gocentral
commented
15 years ago All done, I think; usual call for typo checks and such applies. New terms:
GO:0070227 lymphocyte apoptosis GO:0070228 regulation of lymphocyte apoptosis GO:0070229 negative regulation of lymphocyte apoptosis GO:0070230 positive regulation of lymphocyte apoptosis GO:0070231 T cell apoptosis GO:0070232 regulation of T cell apoptosis GO:0070233 negative regulation of T cell apoptosis GO:0070234 positive regulation of T cell apoptosis GO:0070235 regulation of activation-induced cell death of T cells GO:0070236 negative regulation of activation-induced cell death of T cells GO:0070237 positive regulation of activation-induced cell death of T cells GO:0070238 activated T cell autonomous cell death GO:0070239 regulation of activated T cell autonomous cell death GO:0070240 negative regulation of activated T cell autonomous cell death GO:0070241 positive regulation of activated T cell autonomous cell death GO:0070242 thymocyte apoptosis GO:0070243 regulation of thymocyte apoptosis GO:0070244 negative regulation of thymocyte apoptosis GO:0070245 positive regulation of thymocyte apoptosis GO:0070246 natural killer cell apoptosis GO:0070247 regulation of natural killer cell apoptosis GO:0070248 negative regulation of natural killer cell apoptosis GO:0070249 positive regulation of natural killer cell apoptosis
Original comment by: mah11
I would like a few terms added, including regulation terms, covering processes of lymphocyte apoptosis.
The new term tree is as follows, and the explanations and term definitions follow.
apoptosis ; GO:0006195 --% lymphocyte apoptosis ; GO:NewTer1 ----R regulation of lymphocyte apoptosis ; GO:NewTer2 ------% negative regulation of lymphocyte apoptosis ; GO:NewTer3 ------% positive regulation of lymphocyte apoptosis ; GO:NewTer4 ----% B cell apoptosis ; GO:0001783 [keep existing children] ----% T cell apoptosis ; GO:NewTerm5 ------R regulation of T cell apoptosis ; GO:NewTer6 --------% negative regulation of T cell apoptosis ; GO:NewTer7 --------% positive regulation of T cell apoptosis ; GO:NewTer8 ------% activation-induced cell death of T cells ; GO:0006924 [renamed] --------R regulation of activation-induced cell death of T cells ; GO:NewTer7 ----------% negative regulation of activation-induced cell death of T cells ; GO:NewTer8 ----------% positive regulation of activation-induced cell death of T cells ; GO:NewTer9 ------% activated T cell autonomous cell death ; GO:NewTe10 --------R regulation of activated T cell autonomous cell death ; GO:NewTe11 ----------% negative regulation of activated T cell autonomous cell death ; GO:NewTe12 ----------% positive regulation of activated T cell autonomous cell death ; GO:NewTe13 ------% thymocyte apoptosis ; GO:NewTe14 --------R regulation of thymocyte apoptosis ; GO:NewTe15 ----------% negative regulation of thymocyte apoptosis ; GO:NewTe16 ----------% positive regulation of thymocyte apoptosis ; GO:NewTe17 ----% natural killer cell apoptosis ; GO:NewTe18 ------R regulation of natural killer cell apoptosis ; GO:NewTe19 --------% negative regulation of natural killer cell apoptosis ; GO:NewTe20 --------% positive regulation of natural killer cell apoptosis ; GO:NewTe21
Whoever implements this should make the appropriate relationships between the regulation terms and the parental terms as well as higher level regulation terms. These I omitted for brevity. Note that the 'regulaton of B cell apoptosis' terms need to be rehomed to the 'regulation of lymphocyte apoptosis' terms, rather than being children of 'regulation of apoptosis' terms.
[Term] id: NewTer1 name: lymphocyte apoptosis def: "The process of apopotosis in a lymphocyte." [GOC:add, ISBN:0781765196] comment: Note that a lymphocyte is a cell of the B cell, T cell, or natural killer cell lineage (CL:0000542). is_a: GO:0006195 ! apoptosis
New terms 2-4 are standard regulation terms. Please reference to [GOC:add, ISBN:0781765196].
[Term] id: NewTer5 name: T cell apoptosis def: "The process of apopotosis in a T cell." [GOC:add, ISBN:0781765196] synonym: "T-cell apoptosis" EXACT synonym: "T lymphocyte apoptosis" EXACT synonym: "T-lymphocyte apoptosis" EXACT synonym: "programmed cell death of T cells by apoptosis" EXACT is_a: GO:NewTer1 ! lymphocyte apoptosis
New terms 6-8 are standard regulation terms. Please include the T cell synonyms for these terms and reference the terms to [GOC:add, ISBN:0781765196].
The following term is being renamed to match the literature more closely. The original name is a bit ambiguous. I would also like to remove many of the synonyms, which are redundant.
[Term] id: GO:0006924 name: activation-induced cell death of T cells def: "A type of T cell apoptosis 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, Fas ligand, and TNF and the p55 and p75 TNF receptors." [GOC:add, ISBN:0781765196, PMID:12752672, PMID:12414721] synonym: "AICD" BROAD synonym: "antigen-driven apoptosis" BROAD synonym: "activated T cell apoptosis" BROAD synonym: "activation-induced cell death of T-cells" EXACT synonym: "activation-induced cell death of T lymphocytes" EXACT synonym: "activation-induced cell death of T-lymphocytes" EXACT is_a: GO:NewTer5 ! T cell apoptosis relationship: part_of GO:0043029 ! T cell homeostasis
New terms 7-9 are standard regulation terms. Please include the analogous synonyms for these terms to match GO:0006924 and reference the terms to [GOC:add, ISBN:0781765196, PMID:12752672, PMID:12414721].
[Term] id: GO:NewTe10 name: activated T cell autonomous cell death def: "A type of T cell apoptosis that occurs towards the end of the expansion phase following the initial activation of mature T cells by antigen via the accumulation of pro-apoptotic gene products and decrease in anti-apoptotic gene products." [GOC:add, ISBN:0781765196] synonym: "ACAD" BROAD synonym: "activated cell autonomous cell death" BROAD synonym: "activated T cell apoptosis" BROAD synonym: "activated T-cell autonomous cell death" EXACT synonym: "activated T lymphocyte autonomous cell death" EXACT synonym: "activated T-lymphocyte autonomous cell death" EXACT is_a: GO:NewTer5 ! T cell apoptosis relationship: part_of GO:0043029 ! T cell homeostasis
New terms 11-13 are standard regulation terms. Please include the analogous synonyms for these terms to match GO:NewTe10 and reference the terms to [GOC:add, ISBN:0781765196].
[Term] id: GO:NewTe14 name: thymocyte apoptosis def: "The process of apoptosis in a thymocyte." [GOC:add, ISBN:0781765196] synonym: "immature T cell apoptosis" RELATED comment: "Note that a thymocyte is an immature T cell located in the thymus (CL:0000893). is_a: GO:NewTer5 ! T cell apoptosis relationship: part_of GO:0043029 ! T cell homeostasis
New terms 15-17 are standard regulation terms. Please include the analogous synonyms for these terms to match GO:NewTe14 and reference the terms to [GOC:add, ISBN:0781765196].
[Term] id: GO:NewTe18 name: natural killer cell apoptosis def: "The process of apoptosis in a natural killer cell." [GOC:add, PMID:15728472] synonym: "NK cell apoptosis" EXACT comment: "Note that a thymocyte is an immature T cell located in the thymus (CL:0000893). is_a: GO:NewTer1 ! lymphocyte apoptosis
New terms 19-21 are standard regulation terms. Please include the analogous synonyms for these terms to match GO:NewTe15 and reference the terms to [GOC:add, PMID:15728472].
Thanks,
Alex
Reported by: addiehl
Original Ticket: "geneontology/ontology-requests/5700":https://sourceforge.net/p/geneontology/ontology-requests/5700