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From: Chris Mungall <cmungall@us...>  20080424 18:39:13

Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8prcvs3.sourceforge.net:/tmp/cvsserv19046 Modified Files: mammalian_phenotype_xp.obo Log Message: Georges latest edits. Fixes lots of problems Index: mammalian_phenotype_xp.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype_xp.obo,v retrieving revision 1.66 retrieving revision 1.67 diff C2 d r1.66 r1.67 *** mammalian_phenotype_xp.obo 24 Apr 2008 18:25:14 0000 1.66  mammalian_phenotype_xp.obo 24 Apr 2008 18:39:17 0000 1.67 *************** *** 4,8 **** defaultnamespace: mammalian_phenotype_xp idmapping: during OBO_REL:exists_during ! idmapping: towards OBOL:towards idmapping: qualifier has_qualifier idmapping: output has_output  4,8  defaultnamespace: mammalian_phenotype_xp idmapping: during OBO_REL:exists_during ! idmapping: towards OBO_REL:towards idmapping: qualifier has_qualifier idmapping: output has_output *************** *** 242,245 ****  242,255  [Term] + id: MP:0000060 ! delayed bone ossification + intersection_of: PATO:0000502 ! delayed + intersection_of: inheres_in GO:0001503 ! ossification + + [Term] + id: MP:0000054 ! delayed ear emergence + intersection_of: PATO:0000502 ! delayed + intersection_of: inheres_in GO:0060186 ! outer ear emergence + + [Term] id: MP:0000061 ! fragile skeleton intersection_of: PATO:0001362 ! fragile *************** *** 2715,2719 **** intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000738 ! leukocyte [Term]  2725,2729  intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000473 ! defensive cell [Term] *************** *** 3018,3025 **** intersection_of: OBO_REL:towards MA:0000189 ! hippocampal formation ! [Term] ! id: MP:0000811 ! hippocampal neuron degeneration ! intersection_of: PATO:0000639 ! degenerate ! intersection_of: inheres_in CL:0000598 ! pyramidal cell [Term]  3028,3035  intersection_of: OBO_REL:towards MA:0000189 ! hippocampal formation ! ![Term] ! !id: MP:0000811 ! hippocampal neuron degeneration ! !intersection_of: PATO:0000639 ! degenerate ! !intersection_of: inheres_in CL:0000598 ! pyramidal cell [Term] *************** *** 7932,7936 **** id: MP:0002415 ! abnormal neutrophil differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000775 ! neutrophil [Term]  7942,7947  id: MP:0002415 ! abnormal neutrophil differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0030223 ! neutrophil differentiation ! [Term] *************** *** 8018,8025 **** intersection_of: inheres_in CL:0000546 ! Thelper 2 cell ! [Term] ! id: MP:0002435 ! abnormal effector T cell morphology ! intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000084 ! T cell [Term]  8029,8036  intersection_of: inheres_in CL:0000546 ! Thelper 2 cell ! ![Term] request effector T cell ! !id: MP:0002435 ! abnormal effector T cell morphology ! !intersection_of: PATO:0000460 ! abnormal ! !intersection_of: inheres_in CL:0000084 ! T cell [Term] *************** *** 8043,8047 **** id: MP:0002440 ! abnormal memory B cell morphology intersection_of: PATO:0000460 ! abnormal  intersection_of: OBO_REL:towards GO:0048468 ! cell development intersection_of: inheres_in CL:0000787 ! memory B cell  8054,8057  *************** *** 8060,8064 **** id: MP:0002443 ! abnormal eosinophil differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000771 ! eosinophil [Term]  8070,8074  id: MP:0002443 ! abnormal eosinophil differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in _:eosinophil_cell_differentiation [Term] *************** *** 8069,8075 **** [Term] ! id: MP:0002445 ! abnormal mononuclear leukocyte morphology/development intersection_of: PATO:0000051 ! morphology ! intersection_of: inheres_in CL:0000576 ! monocyte intersection_of: qualifier PATO:0000460 ! abnormal  8079,8085  [Term] ! id: MP:0002445 ! abnormal mononuclear leukocyte differentiation intersection_of: PATO:0000051 ! morphology ! intersection_of: inheres_in _:mononuclear_cell_differentiation intersection_of: qualifier PATO:0000460 ! abnormal *************** *** 8087,8096 **** [Term]  id: MP:0005460 ! abnormal immune cell development  intersection_of: PATO:0000460 ! abnormal  intersection_of: OBO_REL:towards GO:0048468 ! cell development  intersection_of: inheres_in CL:0000738 ! leukocyte   [Term] id: MP:0002450 ! abnormal lymph organ development intersection_of: PATO:0000460 ! abnormal  8097,8100  *************** *** 9531,9534 ****  9535,9539  id: MP:0002872 ! polycythemia intersection_of: PATO:0000420 ! increased number + intersection_of: has_quality PATO:0001869 ! pathological intersection_of: inheres_in CL:0000081 ! blood cell *************** *** 12695,12699 **** intersection_of: PATO:0001662 ! fragility intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000233 ! platelet [Term]  12700,12704  intersection_of: PATO:0001662 ! fragility intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000232 ! erythrocyte [Term] *************** *** 15996,16001 **** intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0032421 ! stereocilium bundle ! intersection_of: part_of CL:0000601 ! outer hair cell [Term]  16001,16005  intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:outer_hair_cell_stereocilia_bundle [Term] *************** *** 16003,16008 **** intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0032421 ! stereocilium bundle ! intersection_of: part_of CL:0000589 ! inner hair cell [Term]  16007,16011  intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:inner_hair_cell_stereocilia_bundle [Term] *************** *** 16064,16099 **** intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0032421 ! stereocilium bundle ! intersection_of: part_of CL:0000609 ! vestibular hair cell [Term] id: MP:0004516 ! fused vestibular hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium ! intersection_of: inheres_in CL:0000609 ! vestibular hair cell [Term] id: MP:0004517 ! decreased vestibular hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000609 ! vestibular hair cell [Term] id: MP:0004518 ! absent vestibular hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in CL:0000609 ! vestibular hair cell ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium [Term] id: MP:0004519 ! thin vestibular hair cell stereocilia intersection_of: PATO:0000592 ! decreased thickness ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000609 ! vestibular hair cell [Term] id: MP:0004520 ! short vestibular hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000609 ! vestibular hair cell [Term]  16067,16096  intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia_bundle [Term] id: MP:0004516 ! fused vestibular hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia [Term] id: MP:0004517 ! decreased vestibular hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia [Term] id: MP:0004518 ! absent vestibular hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia [Term] id: MP:0004519 ! thin vestibular hair cell stereocilia intersection_of: PATO:0000592 ! decreased thickness ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia [Term] id: MP:0004520 ! short vestibular hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in _:vestibular_hair_cell_stereocilia [Term] *************** *** 16101,16106 **** intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0032421 ! stereocilium bundle ! intersection_of: part_of CL:0000202 ! auditory hair cell  16098,16102  intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:cochlear_hair_cell_stereocilia_bundle *************** *** 16116,16145 **** intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000202 ! auditory hair cell ! intersection_of: OBO_REL:towards GO:0032421 ! stereocilium bundle [Term] id: MP:0004523 ! decreased cochlear hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium ! intersection_of: inheres_in CL:0000202 ! auditory hair cell [Term] id: MP:0004524 ! short cochlear hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000202 ! auditory hair cell [Term] id: MP:0004525 ! thin cochlear hair cell stereocilia intersection_of: PATO:0000592 ! decreased thickness ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000202 ! auditory hair cell [Term] id: MP:0004526 ! absent cochlear hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: part_of CL:0000202 ! auditory hair cell ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium [Term]  16112,16136  intersection_of: PATO:0000137 ! orientation intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:cochlear_hair_cell_stereocilia_bundle [Term] id: MP:0004523 ! decreased cochlear hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: OBO_REL:towards _:cochlear_hair_cell_stereocilia [Term] id: MP:0004524 ! short cochlear hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in _:cochlear_hair_cell_stereocilia [Term] id: MP:0004525 ! thin cochlear hair cell stereocilia intersection_of: PATO:0000592 ! decreased thickness ! intersection_of: inheres_in _:cochlear_hair_cell_stereocilia [Term] id: MP:0004526 ! absent cochlear hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in _:cochlear_hair_cell_stereocilia [Term] *************** *** 16158,16181 **** id: MP:0004528 ! fused outer hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium ! intersection_of: inheres_in CL:0000601 ! outer hair cell [Term] id: MP:0004529 ! decreased outer hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000601 ! outer hair cell [Term] id: MP:0004530 ! absent outer hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in CL:0000601 ! outer hair cell ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium [Term] id: MP:0004531 ! short outer hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000601 ! outer hair cell [Term]  16149,16168  id: MP:0004528 ! fused outer hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: inheres_in _:outer_hair_cell_stereocilia [Term] id: MP:0004529 ! decreased outer hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in _:outer_hair_cell_stereocilia [Term] id: MP:0004530 ! absent outer hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in _:outer_hair_cell_stereocilia [Term] id: MP:0004531 ! short outer hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in _:outer_hair_cell_stereocilia [Term] *************** *** 16183,16212 **** intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in GO:0032421 ! stereocilium bundle ! intersection_of: part_of CL:0000589 ! inner hair cell [Term] id: MP:0004533 ! fused inner hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium ! intersection_of: inheres_in CL:0000589 ! inner hair cell [Term] id: MP:0004534 ! decreased inner hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000589 ! inner hair cell [Term] id: MP:0004535 ! absent inner hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in CL:0000589 ! inner hair cell ! intersection_of: OBO_REL:towards GO:0032420 ! stereocilium [Term] id: MP:0004536 ! short inner hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in GO:0032420 ! stereocilium ! intersection_of: part_of CL:0000589 ! inner hair cell [Term]  16170,16194  intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:inner_hair_cell_stereocilia_bundle [Term] id: MP:0004533 ! fused inner hair cell stereocilia intersection_of: PATO:0000642 ! fused ! intersection_of: inheres_in _:inner_hair_cell_stereocilia [Term] id: MP:0004534 ! decreased inner hair cell stereocilia number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in _:inner_hair_cell_stereocilia [Term] id: MP:0004535 ! absent inner hair cell stereocilia intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in _:inner_hair_cell_stereocilia [Term] id: MP:0004536 ! short inner hair cell stereocilia intersection_of: PATO:0000569 ! decreased height ! intersection_of: inheres_in _:inner_hair_cell_stereocilia [Term] *************** *** 19085,19089 **** intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000437 ! follicle stimulating hormone secreting cell [Term]  19067,19071  intersection_of: PATO:0000051 ! morphology intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000173 ! pancreatic D cell [Term] *************** *** 20065,20069 **** id: MP:0005462 ! abnormal mast cell differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000097 ! mast cell [Term]  20047,20051  id: MP:0005462 ! abnormal mast cell differentiation intersection_of: PATO:0000460 ! abnormal ! intersection_of: inheres_in _:mast_cell_differentiation [Term] *************** *** 20940,20944 **** ! PATO:0001803 phototoxic [DEF: "Rendering the skin susceptible to damage by light."] ! MP:0005653 phototoxicity [DEF: "condition caused by overexposure to UV light or from the combination of exposure to specific wavelengths and a phototoxic substance"] ! ! it seems phototoxicity is actually a sensitivity towards UV light that is exacerbated by some substance? [Term] id: MP:0005653 ! phototoxicity  20922,20926  ! PATO:0001803 phototoxic [DEF: "Rendering the skin susceptible to damage by light."] ! MP:0005653 phototoxicity [DEF: "condition caused by overexposure to UV light or from the combination of exposure to specific wavelengths and a phototoxic substance"] ! ! it seems phototoxicity is actually a sensitivity OBO_REL:towards UV light that is exacerbated by some substance? [Term] id: MP:0005653 ! phototoxicity *************** *** 23703,23714 **** id: MP:0008434 ! small somatotroph cell nucelus intersection_of: PATO:0000587 ! decreased size ! intersection_of: inheres_in GO:0005634 ! nucleus ! intersection_of: part_of CL:0000295 ! somatotropin secreting cell [Term] id: MP:0008435 ! large somatotroph cell nucleus intersection_of: PATO:0000586 ! increased size ! intersection_of: inheres_in GO:0005634 ! nucleus ! intersection_of: part_of CL:0000295 ! somatotropin secreting cell [Term]  23685,23694  id: MP:0008434 ! small somatotroph cell nucelus intersection_of: PATO:0000587 ! decreased size ! intersection_of: inheres_in _:somatotropin secreting cell_nucleus [Term] id: MP:0008435 ! large somatotroph cell nucleus intersection_of: PATO:0000586 ! increased size ! intersection_of: inheres_in _:somatotropin secreting cell_nucleus [Term] *************** *** 23749,23753 **** id: MP:0008452 ! increased number of retinal rod cells intersection_of: PATO:0000420 ! increased number ! intersection_of: inheres_in CL:0000287 ! eye photoreceptor cell [Term]  23729,23733  id: MP:0008452 ! increased number of retinal rod cells intersection_of: PATO:0000420 ! increased number ! intersection_of: inheres_in CL:0000604 ! retinal rod cell [Term] *************** *** 23968,23972 **** intersection_of: PATO:0001557 ! lacking physical parts intersection_of: inheres_in MA:0002711 ! immune system ! intersection_of: OBO_REL:towards CL:0000819 ! B1 B cell [Term]  23948,23952  intersection_of: PATO:0001557 ! lacking physical parts intersection_of: inheres_in MA:0002711 ! immune system ! intersection_of: OBO_REL:towards CL:0000821 ! B1b B cell [Term] *************** *** 23997,24001 **** intersection_of: PATO:0001509 ! functionality intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000787 ! memory B cell [Term]  23977,23981  intersection_of: PATO:0001509 ! functionality intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000845 ! marginal zone B cell [Term] *************** *** 24039,24047 **** intersection_of: part_of EMAP:11310 ! TS26,footplate ! [Term] ! id: MP:0008138 ! absent podocyte foot process ! intersection_of: PATO:0001557 ! lacking physical parts ! intersection_of: inheres_in EMAP:11310 ! TS26,footplate ! intersection_of: OBO_REL:towards CL:0000653 ! podocyte [Term]  24019,24027  intersection_of: part_of EMAP:11310 ! TS26,footplate ! ![Term] request podocyte  TODO ! !id: MP:0008138 ! absent podocyte foot process ! !intersection_of: PATO:0001557 ! lacking physical parts ! !intersection_of: inheres_in EMAP:11310 ! TS26,footplate ! !intersection_of: OBO_REL:towards CL:0000653 ! podocyte [Term] *************** *** 24161,24178 **** intersection_of: PATO:0000053 ! count intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in CL:0000624 ! CD4positive, alphabeta T cell ! intersection_of: inheres_in CL:0000625 ! CD8positive, alphabeta T cell [Term] id: MP:0008082 ! increased singlepositive T cell number intersection_of: PATO:0000420 ! increased number ! intersection_of: inheres_in CL:0000624 ! CD4positive, alphabeta T cell ! intersection_of: inheres_in CL:0000625 ! CD8positive, alphabeta T cell [Term] id: MP:0008083 ! decreased singlepositive T cell number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in CL:0000624 ! CD4positive, alphabeta T cell ! intersection_of: inheres_in CL:0000625 ! CD8positive, alphabeta T cell [Term]  24141,24155  intersection_of: PATO:0000053 ! count intersection_of: qualifier PATO:0000460 ! abnormal ! intersection_of: inheres_in _:singlepositive T cell [Term] id: MP:0008082 ! increased singlepositive T cell number intersection_of: PATO:0000420 ! increased number ! intersection_of: inheres_in _:singlepositive T cell [Term] id: MP:0008083 ! decreased singlepositive T cell number intersection_of: PATO:0000419 ! decreased number ! intersection_of: inheres_in _:singlepositive T cell [Term] *************** *** 24180,24185 **** intersection_of: PATO:0001557 ! lacking physical parts intersection_of: inheres_in MA:0002711 ! immune system ! intersection_of: OBO_REL:towards CL:0000624 ! CD4positive, alphabeta T cell ! intersection_of: OBO_REL:towards CL:0000625 ! CD8positive, alphabeta T cell [Term]  24157,24161  intersection_of: PATO:0001557 ! lacking physical parts intersection_of: inheres_in MA:0002711 ! immune system ! intersection_of: OBO_REL:towards _:singlepositive T cell [Term] *************** *** 25085,25088 ****  25061,25079  [Term] + id: _:mast_cell_differentiation + intersection_of: GO:0030154 ! cell differentiation + intersection_of: OBO_REL:results_in_acquisition_of_features_of CL:0000097 ! mast cell + + [Term] + id: _:mononuclear_cell_differentiation + intersection_of: GO:0030154 ! cell differentiation + intersection_of: OBO_REL:results_in_acquisition_of_features_of CL:0000842 ! mononuclear cell + + [Term] + id: _:eosinophil_cell_differentiation + intersection_of: GO:0030154 ! cell differentiation + intersection_of: OBO_REL:results_in_acquisition_of_features_of CL:0000771 ! eosinophil + + [Term] id: _:Purkinje_cell_ganglion intersection_of: GO:0030425 ! dendrite *************** *** 25097,25100 ****  25088,25136  [Term] + id: _:somatotropin secreting cell_nucleus + intersection_of: GO:0005634 ! nucleus + intersection_of: part_of CL:0000295 ! somatotropin secreting cell + + [Term] + id: _:outer_hair_cell_stereocilia + intersection_of: GO:0032420 ! stereocilium + intersection_of: part_of CL:0000601 ! outer hair cell + + [Term] + id: _:inner_hair_cell_stereocilia + intersection_of: GO:0032420 ! stereocilium + intersection_of: CL:0000589 ! inner hair cell + + [Term] + id: _:cochlear_hair_cell_stereocilia + intersection_of: GO:0032420 ! stereocilium + intersection_of: CL:0000202 ! auditory hair cell + + [Term] + id: _:vestibular_hair_cell_stereocilia + intersection_of: GO:0032420 ! stereocilium + intersection_of: CL:0000609 ! vestibular hair cell + + [Term] + id: _:outer_hair_cell_stereocilia_bundle + intersection_of: GO:0032421 ! stereocilium bundle + intersection_of: part_of CL:0000601 ! outer hair cell + + [Term] + id: _:inner_hair_cell_stereocilia_bundle + intersection_of: GO:0032421 ! stereocilium bundle + intersection_of: part_of CL:0000589 ! inner hair cell + + [Term] + id: _:cochlear_hair_cell_stereocilia_bundle + intersection_of: GO:0032421 ! stereocilium bundle + intersection_of: CL:0000202 ! auditory hair cell + + [Term] + id: _:vestibular_hair_cell_stereocilia_bundle + intersection_of: GO:0032421 ! stereocilium bundle + intersection_of: CL:0000609 ! vestibular hair cell + + [Term] id: _:primordial_germ_cell_proliferation is_anonymous: true *************** *** 25108,25111 ****  25144,25153  union_of: MA:0000023 ! head + [Term] + id: _:singlepositive T cell + is_anonymous: true + union_of: CL:0000624 ! CD4positive, alphabeta T cell + union_of: CL:0000625 ! CD8positive, alphabeta T cell + [Typedef] id: qualifier 
From: Chris Mungall <cmungall@us...>  20080424 18:25:14

Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8prcvs3.sourceforge.net:/tmp/cvsserv13503 Modified Files: mammalian_phenotype_xp.obo Log Message: minor formatting changes Index: mammalian_phenotype_xp.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype_xp.obo,v retrieving revision 1.65 retrieving revision 1.66 diff C2 d r1.65 r1.66 *** mammalian_phenotype_xp.obo 14 Apr 2008 01:09:00 0000 1.65  mammalian_phenotype_xp.obo 24 Apr 2008 18:25:14 0000 1.66 *************** *** 61,65 **** id: MP:0000012 ! loss of subcutaneous adipose tissue intersection_of: PATO:0001569 ! having decreased physical parts ! intersection_of: towards MA:0000473 ! subcutaneous adipose tissue [Term]  61,65  id: MP:0000012 ! loss of subcutaneous adipose tissue intersection_of: PATO:0001569 ! having decreased physical parts ! intersection_of: OBO_REL:towards MA:0000473 ! subcutaneous adipose tissue [...12617 lines suppressed...] [Term]  24801,24805  intersection_of: PATO:0001557 ! lacking physical part intersection_of: inheres_in EMAP:2950 ! TS18,neural tube,future spinal cord ! intersection_of: OBO_REL:towards EMAP:2951 ! TS18,floor plate,neural tube,future spinal cord [Term] *************** *** 24823,24827 **** intersection_of: PATO:0001557 ! lacking physical part intersection_of: inheres_in EMAP:2950 ! TS18,neural tube,future spinal cord ! intersection_of: towards EMAP:3534 ! TS19,roof plate,neural tube,future spinal cord [Term]  24813,24817  intersection_of: PATO:0001557 ! lacking physical part intersection_of: inheres_in EMAP:2950 ! TS18,neural tube,future spinal cord ! intersection_of: OBO_REL:towards EMAP:3534 ! TS19,roof plate,neural tube,future spinal cord [Term] 
From: Seth Carbon <sjcarbon@us...>  20080424 07:02:55

Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8prcvs3.sourceforge.net:/tmp/cvsserv31136/phenotype Modified Files: mosquito_insecticide_resistance.obo worm_phenotype.obo Log Message: Automated file update Index: worm_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/worm_phenotype.obo,v retrieving revision 1.8 retrieving revision 1.9 diff C2 d r1.8 r1.9 *** worm_phenotype.obo 23 Apr 2008 07:02:01 0000 1.8  worm_phenotype.obo 24 Apr 2008 07:02:53 0000 1.9 *************** *** 1,4 **** formatversion: 1.2 ! date: 22:04:2008 14:11 savedby: garys autogeneratedby: OBOEdit 1.002  1,4  formatversion: 1.2 ! date: 23:04:2008 20:56 savedby: garys autogeneratedby: OBOEdit 1.002 *************** *** 11,14 ****  11,15  id: WBPhenotype0000000 name: chromosome_instability + def: "Animals exhibit a genetic instability due to chromosome alterations such as increases in the frequencies of translocations, deletions, or gene amplifications and increases in chromosome fusion events and or chromosomal loss." [WB:WBPerson712] is_a: WBPhenotype0000585 ! cell_homeostasis_metabolism_abnormal *************** *** 1501,1506 **** [Term] id: WBPhenotype0000215 ! name: no_germline def: "Animals lack all germline progenitor cells, thereby resulting in the complete absence of a germline." [WB:WBPaper00001477, WB:WBPerson2021] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal  1502,1508  [Term] id: WBPhenotype0000215 ! name: no_germ_line def: "Animals lack all germline progenitor cells, thereby resulting in the complete absence of a germline." [WB:WBPaper00001477, WB:WBPerson2021] + synonym: "no_germline" EXACT [] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal *************** *** 1979,1982 ****  1981,1985  id: WBPhenotype0000288 name: distal_germline_abnormal + synonym: "distal_germ_line_abnormal" RELATED [] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal *************** *** 2402,2405 ****  2405,2409  id: WBPhenotype0000354 name: cell_differentiation_abnormal + def: "The ability of a less specialized cell to become a more specialized cell type is disrupted. Differentiation impacts diverse cellular properties such as size, shape, polarity, gene expression and responsiveness to signals/cues." [WB:WBPerson2021] subset: phenotype_slim_wb is_a: WBPhenotype0000529 ! cell_development_abnormal *************** *** 4111,4114 ****  4115,4119  id: WBPhenotype0000616 name: synapse_morphology_abnormal + def: "Animals exhibit defects in the subcellular junctional structures between presynaptic termini and postsynaptic targets and or the cleft aligning these cellular specializations. Synapse defects may include, for example, alterations in the number or placement of these junctions or alterations in the subcellular localization of synapse components." [WB:WBPaper00027305, WB:WBPerson712] relationship: part_of WBPhenotype0000905 ! neuron_morphology_abnormal *************** *** 4594,4597 ****  4599,4603  name: feminization_of_germline def: "Hermaphrodites transformed into fertile females; XO animals are somatically male but may produce oocytes instead of, or in addition to, sperm." [pmid:3396865, WB:cab] + synonym: "feminization_of_germ line" EXACT [] synonym: "Fog" BROAD three_letter_name [] is_a: WBPhenotype0000687 ! feminization_of_XX_and_XO_animals *************** *** 4602,4605 ****  4608,4612  id: WBPhenotype0000683 name: masculinization_of_germline + synonym: "masculinization of germ line" EXACT [] synonym: "Mog" BROAD three_letter_name [] is_a: WBPhenotype0000688 ! sterile *************** *** 4614,4618 **** synonym: "Fgc" BROAD three_letter_name [] is_a: WBPhenotype0000688 ! sterile ! is_a: WBPhenotype0000823 ! germ_line_proliferation_abnormal  4621,4625  synonym: "Fgc" BROAD three_letter_name [] is_a: WBPhenotype0000688 ! sterile ! is_a: WBPhenotype0000823 ! germline_proliferation_abnormal *************** *** 5551,5557 **** [Term] id: WBPhenotype0000823 ! name: germ_line_proliferation_abnormal def: "Nuclear divisions in the germ line are either expanded are reduced." [WB:cab] synonym: "germ_cell_proliferation_abnormal" RELATED [] synonym: "glp" BROAD three_letter_name [] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal  5558,5565  [Term] id: WBPhenotype0000823 ! name: germline_proliferation_abnormal def: "Nuclear divisions in the germ line are either expanded are reduced." [WB:cab] synonym: "germ_cell_proliferation_abnormal" RELATED [] + synonym: "germ_line_proliferation_abnormal" EXACT [] synonym: "glp" BROAD three_letter_name [] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal *************** *** 5827,5831 **** id: WBPhenotype0000866 name: germ_cell_arrest ! is_a: WBPhenotype0000823 ! germ_line_proliferation_abnormal  5835,5839  id: WBPhenotype0000866 name: germ_cell_arrest ! is_a: WBPhenotype0000823 ! germline_proliferation_abnormal *************** *** 5989,6002 **** [Term] id: WBPhenotype0000892 ! name: hermaphrodite_germ_line_proliferation_abnormal synonym: "hermaphrodite_germ_cell_proliferation_abnormal" RELATED [] ! is_a: WBPhenotype0000823 ! germ_line_proliferation_abnormal [Term] id: WBPhenotype0000893 ! name: male_germ_line_proliferation_abnormal synonym: "male_germ_cell_proliferation_abnormal" RELATED [] ! is_a: WBPhenotype0000823 ! germ_line_proliferation_abnormal  5997,6012  [Term] id: WBPhenotype0000892 ! name: hermaphrodite_germline_proliferation_abnormal synonym: "hermaphrodite_germ_cell_proliferation_abnormal" RELATED [] ! synonym: "hermaphrodite_germ_line_proliferation_abnormal" RELATED [] ! is_a: WBPhenotype0000823 ! germline_proliferation_abnormal [Term] id: WBPhenotype0000893 ! name: male_germline_proliferation_abnormal synonym: "male_germ_cell_proliferation_abnormal" RELATED [] ! synonym: "male_germ_line_proliferation_abnormal" RELATED [] ! is_a: WBPhenotype0000823 ! germline_proliferation_abnormal *************** *** 6444,6447 ****  6454,6459  id: WBPhenotype0000966 name: germline_mortal + def: "progressive decrease in brood size culminating, over generations, in the loss of reproductive ability and thus becoming effectively sterile." [WB:WBPaper00003886, WB:WBPaper00027026, WB:WBPerson712] + synonym: "Mrt" BROAD three_letter_name [] is_a: WBPhenotype0000987 ! germ_cell_physiology_abnormal *************** *** 6920,6923 ****  6932,6936  name: tumorous_germline synonym: "Tum" BROAD three_letter_name [] + synonym: "tumorous_germ_line" EXACT [] is_a: WBPhenotype0000812 ! germ_cell_development_abnormal *************** *** 7972,7975 ****  7985,7989  name: high_incidence_male_progeny def: "Higher numbers of male progeny occur in the population as a result of an increase in X chromosome nondisjunction" [WB:cab, WB:WBPaper00004402, WB:WBPaper00005654, WB:WBPerson712] + synonym: "high_frequency_X_chromosome_nondisjunction" RELATED [] synonym: "Him" BROAD three_letter_name [] is_a: WBPhenotype0001664 ! X_chromosome_nondisjunction *************** *** 8239,8243 **** name: germ_cell_mitosis_abnormal def: "Any abnormality that perturbs the constant mitotic proliferation of germ cells during development. Such defects often result in the germ cells prematurely entering into meiosis. " [WB:WBPaper00001007, WB:WBPerson2021] ! is_a: WBPhenotype0000823 ! germ_line_proliferation_abnormal  8253,8257  name: germ_cell_mitosis_abnormal def: "Any abnormality that perturbs the constant mitotic proliferation of germ cells during development. Such defects often result in the germ cells prematurely entering into meiosis. " [WB:WBPaper00001007, WB:WBPerson2021] ! is_a: WBPhenotype0000823 ! germline_proliferation_abnormal *************** *** 10524,10528 **** id: WBPhenotype0001566 name: ventral_enclosure_abnormal ! def: "the process by which ventral epidermal cells migrate toward the ventral midline to encase underlying cells in an epithelial monolayer" [WB:WBPaper00027244] is_a: WBPhenotype0000749 ! embryonic_development_abnormal  10538,10542  id: WBPhenotype0001566 name: ventral_enclosure_abnormal ! def: "The process that regulates the migration of ventral epidermal cells toward the ventral midline (to encase underlying cells in an epithelial monolayer) in developing embryos is perturbed." [WB:WBPaper00027244, WB:WBPerson2021] is_a: WBPhenotype0000749 ! embryonic_development_abnormal *************** *** 11005,11009 **** id: WBPhenotype0001635 name: excess_pharyngeal_cells ! def: "Embryos generate an excess number of MSlike pharyngeal cells that are derived from the ABa, ABp, E or P2 blastomeres. The overproduction of pharyngeal tissue is not dependent on cellcell interactions and is an outcome of multiple early blastomeres adopting a fate similar to that of the MS blastomere. " [WB:WBPaper00001584, WB:WBperson2021] is_a: WBPhenotype0000707 ! pharyngeal_development_abnormal  11019,11023  id: WBPhenotype0001635 name: excess_pharyngeal_cells ! def: "Embryos generate an excess number of MSlike pharyngeal cells that are derived from the ABa, ABp, E or P2 blastomeres. The overproduction of pharyngeal tissue is often an outcome of multiple early blastomeres adopting a fate similar to that of the MS blastomere." [WB:WBPaper00001584, WB:WBPaper00002922, WB:WBperson2021] is_a: WBPhenotype0000707 ! pharyngeal_development_abnormal *************** *** 11012,11016 **** id: WBPhenotype0001636 name: excess_intestinal_cells ! def: "Embryos generate an excess number of intestinal cells that are derived from the P2 blastomere. Such defects occur when the P2 blastomere adopts a fate that is similar to that of the EMS blastomere." [WB:WBPaper00001584, WB:WBperson2021] is_a: WBPhenotype0000708 ! intestinal_development_abnormal  11026,11030  id: WBPhenotype0001636 name: excess_intestinal_cells ! def: "Embryos generate an excess number of intestinal cells that are derived from a non Eblastomere. For example, the P2 or MS blastomere adopts a fate that is similar to that of the E blastomere." [WB:WBPaper00001584, WB:WBPaper00002330, WB:WBperson2021] is_a: WBPhenotype0000708 ! intestinal_development_abnormal *************** *** 11082,11085 ****  11096,11100  id: WBPhenotype0001646 name: no_pharynx + def: "Embryos completely lack any structures that morphologically resemble a pharynx." [WB:WBPaper00001521, WB:WBPerson2021] is_a: WBPhenotype0000707 ! pharyngeal_development_abnormal *************** *** 11094,11097 ****  11109,11113  id: WBPhenotype0001648 name: no_posterior_pharynx + def: "Embryos fail to generate the MS blastomere derived pharyngeal cells, which constitute the posterior portion of the pharynx." [WB:WBPaper00002330, WB:WBPerson2021] is_a: WBPhenotype0001646 ! no_pharynx is_a: WBPhenotype0001647 ! posterior_pharynx_abnormal *************** *** 11175,11178 ****  11191,11195  id: WBPhenotype0001660 name: loss_of_asymmetry_ASE + def: "The two morphologically bilaterally symmetric gustatory neurons ASE left (ASEL) and ASE right (ASER) fail to undergo a left/right asymmetric diversification in cell fate." [WB:WBPaper00030973, WB:WBPerson2021] synonym: "2ASEL" NARROW [] synonym: "2ASER" NARROW [] *************** *** 11183,11186 ****  11200,11204  id: WBPhenotype0001661 name: loss_of_asymmetry_AWC + def: "The two morphologically bilaterally symmetric olfactory neurons AWC left (AWCL) and AWC right (AWCR) fail to undergo a left/right asymmetric diversification in cell fate." [WB:WBPaper00003760, WB:WBPerson2021] synonym: "2 AWC off" NARROW [] synonym: "2 AWC on" NARROW [] 