!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! * SELFIE: a logical def that references itself. obviously wrong, but is often indicative of a bad smell - e.g. a weird synonym. ACTION: low priority, can be ignore * OBVIOUS the label clearly indicates the logical def should be made ACTION: make the logical def, or, in some cases, rexamine the label * OBVIOUS, IMMUNE as above, but also an immune process. The label may be misleading. ACTION: in all cases EITHER make the logical def OR change the label, as it is necessarily wrong * NON-OBVIOUS Derived by exact synonym rather than label. ACTION: The exact syns should be checked. * CHECK-NESTING An equivalence axiom obviously needs to be made, but there may be two possibilities due to an ambiguous parse. Think: lego diagrams ACTION: Make an equivalence axiom !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !! SELFIE [Term] id: GO:0000910 ! cytokinesis intersection_of: GO:0000910 ! cytokinesis intersection_of: part_of GO:0007049 ! cell cycle !! NON-OBVIOUS [Term] id: GO:0000916 ! actomyosin contractile ring contraction intersection_of: GO:0036213 ! contractile ring contraction intersection_of: part_of GO:0000910 ! cytokinesis !! SELFIE [Term] id: GO:0000920 ! cytokinetic cell separation intersection_of: GO:0000920 ! cytokinetic cell separation intersection_of: part_of GO:0000910 ! cytokinesis !! OBVIOUS *challenging, parentage has cellular vs. not cellular issues* [Term] id: GO:0001316 ! age-dependent response to reactive oxygen species involved in replicative cell aging intersection_of: GO:0001315 ! age-dependent response to reactive oxygen species intersection_of: part_of GO:0001302 ! replicative cell aging !! OBVIOUS, IMMUNE [Term] id: GO:0002205 ! somatic hypermutation of immunoglobulin genes involved in immune response intersection_of: GO:0016446 ! somatic hypermutation of immunoglobulin genes intersection_of: part_of GO:0006955 ! immune response !! OBVIOUS, IMMUNE [Term] id: GO:0002207 ! gene conversion of immunoglobulin genes involved in immune response intersection_of: GO:0002206 ! gene conversion of immunoglobulin genes intersection_of: part_of GO:0006955 ! immune response !! OBVIOUS, IMMUNE [Term] id: GO:0002208 ! somatic diversification of immunoglobulins involved in immune response intersection_of: GO:0016445 ! somatic diversification of immunoglobulins intersection_of: part_of GO:0006955 ! immune response !! OBVIOUS *DONE* [Term] id: GO:0007305 ! vitelline membrane formation involved in chorion-containing eggshell formation intersection_of: GO:0030704 ! vitelline membrane formation intersection_of: part_of GO:0007304 ! chorion-containing eggshell formation !! NON-OBVIOUS [Term] id: GO:0008979 ! prophage integrase activity intersection_of: GO:0008907 ! integrase activity intersection_of: part_of GO:0075713 ! establishment of integrated proviral latency !! OBVIOUS *DONE* [Term] id: GO:0010790 ! meiotic sister chromatid cohesion involved in meiosis II intersection_of: GO:0051177 ! meiotic sister chromatid cohesion intersection_of: part_of GO:0007135 ! meiosis II !! NON-OBVIOUS [Term] id: GO:0031566 ! actomyosin contractile ring maintenance intersection_of: GO:0036212 ! contractile ring maintenance intersection_of: part_of GO:0000910 ! cytokinesis !! CHECK-NESTING *DONE* [Term] id: GO:0031657 ! regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle intersection_of: GO:0000079 ! regulation of cyclin-dependent protein serine/threonine kinase activity intersection_of: part_of GO:0000082 ! G1/S transition of mitotic cell cycle !! CHECK-NESTING *DONE* [Term] id: GO:0031658 ! negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle intersection_of: GO:0045736 ! negative regulation of cyclin-dependent protein serine/threonine kinase activity intersection_of: part_of GO:0000082 ! G1/S transition of mitotic cell cycle !! CHECK-NESTING *DONE* [Term] id: GO:0031659 ! positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle intersection_of: GO:0045737 ! positive regulation of cyclin-dependent protein serine/threonine kinase activity intersection_of: part_of GO:0000082 ! G1/S transition of mitotic cell cycle !! SELFIE !! comes from this syn: !! synonym: "positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response" EXACT [GOC:dph, GOC:tb] !! this is kind of cute and logically correct but we have to question at what point something is really a synonym !! What we have here is a hidden GCI, it would be good to indicate this explicitly somehow [Term] id: GO:0032933 ! SREBP signaling pathway intersection_of: GO:0032933 ! SREBP signaling pathway intersection_of: part_of GO:0006991 ! response to sterol depletion !! SELFIE !! hidden-GCI type [Term] id: GO:0035105 ! sterol regulatory element binding protein import into nucleus intersection_of: GO:0035105 ! sterol regulatory element binding protein import into nucleus intersection_of: part_of GO:0006991 ! response to sterol depletion !! NON-OBVIOUS [Term] id: GO:0039638 ! lipopolysaccharide-mediated virion attachment to host cell intersection_of: GO:0001530 ! lipopolysaccharide binding intersection_of: part_of VZ:956 ! Viral attachment to host cell !! NON-OBVIOUS [Term] id: GO:0039700 ! fusion of viral membrane with host outer nuclear membrane intersection_of: GO:0039700 ! fusion of viral membrane with host outer nuclear membrane intersection_of: part_of GO:0046802 ! exit of virus from host cell nucleus by nuclear egress !! OBVIOUS *DONE* [Term] id: GO:0043027 ! cysteine-type endopeptidase inhibitor activity involved in apoptotic process intersection_of: GO:0004869 ! cysteine-type endopeptidase inhibitor activity intersection_of: part_of GO:0006915 ! apoptotic process !! MULTI-ORGANISM [Term] id: GO:0051801 ! cytolysis in other organism involved in symbiotic interaction intersection_of: GO:0051715 ! cytolysis in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0051818 ! disruption of cells of other organism involved in symbiotic interaction intersection_of: GO:0044364 ! disruption of cells of other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052180 ! negative regulation of peptidase activity in other organism involved in symbiotic interaction intersection_of: GO:0035940 ! negative regulation of peptidase activity in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052204 ! negative regulation of molecular function in other organism involved in symbiotic interaction intersection_of: GO:0044362 ! negative regulation of molecular function in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052205 ! modulation of molecular function in other organism involved in symbiotic interaction intersection_of: GO:0044359 ! modulation of molecular function in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052248 ! modulation of programmed cell death in other organism involved in symbiotic interaction intersection_of: GO:0044531 ! modulation of programmed cell death in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052250 ! modulation of signal transduction in other organism involved in symbiotic interaction intersection_of: GO:0044501 ! modulation of signal transduction in other organism intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! MULTI-ORGANISM [Term] id: GO:0052261 ! suppression of defense response of other organism involved in symbiotic interaction intersection_of: GO:0052261 ! suppression of defense response of other organism involved in symbiotic interaction intersection_of: part_of GO:0044403 ! symbiosis, encompassing mutualism through parasitism !! NON-OBVIOUS !! this is kind of cute... !! we're encoding a hidden GCI here in the exact synonym !! synonym: "synaptic transmission involved in urination" EXACT [] !! but should this be an exact synonym? !! Are there not other synaptic transmission events in urination? !! there's bladder muscles doing one thing, other muscles doing other things, !! synaptic events upstream, synaptic transmission involved in aiming the flow.... [Term] id: GO:0060085 ! smooth muscle relaxation of the bladder outlet intersection_of: GO:0007268 ! synaptic transmission intersection_of: part_of GO:0060073 ! micturition !! OBVIOUS [Term] id: GO:0061226 ! proximal/distal pattern formation involved in mesonephric nephron development intersection_of: GO:0009954 ! proximal/distal pattern formation intersection_of: part_of GO:0061215 ! mesonephric nephron development !! OBVIOUS [Term] id: GO:0061239 ! mesenchymal stem cell differentiation involved in mesonephric nephron morphogenesis intersection_of: GO:0072497 ! mesenchymal stem cell differentiation intersection_of: part_of GO:0061228 ! mesonephric nephron morphogenesis !! NON-OBVIOUS [Term] id: GO:0061345 ! planar cell polarity pathway involved in cardiac muscle cell fate commitment intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0060923 ! cardiac muscle cell fate commitment !! NON-OBVIOUS [Term] id: GO:0061346 ! planar cell polarity pathway involved in heart morphogenesis intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0003007 ! heart morphogenesis !! NON-OBVIOUS [Term] id: GO:0061348 ! planar cell polarity pathway involved in ventricular septum morphogenesis intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0060412 ! ventricular septum morphogenesis !! NON-OBVIOUS [Term] id: GO:0061349 ! planar cell polarity pathway involved in cardiac right atrium morphogenesis intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0003213 ! cardiac right atrium morphogenesis !! NON-OBVIOUS [Term] id: GO:0061350 ! planar cell polarity pathway involved in cardiac muscle tissue morphogenesis intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0055008 ! cardiac muscle tissue morphogenesis !! NON-OBVIOUS [Term] id: GO:0061354 ! planar cell polarity pathway involved in pericardium morphogenesis intersection_of: GO:0060071 ! Wnt signaling pathway, planar cell polarity pathway intersection_of: part_of GO:0003344 ! pericardium morphogenesis !! CHECK-NESTING [Term] id: GO:0072042 ! regulation of mesenchymal stem cell proliferation involved in nephron morphogenesis intersection_of: GO:1902460 ! regulation of mesenchymal stem cell proliferation intersection_of: part_of GO:0072028 ! nephron morphogenesis !! OBVIOUS [Term] id: GO:0072090 ! mesenchymal stem cell proliferation involved in nephron morphogenesis intersection_of: GO:0097168 ! mesenchymal stem cell proliferation intersection_of: part_of GO:0072028 ! nephron morphogenesis !! CHECK-NESTING [Term] id: GO:0086039 ! calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential intersection_of: GO:0005388 ! calcium-transporting ATPase activity intersection_of: part_of GO:0086036 ! regulation of cardiac muscle cell membrane potential !! OBVIOUS [Term] id: GO:0086040 ! sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential intersection_of: GO:0015385 ! sodium:proton antiporter activity intersection_of: part_of GO:0086036 ! regulation of cardiac muscle cell membrane potential !! SELFIE !! OK, something is fishy here. The parse came from one of the many auto-generated TG synonyms. !! But what's a TG templated term doing without an equivalence axiom? !! If it was removed for some reason, then really the corresponding synonyms should also be removed [Term] id: GO:1902178 ! fibroblast growth factor receptor apoptotic signaling pathway intersection_of: GO:0008543 ! fibroblast growth factor receptor signaling pathway intersection_of: part_of GO:0006915 ! apoptotic process !! OBVIOUS [Term] id: GO:1990001 ! inhibition of cysteine-type endopeptidase activity involved in apoptotic process intersection_of: GO:0097340 ! inhibition of cysteine-type endopeptidase activity intersection_of: part_of GO:0006915 ! apoptotic process