LiteFold/GO huggingface dataset:
obsolete DNA catabolic process, endonucleolytic (GO:0000737)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
Synonyms: DNA breakdown, endonucleolytic; DNA degradation, endonucleolytic; endonucleolytic degradation of DNA; endonucleolytic DNA catabolism
Comment: The reason is that these terms represent Molecular functions in the Biological Process ontology.
obsolete DNA catabolic process, exonucleolytic (GO:0000738)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
Synonyms: DNA breakdown, exonucleolytic; DNA degradation, exonucleolytic; exonucleolytic degradation of DNA
Comment: The reason is that these terms represent Molecular functions in the Biological Process ontology.
obsolete DNA strand annealing activity (GO:0000739)
Namespace: molecular_function
Definition: OBSOLETE. Facilitates the base-pairing of complementary single-stranded DNA.
Synonyms: DNA strand annealing activity
Comment: This term was made obsolete because it describes a process and not an activity.
nuclear membrane fusion (GO:0000740)
Namespace: biological_process
Definition: The joining of 2 or more lipid bilayer membranes that surround the nucleus.
karyogamy (GO:0000741)
Namespace: biological_process
Definition: The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei.
Synonyms: nuclear fusion; nuclear fusion during karyogamy
karyogamy involved in conjugation with cellular fusion (GO:0000742)
Namespace: biological_process
Definition: During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after cytogamy.
Synonyms: karyogamy during conjugation with cellular fusion
nuclear migration involved in conjugation with cellular fusion (GO:0000743)
Namespace: biological_process
Definition: The microtubule-based movement of nuclei towards one another as a prelude to karyogamy in organisms undergoing conjugation with cellular fusion.
Synonyms: nuclear congression; nuclear migration during conjugation with cellular fusion
obsolete karyogamy involved in conjugation with mutual genetic exchange (GO:0000744)
Namespace: biological_process
Definition: OBSOLETE. During sexual reproduction, the creation of a single nucleus from two nuclei as a result of fusing the nuclear envelopes that surround each nuclei. This takes place following the mutual exchange of one of the two nuclei produced by the mitosis that follows the second meiotic nuclear division. This occurs in ciliated protozoans such as Tetrahymena.
Synonyms: karyogamy involved in conjugation without cellular fusion
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
obsolete nuclear migration involved in conjugation with mutual genetic exchange (GO:0000745)
Namespace: biological_process
Definition: OBSOLETE. The net movement of nuclei towards one another, leading to the bilateral transfer of genetic material in organisms undergoing conjugation without cellular fusion.
Synonyms: nuclear exchange during conjugation without cellular fusion; nuclear migration involved in conjugation without cellular fusion
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
obsolete conjugation (GO:0000746)
Namespace: biological_process
Definition: OBSOLETE. The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
Comment: This term was obsoleted because it is an unnecessary grouping class.
conjugation with cellular fusion (GO:0000747)
Namespace: biological_process
Definition: A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
Synonyms: cell fusion; mating
conjugation with mutual genetic exchange (GO:0000748)
Namespace: biological_process
Definition: A conjugation process that results in the mutual exchange and union of only genetic information between compatible mating types. Conjugation without cellular fusion requires direct cellular contact between the organisms without plasma membrane fusion. The organisms involved in conjugation without cellular fusion separate after nuclear exchange.
Synonyms: conjugation without cellular fusion
response to pheromone triggering conjugation with cellular fusion (GO:0000749)
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 pheromone stimulus that positively regulates the process of conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.
Synonyms: response to pheromone during conjugation with cellular fusion
pheromone-dependent signal transduction involved in conjugation with cellular fusion (GO:0000750)
Namespace: biological_process
Definition: A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.
Synonyms: transduction of mating signal
agglutination involved in conjugation with cellular fusion (GO:0000752)
Namespace: biological_process
Definition: The aggregation or adhesion of compatible mating types via complementary cell-cell interactions during conjugation with cellular fusion of a unicellular organism. An example of this process is agglutination in Saccharomyces cerevisiae.
Synonyms: agglutination; cell-cell adhesion during conjugation with cellular fusion; cell-cell adhesion during mating
cell morphogenesis involved in conjugation with cellular fusion (GO:0000753)
Namespace: biological_process
Definition: The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation cellular fusion.
Synonyms: shmoo orientation; shmooing
obsolete adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion (GO:0000754)
Namespace: biological_process
Definition: OBSOLETE. In organisms that undergo conjugation with cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses. An example of this is the adaptation to pheromone during conjugation with cellular fusion in Saccharomyces cerevisiae.
Synonyms: adaptation of signalling pathway by response to pheromone involved in conjugation with cellular fusion; adaptation to pheromone during conjugation with cellular fusion; desensitization to pheromone during conjugation with cellular fusion
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
cytogamy (GO:0000755)
Namespace: biological_process
Definition: A reproductive process in a single-celled organism in which the cytoplasm of two mating cells fuse, resulting in the formation of a single cell containing the combined cellular contents.
Synonyms: zygote formation
Comment: Cytogamy follows cell recognition and mating projection formation (when present) and precedes or accompanies nuclear fusion (karyogamy).
response to pheromone regulating conjugation with mutual genetic exchange (GO:0000756)
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 pheromone stimulus regulating the process of conjugation without cellular fusion.
Synonyms: response to pheromone triggering conjugation without cellular fusion
obsolete signal transduction involved in regulation of conjugation with mutual genetic exchange (GO:0000757)
Namespace: biological_process
Definition: OBSOLETE. A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation without cellular fusion.
Synonyms: signal transduction involved in conjugation without cellular fusion
Comment: This term was obsoleted because its label and definitions were not clear. It had never been used for annotation.
obsolete agglutination involved in conjugation with mutual genetic exchange (GO:0000758)
Namespace: biological_process
Definition: OBSOLETE. The aggregation or adhesion of compatible mating types via complementary cell-cell interactions during conjugation without cellular fusion of a unicellular organism.
Synonyms: agglutination involved in conjugation without cellular fusion; sexual flocculation
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
obsolete cell morphogenesis involved in conjugation with mutual genetic exchange (GO:0000759)
Namespace: biological_process
Definition: OBSOLETE. The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation without cellular fusion.
Synonyms: cellular morphogenesis involved in conjugation without cellular fusion
Comment: This term was obsoleted because there is no evidence that this process exists.
adaptation to pheromone regulating conjugation with mutual genetic exchange (GO:0000760)
Namespace: biological_process
Definition: In organisms that undergo conjugation without cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses.
Synonyms: adaptation to pheromone involved conjugation without cellular fusion; desensitization to pheromone during conjugation without cellular fusion
conjugant formation (GO:0000761)
Namespace: biological_process
Definition: During conjugation without cellular fusion, the process that results in pairing complementary mating types. Localized morphological, cytological, and cytoskeletal changes connect the mating types without cytoplasmic mixing.
pheromone-induced unidirectional conjugation (GO:0000762)
Namespace: biological_process
Definition: Unidirectional transfer of genetic information triggered by to a pheromone signal.
obsolete cell morphogenesis involved in unidirectional conjugation (GO:0000763)
Namespace: biological_process
Definition: OBSOLETE. The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo unidirectional conjugation.
Synonyms: cell morphogenesis involved in unidirectional conjugation
Comment: This term was made obsolete because unidirectional conjugation occurs only in prokaryotes, which do not undergo morphogenetic changes associated with conjugation. In short, the process described by this term does not occur.
obsolete cellular morphogenesis involved in pheromone-induced unidirectional conjugation (GO:0000764)
Namespace: biological_process
Definition: OBSOLETE. The change in form (cell shape and size) that contributes to sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo pheromone-induced unidirectional conjugation.
Synonyms: cellular morphogenesis during pheromone-induced unidirectional; cellular morphogenesis involved in pheromone-induced unidirectional conjugation
Comment: This term was made obsolete because unidirectional conjugation occurs only in prokaryotes, which do not undergo morphogenetic changes associated with conjugation. In short, the process described by this term does not occur.
response to pheromone regulating pheromone-induced unidirectional conjugation (GO:0000765)
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 pheromone stimulus that regulates the process of pheromone-induced unidirectional conjugation.
Synonyms: response to pheromone during pheromone-induced unidirectional
obsolete cell morphogenesis involved in conjugation (GO:0000767)
Namespace: biological_process
Definition: OBSOLETE. The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types.
Comment: This term was obsoleted because it is an unnecessary grouping class.
syncytium formation by cell-cell fusion (GO:0000768)
Namespace: biological_process
Definition: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
Synonyms: syncytium formation by plasma membrane fusion
syncytium formation by mitosis without cytokinesis (GO:0000769)
Namespace: biological_process
Definition: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by one or more rounds of nuclear division without cytokinesis.
Synonyms: syncytium formation by mitosis without cell division
peptide pheromone export (GO:0000770)
Namespace: biological_process
Definition: The directed movement of a peptide pheromone out of a cell by a secretion or export pathway used solely for the export of peptide pheromones.
Synonyms: a-factor export
obsolete agglutination involved in conjugation (GO:0000771)
Namespace: biological_process
Definition: OBSOLETE. The aggregation or adhesion of compatible mating types via complementary cell-cell interactions prior to the formation of irreversible cellular contacts during conjugation.
Comment: This term was obsoleted because it is an unnecessary grouping class.
mating pheromone activity (GO:0000772)
Namespace: molecular_function
Definition: The activity of binding to and activating specific cell surface receptors, thereby inducing a behavioral or physiological response(s) from a responding organism or cell that leads to the transfer or union of genetic material between organisms or cells. The mating pheromone can either be retained on the cell surface or secreted.
phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + phosphatidyl-N-methylethanolamine = S-adenosyl-L-homocysteine + phosphatidyl-N-dimethylethanolamine. Also catalyzes the transfer of a further methylgroup, producing phosphatidylcholine.
Synonyms: methyltransferase II; phosphatidyl-N-methylethanolamine methyltransferase activity; phosphatidyl-N-monomethylethanolamine methyltransferase activity; phosphatidylethanolamine methyltransferase I; phosphatidylmonomethylethanolamine methyltransferase activity; phospholipid methyltransferase activity; PLMT; S-adenosyl-L-methionine:phosphatidyl-N-methylethanolamine N-methyltransferase activity
adenyl-nucleotide exchange factor activity (GO:0000774)
Namespace: molecular_function
Definition: Binds to and stimulates the hydrolysis and exchange of adenyl nucleotides by other proteins.
chromosome, centromeric region (GO:0000775)
Namespace: cellular_component
Definition: The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
Synonyms: centromere; centromere complex; chromosome, centric region; chromosome, pericentric region
Comment: Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'.
kinetochore (GO:0000776)
Namespace: cellular_component
Definition: A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
Synonyms: condensed chromosome kinetochore; condensed nuclear chromosome kinetochore; NMS complex
Comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore.
condensed chromosome, centromeric region (GO:0000779)
Namespace: cellular_component
Definition: The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
Synonyms: condensed chromosome, centric region; condensed chromosome, centromere; condensed chromosome, pericentric region; condensed nuclear chromosome, centromeric region
Comment: Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex.
chromosome, telomeric region (GO:0000781)
Namespace: cellular_component
Definition: The end of a linear chromosome, required for the integrity and maintenance of the end. A chromosome telomere usually includes a region of telomerase-encoded repeats the length of which rarely exceeds 20 bp each and that permits the formation of a telomeric loop (T-loop). The telomeric repeat region is usually preceded by a sub-telomeric region that is gene-poor but rich in repetitive elements. Some telomeres only consist of the latter part (for eg. D. melanogaster telomeres).
Synonyms: nuclear chromosome, telomere; nuclear chromosome, telomeric region; telomere
Comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex.
nuclear telomere cap complex (GO:0000783)
Namespace: cellular_component
Definition: A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
Comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome.
chromatin (GO:0000785)
Namespace: cellular_component
Definition: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
Synonyms: chromosome scaffold; cytoplasmic chromatin; nuclear chromatin
Comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
nucleosome (GO:0000786)
Namespace: cellular_component
Definition: A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
Synonyms: cytoplasmic nucleosome; nuclear nucleosome
euchromatin (GO:0000791)
Namespace: cellular_component
Definition: A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation.
Synonyms: nuclear euchromatin; transcriptionally active chromatin
heterochromatin (GO:0000792)
Namespace: cellular_component
Definition: A compact and highly condensed form of chromatin that is refractory to transcription.
Synonyms: nuclear heterochromatin; transcriptionally inactive chromatin; transcriptionally silent chromatin
condensed chromosome (GO:0000793)
Namespace: cellular_component
Definition: A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
Synonyms: cytoplasmic mitotic chromosome; metaphase chromosome; mitotic chromosome
Comment: Note that this term can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes an 'open mitosis' in which the nuclear envelope breaks down during mitosis.
condensed nuclear chromosome (GO:0000794)
Namespace: cellular_component
Definition: A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
Synonyms: meiotic chromosome; nuclear mitotic chromosome
Comment: Note that this term and its children can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes a 'closed mitosis' in which the nuclear envelope does not break down during mitosis and for gene products that localize to a meiotic chromosome.
synaptonemal complex (GO:0000795)
Namespace: cellular_component
Definition: A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
condensin complex (GO:0000796)
Namespace: cellular_component
Definition: A multisubunit protein complex that plays a central role in chromosome condensation in meiosis and mitosis.
Synonyms: 13S condensin complex; 8S condensin complex; condensin core heterodimer; condensin I complex; nuclear condensin complex; SMC complex; Smc2-Smc4 complex
lateral element (GO:0000800)
Namespace: cellular_component
Definition: A proteinaceous core found between sister chromatids during meiotic prophase.
Synonyms: axial element
Comment: In species that have a synaptonemal complex, the lateral elements are part of this complex. S.pombe is an example of a species that lacks a (canonical) synaptonemal complex, but still has lateral elements.
central element (GO:0000801)
Namespace: cellular_component
Definition: A structural unit of the synaptonemal complex found between the lateral elements.
transverse filament (GO:0000802)
Namespace: cellular_component
Definition: A structural unit of the synaptonemal complex that spans the regions between the lateral elements and connects them.
sex chromosome (GO:0000803)
Namespace: cellular_component
Definition: A chromosome involved in sex determination.
W chromosome (GO:0000804)
Namespace: cellular_component
Definition: The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females.
X chromosome (GO:0000805)
Namespace: cellular_component
Definition: The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.
Y chromosome (GO:0000806)
Namespace: cellular_component
Definition: The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males.
Z chromosome (GO:0000807)
Namespace: cellular_component
Definition: The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females.
cytoplasmic origin of replication recognition complex (GO:0000809)
Namespace: cellular_component
Definition: A multisubunit complex that is located at the replication origins of a chromosome in the cytoplasm.
Synonyms: cytoplasmic ORC; prokaryotic ORC