initiation methionine is cleaved, so the first residue is S1.
histone H3S28 kinase activity (GO:0044022)
Namespace: molecular_function
Definition: Catalysis of the reaction: histone H3-serine (position 28) + ATP = histone H3-phosphoserine (position 28) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 28 of histone H3.
Synonyms: histone kinase activity (H3-S28 specific); histone serine kinase activity (H3-S28 specific); histone-serine kinase activity (H3-S28 specific)
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes, except for S. pombe. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H4S1 kinase activity (GO:0044023)
Namespace: molecular_function
Definition: Catalysis of the reaction: histone H4-serine (position 1) + ATP = histone H4-phosphoserine (position 1) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 1 of histone H4.
Synonyms: histone kinase activity (H4-S1 specific); histone serine kinase activity (H4-S1 specific); histone-serine kinase activity (H4-S1 specific)
Comment: Note that the residue position corresponds to the canonical human H4 histone (UniProtKB:P02309); this residue is conserved across all eukaryotes, but is a Thr in Drosophila. Note that the initiation methionine is cleaved, so the first residue is S1.
histone H2AS1 kinase activity (GO:0044024)
Namespace: molecular_function
Definition: Catalysis of the reaction: histone H2A-serine (position 1) + ATP = histone H2A-phosphoserine (position 1) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 1 of histone H2A.
Synonyms: histone kinase activity (H2A-S1 specific); histone serine kinase activity (H2A-S1 specific); histone-serine kinase activity (H2A-S1 specific)
Comment: Note that the residue position corresponds to the canonical human H2A2A histone (UniProtKB:Q6FI13); this residue is conserved across all eukaryotes, but missing from Drosophila histone H2AV. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H2BS14 kinase activity (GO:0044025)
Namespace: molecular_function
Definition: Catalysis of the reaction: histone H2B-serine (position 14) + ATP = histone H2B-phosphoserine (position 14) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 14 of histone H2B.
Synonyms: histone kinase activity (H2B-S14 specific); histone serine kinase activity (H2B-S14 specific); histone-serine kinase activity (H2B-S14 specific)
Comment: Note that the residue position corresponds to the canonical human H2B histone (UniProtKB:P62807); the N-terminus of histone H2B is divergent across eukaryotes; make sure that the paper clearly references the human protein for the position of this modification to use this term. Residue 1 is the first residue following removal of the initiating Methionine (Met). Corresponds to Serine 10 in yeast (PMID:15652479). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
negative regulation of gene expression via chromosomal CpG island methylation (GO:0044027)
Namespace: biological_process
Definition: An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide associated with the transcription start site of genes.
Synonyms: DNA hypermethylation of CG island; DNA hypermethylation of CpG island; epigenetic regulation of gene expression via CpG island hypermethylation; hypermethylation of CpG island; maintenance of DNA methylation; negative regulation of gene expression via chromosomal CG dinucleotide methylation; negative regulation of gene expression via chromosomal CpG dinucleotide methylation; negative regulation of gene expression via chromosomal DNA cytosine methylation; negative regulation of gene expression via CpG island hypermethylation; negative regulation of gene expression via CpG island methylation
obsolete DNA hypomethylation (GO:0044028)
Namespace: biological_process
Definition: OBSOLETE. An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA.
Comment: The reason for obsoletion is that this is a readout.
positive regulation of gene expression via chromosomal CpG island demethylation (GO:0044029)
Namespace: biological_process
Definition: An epigenetic gene regulation mechanism that positively regulates gene expression by demethylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
Synonyms: DNA demethylation; DNA hypomethylation of CpG island; hypomethylation of CpG island; positive regulation of gene expression via chromosomal CpG dinucleotide demethylation
obsolete regulation of DNA methylation (GO:0044030)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
Comment: This term was obsoleted because it represents regulation of a molecular function.
obsolete modification by symbiont of host protein by phosphorylation (GO:0044031)
Namespace: biological_process
Definition: OBSOLETE. The process in which an organism adds a phosphate group to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it represents a molecular function.
obsolete modulation by symbiont of indole acetic acid levels in host (GO:0044032)
Namespace: biological_process
Definition: OBSOLETE. The alteration by an organism of the levels of indole acetic acid in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: modulation by symbiont of auxin levels in host; modulation by symbiont of IAA levels in host
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism metabolic process (GO:0044033)
Namespace: biological_process
Definition: OBSOLETE. A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism.
Synonyms: multi-organism metabolism; multi-organismal metabolic process; multi-organismal metabolism
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism biosynthetic process (GO:0044034)
Namespace: biological_process
Definition: OBSOLETE. A biosynthetic process - chemical reactions and pathways resulting in the formation of substances - which involves more than one organism.
Synonyms: multi-organism biosynthesis; multi-organismal biosynthesis; multi-organismal biosynthetic process
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism catabolic process (GO:0044035)
Namespace: biological_process
Definition: OBSOLETE. A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves more than one organism.
Synonyms: multi-organism catabolism; multi-organismal catabolic process; multi-organismal catabolism
Comment: This term was obsoleted because there is no evidence that this process exists.
cell wall macromolecule metabolic process (GO:0044036)
Namespace: biological_process
Definition: The chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
Synonyms: cellular cell wall macromolecule metabolic process; cellular cell wall macromolecule metabolism
cell wall macromolecule biosynthetic process (GO:0044038)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall.
Synonyms: cell wall macromolecule anabolism; cell wall macromolecule biosynthesis; cell wall macromolecule biosynthetic process at cellular level; cell wall macromolecule synthesis; cellular cell wall macromolecule biosynthetic process
obsolete multi-organism carbohydrate metabolic process (GO:0044040)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, that involve more than one organism.
Synonyms: main pathways of carbohydrate metabolic process; main pathways of carbohydrate metabolism; multi-organism carbohydrate metabolism
Comment: This term was obsoleted because there is no evidence that this process exists.
obsolete multi-organism carbohydrate catabolic process (GO:0044041)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, involving more than one organism.
Synonyms: multi-organism carbohydrate breakdown; multi-organism carbohydrate catabolism; multi-organism carbohydrate degradation
Comment: This term was obsoleted because there is no evidence that this process exists.
glucan metabolic process (GO:0044042)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
Synonyms: glucan metabolism
obsolete multi-organism glucan metabolic process (GO:0044043)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, involving more than one organism.
Synonyms: multi-organism glucan metabolism
Comment: This term was obsoleted because there is no evidence it exists.
obsolete interaction with host via substance in symbiont surface (GO:0044044)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance on the surface of the other (symbiont) organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: The reason for obsoletion is that these terms conflate a process and the mechanism of secretion of the compound mediating the process.
obsolete interaction with host via substance in symbiont cell outer membrane (GO:0044045)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance in the symbiont cell outer membrane - a lipid bilayer that forms the outermost layer of the symbiont cell envelope. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: The reason for obsoletion is that these terms conflate a process and the mechanism of secretion of the compound mediating the process.
obsolete interaction with host via substance released outside of symbiont (GO:0044046)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance that is released by the other organism. This includes substances that are released via pathogen cell lysis.
Synonyms: interaction with host via substance released outside of symbiont cells
Comment: This term was obsoleted because it conflates a process and the mechanism of secretion of the gene product mediating the process.
obsolete interaction with host via protein secreted by type I secretion system (GO:0044047)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance secreted by the other (symbiont) organism via a type I secretion system. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it conflated the process in which a gene product is involved with the secretion system by which it reaches its target.
obsolete interaction with host via protein secreted by type V secretion system (GO:0044048)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance secreted by the other (symbiont) organism via a type V secretion system. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it conflated the process in which a gene product is involved with the secretion system by which it reaches its target.
obsolete interaction with host via protein secreted by type VI secretion system (GO:0044049)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance secreted by the other (symbiont) organism via a type VI secretion system. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Comment: This term was obsoleted because it conflated the process in which a gene product is involved with the secretion system by which it reaches its target.
obsolete interaction with host via substance released by sporangium lysis (GO:0044050)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance released via rupture of symbiont sporangia, structures producing and containing spores. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: interaction with host via substance released by lysis of symbiont sporangium; interaction with host via substance released by sporangia lysis
Comment: This term was obsoleted because it conflates a process and the mechanism of secretion of the gene product mediating the process.
obsolete interaction with host via substance released by symbiont cytolysis (GO:0044051)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance released via cytolysis of symbiont cells. Cytolysis is the rupture of cell membranes and the loss of cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: interaction with host via substance released by cytolysis of symbiont
Comment: This term was obsoleted because it conflates a process and the mechanism of secretion of the gene product mediating the process.
obsolete interaction with host via substance released by membrane budding (GO:0044052)
Namespace: biological_process
Definition: OBSOLETE. An interaction with the host organism mediated by a substance released via symbiont membrane budding, the evagination of a membrane resulting in formation of a vesicle.
Synonyms: interaction with host via substance released by symbiont membrane budding
Comment: This term was obsoleted because it conflates a process and the mechanism of secretion of the gene product mediating the process.
translocation of peptides or proteins into host cell cytoplasm (GO:0044053)
Namespace: biological_process
Definition: The directed movement of peptides or proteins produced by a symbiont organism to a location within the host cell cytoplasm.
Synonyms: translocation of symbiont peptides or proteins into host cell cytoplasm; transport of peptides or proteins into host cell cytoplasm