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From: Seth C. <sjc...@us...> - 2008-07-30 07:02:56
|
Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv15493/phenotype Modified Files: mammalian_phenotype.obo mosquito_insecticide_resistance.obo Log Message: Automated file update Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.188 retrieving revision 1.189 diff -C2 -d -r1.188 -r1.189 *** mammalian_phenotype.obo 23 Jul 2008 07:04:07 -0000 1.188 --- mammalian_phenotype.obo 30 Jul 2008 07:02:58 -0000 1.189 *************** *** 1,4 **** format-version: 1.2 ! date: 22:07:2008 16:36 saved-by: csmith auto-generated-by: OBO-Edit 1.101 --- 1,4 ---- format-version: 1.2 ! date: 29:07:2008 16:54 saved-by: csmith auto-generated-by: OBO-Edit 1.101 *************** *** 2877,2880 **** --- 2877,2881 ---- synonym: "abnormal enterocyte" EXACT [] synonym: "abnormal intestinal cell morphology" BROAD [] + synonym: "abnormal intestinal epithelial cell" EXACT [] synonym: "intestinal cell abnormalities" BROAD [] is_a: MP:0000488 ! abnormal intestinal epithelium morphology *************** *** 16104,16109 **** name: abnormal response/metabolism to xenobiotics def: "altered ability or inability to metabolize or respond to foreign substances" [J:55555, MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] synonym: "abnormal metabolism of xenobiotics" EXACT [] ! is_a: MP:0005266 ! abnormal metabolism [Term] --- 16105,16111 ---- name: abnormal response/metabolism to xenobiotics def: "altered ability or inability to metabolize or respond to foreign substances" [J:55555, MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] + comment: This term has been rendered obsolete. Please use instead the terms abnormal pharmacogenetics of xenobiotics (MP:0008875) or abnormal response to xenobiotics (MP:0008872). synonym: "abnormal metabolism of xenobiotics" EXACT [] ! is_obsolete: true [Term] *************** *** 19635,19638 **** --- 19637,19641 ---- name: abnormal nucleus morphology def: "any structural anomaly of the part of the cell or its surrounding membrane that contains DNA and RNA and is responsible for growth and reproduction of the cell" [J:91473, MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + synonym: "abnormal nuclear compartment morphology" EXACT [] is_a: MP:0000358 ! abnormal cell content/ morphology *************** *** 19665,19668 **** --- 19668,19672 ---- name: rickets def: "overproduction and deficient calcification of osteoid tissue due to vitamin D deficiency; can lead to skeletal deformities, growth defects, hypocalcemia, and sometimes tetany; skeletal fractures occur frequently" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] + synonym: "abnormal bone calcification" RELATED [] is_a: MP:0002896 ! abnormal bone mineralization *************** *** 19697,19701 **** name: genomic imprinting def: "phenotype resulting from inactivation of specific loci during gametogenesis, but not encoded by the DNA itself" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! is_a: MP:0005621 ! abnormal cell physiology [Term] --- 19701,19706 ---- name: genomic imprinting def: "phenotype resulting from inactivation of specific loci during gametogenesis, but not encoded by the DNA itself" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! synonym: "genetic imprinting" EXACT [] ! is_a: MP:0005384 ! cellular phenotype [Term] *************** *** 36046,36050 **** [Term] id: MP:0005466 ! name: abnormal T helper 2 physiology def: "abnormal function of the type of T-helper cell whose cytokine production promotes defense against extracellular parasites and humoral immune responses typical of allergy" [CL:0000546, ISBN:0781735149] synonym: "abnormal helper T cell type 2 function" EXACT [] --- 36051,36055 ---- [Term] id: MP:0005466 ! name: abnormal T-helper 2 physiology def: "abnormal function of the type of T-helper cell whose cytokine production promotes defense against extracellular parasites and humoral immune responses typical of allergy" [CL:0000546, ISBN:0781735149] synonym: "abnormal helper T cell type 2 function" EXACT [] *************** *** 36053,36056 **** --- 36058,36062 ---- synonym: "abnormal helper T-lymphocyte type 2 function" EXACT [] synonym: "abnormal T helper 2 function" EXACT [] + synonym: "abnormal T helper 2 physiology" EXACT [] synonym: "abnormal TH2 cell function" EXACT [] synonym: "T helper 2 functional abnormalities" EXACT [] *************** *** 40700,40707 **** name: absent uterine NK cells def: "absence of the uterine subset of the non-T, non-B lymphocytes, having a granular morphology and which are important in innate immunity to viruses and other intracellular pathogens; in addition, these cells can kill certain tumor cells" [ISBN:0-8153-1691-7 "Immunobiology, The Immune System in Health and Disease"] synonym: "absent uNK cells" EXACT [] synonym: "absent uterine natural killer cells" EXACT [] is_a: MP:0008046 ! absent NK cells ! is_a: MP:0008054 ! abnormal uterine NK cell morphology [Term] --- 40706,40715 ---- name: absent uterine NK cells def: "absence of the uterine subset of the non-T, non-B lymphocytes, having a granular morphology and which are important in innate immunity to viruses and other intracellular pathogens; in addition, these cells can kill certain tumor cells" [ISBN:0-8153-1691-7 "Immunobiology, The Immune System in Health and Disease"] + synonym: "absent GMG cells" EXACT [] + synonym: "absent granulated metrial gland cells" EXACT [] synonym: "absent uNK cells" EXACT [] synonym: "absent uterine natural killer cells" EXACT [] is_a: MP:0008046 ! absent NK cells ! is_a: MP:0008876 ! decreased uterine NK cell number [Term] *************** *** 40751,40754 **** --- 40759,40764 ---- name: abnormal uterine NK cell morphology def: "any structural anomaly of the uterine subset of the non-T, non-B lymphocytes, having a granular morphology and which are important in innate immunity to viruses and other intracellular pathogens; in addition, these cells can kill certain tumor cells" [ISBN:0-8153-1691-7 "Immunobiology, The Immune System in Health and Disease"] + synonym: "abnormal GMG cell morphology" EXACT [] + synonym: "abnormal granulated metrial gland cell morphology" EXACT [] synonym: "abnormal uNK cell morphology" EXACT [] synonym: "abnormal uterine natural killer cell morphology" EXACT [] *************** *** 48194,48198 **** [Term] id: MP:0008870 ! name: increased mature ovarian follicle number def: "than normal numbers of spheroid cell aggregations in the ovary containing the ovum" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] is_a: MP:0008871 ! abnormal ovarian follicle number --- 48204,48208 ---- [Term] id: MP:0008870 ! name: increased mature ovarian follicle number def: "than normal numbers of spheroid cell aggregations in the ovary containing the ovum" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] is_a: MP:0008871 ! abnormal ovarian follicle number *************** *** 48232,48235 **** --- 48242,48365 ---- is_a: MP:0005266 ! abnormal metabolism + [Term] + id: MP:0008876 + name: decreased uterine NK cell number + def: "reduced number of the uterine subset of the non-T, non-B lymphocytes, having a granular morphology and which are important in innate immunity to viruses and other intracellular pathogens; in addition, these cells can kill certain tumor cells" [ISBN:0-8153-1691-7 "Immunobiology, The Immune System in Health and Disease"] + synonym: "decreased GMG cell number" EXACT [] + synonym: "decreased granulated metrial gland cell number" EXACT [] + synonym: "decreased uNK cell number" EXACT [] + synonym: "decreased uterine natural killer cell number" EXACT [] + synonym: "reduced GMG cell number" EXACT [] + synonym: "reduced granulated metrial gland cell number" EXACT [] + synonym: "reduced uNK cell number" EXACT [] + synonym: "reduced uterine natural killer cell number" EXACT [] + is_a: MP:0008054 ! abnormal uterine NK cell morphology + + [Term] + id: MP:0008877 + name: abnormal DNA methylation + def: "any anomaly in the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine of DNA" [GO:0006306] + is_a: MP:0005621 ! abnormal cell physiology + + [Term] + id: MP:0008878 + name: abnormal DNA methylation during gametogenesis + def: "any anomaly of the covalent transfer of a methyl group to C-5 of cytosine during gamete generation, when DNA methylation patterns are established" [GO:0043046] + synonym: "abnormal de novo DNA methylation" EXACT [] + is_a: MP:0001929 ! abnormal gametogenesis + is_a: MP:0008877 ! abnormal DNA methylation + + [Term] + id: MP:0008879 + name: submandibular gland inflammation + def: "local accumulation of fluid, plasma proteins, and leukocytes in either of the large major salivary glands situated beneath the mandible" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + is_a: MP:0001870 ! salivary gland inflammation + + [Term] + id: MP:0008880 + name: lacrimal gland inflammation + def: "local accumulation of fluid, plasma proteins, and leukocytes in the glands that secrete tears" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + is_a: MP:0001348 ! abnormal lacrimal gland physiology + is_a: MP:0001846 ! increased inflammatory response + + [Term] + id: MP:0008881 + name: absent Harderian gland + def: "absence of the sebaceous gland located behind the eyeball in the orbit that excretes fluid that facilitates movement of the third eyelid" [MESH:A13.445] + is_a: MP:0005248 ! abnormal Harderian gland morphology + + [Term] + id: MP:0008882 + name: abnormal enterocyte physiology + def: "any functional anomaly of the epithelial cells that have an apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen" [CL:0000584, MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + synonym: "abnormal intestinal cell physiology" EXACT [] + synonym: "abnormal intestinal epithelial cell physiology" EXACT [] + is_a: MP:0001663 ! abnormal digestive system physiology + + [Term] + id: MP:0008883 + name: abnormal enterocyte proliferation + def: "anomaly in the ability of the enterocyte cell population to undergo expansion by cell division" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + synonym: "abnormal intestinal cell proliferation" EXACT [] + synonym: "abnormal intestinal epithelial cell proliferation" EXACT [] + is_a: MP:0008882 ! abnormal enterocyte physiology + + [Term] + id: MP:0008884 + name: abnormal enterocyte apoptosis + def: "change in the timing or the number of enterocytes undergoing programmed cell death" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + synonym: "abnormal enterocyte programmed cell death" EXACT [] + synonym: "abnormal intestinal cell apoptosis" EXACT [] + synonym: "abnormal intestinal epithelial cell apoptosis" EXACT [] + is_a: MP:0008882 ! abnormal enterocyte physiology + + [Term] + id: MP:0008885 + name: increased enterocyte apoptosis + def: "increase in the timing or the number of B cells undergoing programmed cell death" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + synonym: "increased intestinal cell apoptosis" EXACT [] + synonym: "increased intestinal epithelial cell apoptosis" EXACT [] + is_a: MP:0008884 ! abnormal enterocyte apoptosis + + [Term] + id: MP:0008886 + name: abnormal PML bodies + def: "alteration in structure, number or location of the subnuclear structures associated with functions including transcription, DNA repair, viral defense, stress, cell cycle regulation, proteolysis and apoptosis" [https://npd.hgu.mrc.ac.uk/compartments.html, MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + synonym: "abnormal Kr bodies" EXACT [] + synonym: "abnormal ND10 morphology" EXACT [] + synonym: "abnormal nuclear dot morphology" EXACT [] + synonym: "abnormal PML NBs" EXACT [] + synonym: "abnormal Promyelocytic leukaemia nuclear body" EXACT [] + synonym: "abnormal SP-100 bodies" EXACT [] + is_a: MP:0003111 ! abnormal nucleus morphology + + [Term] + id: MP:0008887 + name: abnormal splicing factor domain morphology + def: "alteration in structure, number or location of subnuclear structures comprising storage locations for elements responsible for excising non-coding regions from a primary messenger RNA transcript and joining coding regions to produce mature messenger RNA" [https://npd.hgu.mrc.ac.uk/compartments.html, MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + comment: Same as nuclear speck (GO0016607)? + synonym: "abnormal splicing speckle morphology" EXACT [] + is_a: MP:0003111 ! abnormal nucleus morphology + + [Term] + id: MP:0008888 + name: abnormal Cajal body morphology + def: "alteration in structure, number or location of subnuclear structures involved in snRNP biogenesis and in the trafficking of snoRNPs and snRNPs" [https://npd.hgu.mrc.ac.uk/compartments.html, MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + synonym: "abnormal coiled body morphology" EXACT [] + is_a: MP:0003111 ! abnormal nucleus morphology + + [Term] + id: MP:0008889 + name: abnormal Gems + def: "alteration in structure, number or location of subnuclear structures involved in snRNP biogenesis and in the trafficking of snoRNPs and snRNPs and found paired or juxtaposed to Cajal bodies" [https://npd.hgu.mrc.ac.uk/compartments.html, MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + synonym: "abnormal SMN gem morphology" EXACT [] + is_a: MP:0003111 ! abnormal nucleus morphology + + [Term] + id: MP:0008890 + name: abnormal nuclear lamina morphology + def: "alteration in the structure of the inner nuclear membrane surrounding the nuclear periphery, comprising a scaffold-like network of protein filaments responsible for trafficking of mRNA to the cytoplasm" [https://npd.hgu.mrc.ac.uk/compartments.html, MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0003111 ! abnormal nucleus morphology + [Typedef] id: part_of |
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From: Georgios V. G. <gk...@us...> - 2008-07-29 12:22:50
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv6948 Modified Files: quality.obo Log Message: update Index: quality.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/quality.obo,v retrieving revision 1.115 retrieving revision 1.116 diff -C2 -d -r1.115 -r1.116 *** quality.obo 6 Jul 2008 12:46:34 -0000 1.115 --- quality.obo 29 Jul 2008 12:22:49 -0000 1.116 *************** *** 1,4 **** format-version: 1.0 ! date: 06:07:2008 13:42 saved-by: George Gkoutos auto-generated-by: OBO-Edit 1.100 --- 1,4 ---- format-version: 1.0 ! date: 29:07:2008 13:17 saved-by: George Gkoutos auto-generated-by: OBO-Edit 1.100 *************** *** 11657,11661 **** subset: cell_quality subset: value_slim ! is_a: PATO:0000052 ! shape [Term] --- 11657,11661 ---- subset: cell_quality subset: value_slim ! is_a: PATO:0001988 ! quadrangular [Term] *************** *** 12518,12521 **** --- 12518,12533 ---- is_a: PATO:0000141 ! structure + [Term] + id: PATO:0001988 + name: quadrangular + def: "A shape quality inhering in a bearer by virtue of having four angles and four sides." [Oxford English Dictionary:Oxford English Dictionary "http://www.oed.com/"] + is_a: PATO:0000052 ! shape + + [Term] + id: PATO:0001989 + name: sinuous + def: "A shape having many curves and turns." [Oxford American Dictionary:Oxford American Dictionary "Oxford American Dictionary"] + is_a: PATO:0001591 ! curvature + [Typedef] id: is_magnitude_of |
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From: Seth C. <sjc...@us...> - 2008-07-29 07:03:28
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv16667/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-28 07:02:36
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv10481/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-27 07:02:50
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv22059/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-26 07:01:53
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv31677/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-25 07:02:57
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv4066/phenotype Modified Files: human_disease.obo mosquito_insecticide_resistance.obo worm_phenotype.obo Log Message: Automated file update Index: human_disease.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/human_disease.obo,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** human_disease.obo 22 Jul 2008 07:04:08 -0000 1.7 --- human_disease.obo 25 Jul 2008 07:02:47 -0000 1.8 *************** *** 0 **** --- 1,505866 ---- + format-version: 1.0 + date: 19:09:2007 11:23 + saved-by: lschriml + auto-generated-by: OBO-Edit 1.101 + default-namespace: disease_ontology + namespace-id-rule: * DOID:$sequence(7,50000,50999)$ + remark: version\: $Revision\: 1.1 $ + + [Term] [...505837 lines suppressed...] + xref_analog: ICD9CM_2004:674.2 + xref_analog: ICD9CM_2004:674.20 + xref_analog: ICD9CM_2004:674.22 + xref_analog: ICD9CM_2005:674.2 + xref_analog: ICD9CM_2005:674.20 + xref_analog: ICD9CM_2005:674.22 + xref_analog: UMLS_CUI:C0157582 + xref_analog: UMLS_CUI:C0157583 + xref_analog: UMLS_CUI:C0269966 + xref_analog: UMLS_ICD9CM_2005_AUI:A0280714 + xref_analog: UMLS_ICD9CM_2005_AUI:A0280716 + xref_analog: UMLS_ICD9CM_2005_AUI:A0280718 + xref_analog: UMLS_ST:T033 + xref_analog: UMLS_ST:T037 + is_obsolete: true + + [Typedef] + id: part_of + name: part_of + Index: worm_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/worm_phenotype.obo,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -d -r1.30 -r1.31 *** worm_phenotype.obo 23 Jul 2008 07:04:10 -0000 1.30 --- worm_phenotype.obo 25 Jul 2008 07:02:59 -0000 1.31 *************** *** 1,4 **** format-version: 1.2 ! date: 22:07:2008 11:47 saved-by: garys auto-generated-by: OBO-Edit 1.002 --- 1,4 ---- format-version: 1.2 ! date: 24:07:2008 11:59 saved-by: garys auto-generated-by: OBO-Edit 1.002 *************** *** 6959,6962 **** --- 6959,6963 ---- id: WBPhenotype:0001022 name: hermaphrodite_sexual_development_abnormal + def: "XX animals develop as males or intersexuals instead of self-fertile hermaphrodites." [WB:WBPerson2021] is_a: WBPhenotype:0000822 ! sex_determination_abnormal *************** *** 11626,11630 **** def: "Germ nuclei are misplaced in the gonad and are observed in the rachis. Sheath cells are observed protruding between these nuclei. Meiotic or mitotic specification of germ nuclei is not affected." [WB:WBPaper00031889, WB:WBPerson712] synonym: "germ_line_morphogenesis(Glm)" NARROW [] ! is_a: WBPhenotype:0000900 ! germ_cell_morphology_abnormal --- 11627,11631 ---- def: "Germ nuclei are misplaced in the gonad and are observed in the rachis. Sheath cells are observed protruding between these nuclei. Meiotic or mitotic specification of germ nuclei is not affected." [WB:WBPaper00031889, WB:WBPerson712] synonym: "germ_line_morphogenesis(Glm)" NARROW [] ! is_a: WBPhenotype:0000977 ! somatic_gonad_morphology_abnormal |
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From: Seth C. <sjc...@us...> - 2008-07-24 07:04:22
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv30425/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-23 07:04:06
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv15287/phenotype Modified Files: mammalian_phenotype.obo 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 1.29 retrieving revision 1.30 diff -C2 -d -r1.29 -r1.30 *** worm_phenotype.obo 24 Jun 2008 07:01:55 -0000 1.29 --- worm_phenotype.obo 23 Jul 2008 07:04:10 -0000 1.30 *************** *** 1,4 **** format-version: 1.2 ! date: 23:06:2008 14:51 saved-by: garys auto-generated-by: OBO-Edit 1.002 --- 1,4 ---- format-version: 1.2 ! date: 22:07:2008 11:47 saved-by: garys auto-generated-by: OBO-Edit 1.002 *************** *** 11716,11719 **** --- 11716,11726 ---- [Term] + id: WBPhenotype:0001704 + name: multiple_alae + def: "Alae are composed of more than three cuticular ridges." [WB:WBPaper00026841, WB:WBPerson557] + is_a: WBPhenotype:0001412 ! alae_morphology_abnormal + + + [Term] id: WBPhenotype:0004001 name: hermaphrodite_mating_abnormal Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.187 retrieving revision 1.188 diff -C2 -d -r1.187 -r1.188 *** mammalian_phenotype.obo 20 Jul 2008 07:02:31 -0000 1.187 --- mammalian_phenotype.obo 23 Jul 2008 07:04:07 -0000 1.188 *************** *** 1,4 **** format-version: 1.2 ! date: 18:07:2008 16:23 saved-by: csmith auto-generated-by: OBO-Edit 1.101 --- 1,4 ---- format-version: 1.2 ! date: 22:07:2008 16:36 saved-by: csmith auto-generated-by: OBO-Edit 1.101 *************** *** 5873,5877 **** def: "seizure activity that is brought about by treatment with pharmacological agents" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] is_a: MP:0002064 ! seizures ! is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics [Term] --- 5873,5877 ---- def: "seizure activity that is brought about by treatment with pharmacological agents" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] is_a: MP:0002064 ! seizures ! is_a: MP:0008872 ! abnormal response to xenobiotics [Term] *************** *** 7411,7414 **** --- 7411,7415 ---- name: atelectasis def: "collapse of the lung or any portion of the lung, or decreased or absent air in the lung, may be the result of trauma, blockage or congenital defect" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator", PMID:10357937] + synonym: "collapsed lung" EXACT [] is_a: MP:0002133 ! abnormal respiratory system physiology *************** *** 16740,16744 **** synonym: "reduced mature ovarian follicle number" EXACT [] synonym: "reduced number of mature ovarian follicles" EXACT [] ! is_a: MP:0001131 ! abnormal ovarian follicle morphology [Term] --- 16741,16745 ---- synonym: "reduced mature ovarian follicle number" EXACT [] synonym: "reduced number of mature ovarian follicles" EXACT [] ! is_a: MP:0008871 ! abnormal ovarian follicle number [Term] *************** *** 18966,18970 **** id: MP:0003014 name: abnormal kidney medulla morphology ! def: "any structural anomaly of the inner portion of the kidney consisting of the renal pyramids" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", J:88636, MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] synonym: "abnormal renal medulla" EXACT [] is_a: MP:0002135 ! abnormal kidney morphology --- 18967,18971 ---- id: MP:0003014 name: abnormal kidney medulla morphology ! def: "any structural anomaly of the inner portion of the kidney consisting of the renal pyramids" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] synonym: "abnormal renal medulla" EXACT [] is_a: MP:0002135 ! abnormal kidney morphology *************** *** 19696,19700 **** name: genomic imprinting def: "phenotype resulting from inactivation of specific loci during gametogenesis, but not encoded by the DNA itself" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! is_a: MP:0005395 ! other phenotype [Term] --- 19697,19701 ---- name: genomic imprinting def: "phenotype resulting from inactivation of specific loci during gametogenesis, but not encoded by the DNA itself" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator", MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! is_a: MP:0005621 ! abnormal cell physiology [Term] *************** *** 21280,21285 **** id: MP:0003357 name: impaired granulosa cell differentiation ! def: "atypical differentiation of the layer of small cells that forms the wall of an ovarian follicle" [J:43075, MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] ! is_a: MP:0001131 ! abnormal ovarian follicle morphology [Term] --- 21281,21286 ---- id: MP:0003357 name: impaired granulosa cell differentiation ! def: "atypical production of or inability to produce the supporting cells for the developing female gamete in the ovary of mammals; granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle" [MESH:A.05.360.319.114.630.535.200] ! is_a: MP:0008868 ! abnormal granulosa cell morphology [Term] *************** *** 28935,28939 **** def: "higher than normal frequency of tumor incidence induced by one or more chemical carcinogens or mutagens" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0002021 ! increased incidence of induced tumors ! is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics [Term] --- 28936,28940 ---- def: "higher than normal frequency of tumor incidence induced by one or more chemical carcinogens or mutagens" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0002021 ! increased incidence of induced tumors ! is_a: MP:0008873 ! increased sensitivity to xenobiotics [Term] *************** *** 29714,29719 **** name: increased susceptibility to ototoxicity-induced hearing loss def: "greater than normal reduction in hearing sensitivity following exposure to an ototoxic compound, such as aminoglycoside-induced hearing loss mediated via a glutamate excitotoxic process" [MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] - is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics is_a: MP:0006334 ! abnormal susceptibility to hearing loss [Term] --- 29715,29720 ---- name: increased susceptibility to ototoxicity-induced hearing loss def: "greater than normal reduction in hearing sensitivity following exposure to an ototoxic compound, such as aminoglycoside-induced hearing loss mediated via a glutamate excitotoxic process" [MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] is_a: MP:0006334 ! abnormal susceptibility to hearing loss + is_a: MP:0008873 ! increased sensitivity to xenobiotics [Term] *************** *** 32899,32903 **** def: "a reaction that differs from normal to compounds that reversibly depress neuronal function" [MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] synonym: "altered sensitivity to anesthetics" EXACT [] ! is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics [Term] --- 32900,32904 ---- def: "a reaction that differs from normal to compounds that reversibly depress neuronal function" [MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] synonym: "altered sensitivity to anesthetics" EXACT [] ! is_a: MP:0008872 ! abnormal response to xenobiotics [Term] *************** *** 35871,35875 **** def: "altered ability to metabolize the clear, colorless liquid that is the primary ingredient in alcoholic beverages" [J:55555, MESH:National Library of Medicine_Medical Subject Headings, MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] synonym: "abnormal alcohol metabolism" EXACT [] ! is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics [Term] --- 35872,35876 ---- def: "altered ability to metabolize the clear, colorless liquid that is the primary ingredient in alcoholic beverages" [J:55555, MESH:National Library of Medicine_Medical Subject Headings, MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] synonym: "abnormal alcohol metabolism" EXACT [] ! is_a: MP:0008875 ! abnormal pharmacokinetics of xenobiotics [Term] *************** *** 42268,42273 **** def: "greater than normal amount of neuronal cell death following exposure to a neurotoxic compound, such as kaniate-induced neuronal cell death mediated via a glutamate excitotoxic process" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] synonym: "increased susceptibility to neurotoxicity-induced cell death" EXACT [] - is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics is_a: MP:0003203 ! increased neuron apoptosis [Term] --- 42269,42274 ---- def: "greater than normal amount of neuronal cell death following exposure to a neurotoxic compound, such as kaniate-induced neuronal cell death mediated via a glutamate excitotoxic process" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] synonym: "increased susceptibility to neurotoxicity-induced cell death" EXACT [] is_a: MP:0003203 ! increased neuron apoptosis + is_a: MP:0008873 ! increased sensitivity to xenobiotics [Term] *************** *** 42277,42282 **** synonym: "decreased susceptibility to neurotoxicity-induced cell death" EXACT [] synonym: "reduced susceptibility to neuronal excitotoxicity" EXACT [] - is_a: MP:0002585 ! abnormal response/metabolism to xenobiotics is_a: MP:0003204 ! decreased neuron apoptosis [Term] --- 42278,42283 ---- synonym: "decreased susceptibility to neurotoxicity-induced cell death" EXACT [] synonym: "reduced susceptibility to neuronal excitotoxicity" EXACT [] is_a: MP:0003204 ! decreased neuron apoptosis + is_a: MP:0008874 ! decreased sensitivity to xenobiotics [Term] *************** *** 48150,48154 **** id: MP:0008863 name: craniofacial asymmetry ! def: "head or facila features that lack mirrored identity on either side of the median plane" [MGI:mberry "Melissa Berry, Genetics Resources Curator"] is_a: MP:0003935 ! abnormal craniofacial development --- 48151,48155 ---- id: MP:0008863 name: craniofacial asymmetry ! def: "head or facial features that lack mirrored identity on either side of the median plane" [MGI:mberry "Melissa Berry, Genetics Resources Curator"] is_a: MP:0003935 ! abnormal craniofacial development *************** *** 48168,48174 **** id: MP:0008866 name: chromosomal instability ! def: "increase in the probability that whole chromosomes or large fractions of chromosomes are gained or lost during cell division, resulting in an imbalance in the number of chromosomes per cell (aneuploidy) and an enhanced rate of loss of heterozygosity" [PMID:12446840] is_a: MP:0005621 ! abnormal cell physiology [Typedef] id: part_of --- 48169,48235 ---- id: MP:0008866 name: chromosomal instability ! def: "abnormalities of DNA metabolism, DNA repair, cell-cycle governance, or control of apoptosis that increase the probability that whole chromosomes or pieces of chromosomes are gained or lost during cell division, resulting in an imbalance in the number of chromosomes per cell (aneuploidy) and an enhanced rate of loss of heterozygosity" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator", PMID:12446840] is_a: MP:0005621 ! abnormal cell physiology + [Term] + id: MP:0008867 + name: uniparental disomy + def: "abnormal assortment of chromosomes from parent to offspring whereby the chromosome number is correct, but both members of a chromosome pair or segments of a chromosome pair are inherited from the same parent" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0001930 ! abnormal meiosis + + [Term] + id: MP:0008868 + name: abnormal granulosa cell morphology + def: "any structural anomaly of a supporting cell for the developing female gamete in the ovary of mammals; granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle" [MESH:A.05.360.319.114.630.535.200] + is_a: MP:0001131 ! abnormal ovarian follicle morphology + + [Term] + id: MP:0008869 + name: anovulation + def: "complete failure of ovum to be released from an ovarian follicle" [MESH:C13.351.500.056.630.050, MGI:mnk "Michelle Knowlton, Mouse Genome Informatics Curator"] + synonym: "absence of ovulation" EXACT [] + synonym: "absent ovulation" EXACT [] + is_a: MP:0001928 ! abnormal ovulation + + [Term] + id: MP:0008870 + name: increased mature ovarian follicle number + def: "than normal numbers of spheroid cell aggregations in the ovary containing the ovum" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] + is_a: MP:0008871 ! abnormal ovarian follicle number + + [Term] + id: MP:0008871 + name: abnormal ovarian follicle number + def: "abnormal numbers of spheroid cell aggregations in the ovary" [MGI:mnk "Michelle Knowlton, Mouse Genome Informatics Curator"] + is_a: MP:0001131 ! abnormal ovarian follicle morphology + + [Term] + id: MP:0008872 + name: abnormal response to xenobiotics + def: "any anomaly in the physiological or morphological changes induced by a foreign compound, such as changes in blood pressure, changes in hormone or protein levels or hypertrophy or hypotrophy of an organ" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + is_a: MP:0005376 ! homeostasis/metabolism phenotype + + [Term] + id: MP:0008873 + name: increased sensitivity to xenobiotics + def: "decrease in the dose or concentration of a foreign compound required to induce a specific level of response" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + synonym: "decreased resistance to xenobiotics " EXACT [] + synonym: "increased susceptibility to xenobiotics" EXACT [] + is_a: MP:0008872 ! abnormal response to xenobiotics + + [Term] + id: MP:0008874 + name: decreased sensitivity to xenobiotics + def: "increase in the dose or concentration of a foreign compound required to induce a specific level of response" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + synonym: "decreased susceptibility to xenobiotics" EXACT [] + synonym: "increased resistance to xenobiotics " EXACT [] + is_a: MP:0008872 ! abnormal response to xenobiotics + + [Term] + id: MP:0008875 + name: abnormal pharmacokinetics of xenobiotics + def: "any anomaly in the absorbtion, distribution, metabolism or elimination of a foreign compound" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + is_a: MP:0005266 ! abnormal metabolism + [Typedef] id: part_of |
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From: Seth C. <sjc...@us...> - 2008-07-22 07:04:16
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv18654/phenotype Modified Files: human_disease.obo mosquito_insecticide_resistance.obo Log Message: Automated file update Index: human_disease.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/human_disease.obo,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** human_disease.obo 20 Mar 2008 07:01:48 -0000 1.6 --- human_disease.obo 22 Jul 2008 07:04:08 -0000 1.7 *************** *** 1,505866 **** - format-version: 1.0 - date: 19:09:2007 11:23 - saved-by: lschriml - auto-generated-by: OBO-Edit 1.101 - default-namespace: disease_ontology - namespace-id-rule: * DOID:$sequence(7,50000,50999)$ - remark: version\: $Revision\: 1.1 $ - - [Term] - id: DOID:0000000 [...505837 lines suppressed...] - xref_analog: ICD9CM_2004:674.20 - xref_analog: ICD9CM_2004:674.22 - xref_analog: ICD9CM_2005:674.2 - xref_analog: ICD9CM_2005:674.20 - xref_analog: ICD9CM_2005:674.22 - xref_analog: UMLS_CUI:C0157582 - xref_analog: UMLS_CUI:C0157583 - xref_analog: UMLS_CUI:C0269966 - xref_analog: UMLS_ICD9CM_2005_AUI:A0280714 - xref_analog: UMLS_ICD9CM_2005_AUI:A0280716 - xref_analog: UMLS_ICD9CM_2005_AUI:A0280718 - xref_analog: UMLS_ST:T033 - xref_analog: UMLS_ST:T037 - is_obsolete: true - - [Typedef] - id: part_of - name: part_of - --- 0 ---- |
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From: Seth C. <sjc...@us...> - 2008-07-21 07:02:24
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv4428/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-20 07:02:30
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv13229/phenotype Modified Files: mammalian_phenotype.obo mosquito_insecticide_resistance.obo Log Message: Automated file update Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.186 retrieving revision 1.187 diff -C2 -d -r1.186 -r1.187 *** mammalian_phenotype.obo 17 Jul 2008 07:01:54 -0000 1.186 --- mammalian_phenotype.obo 20 Jul 2008 07:02:31 -0000 1.187 *************** *** 1,4 **** format-version: 1.2 ! date: 16:07:2008 16:46 saved-by: csmith auto-generated-by: OBO-Edit 1.101 --- 1,4 ---- format-version: 1.2 ! date: 18:07:2008 16:23 saved-by: csmith auto-generated-by: OBO-Edit 1.101 *************** *** 2484,2488 **** id: MP:0000427 name: abnormal hair cycle ! def: "aberrant growth or asynchronous timing of the hair growth " [J:65302] is_a: MP:0002073 ! abnormal hair growth --- 2484,2488 ---- id: MP:0000427 name: abnormal hair cycle ! def: "aberrant timing of growth and loss of hair (coat)" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] is_a: MP:0002073 ! abnormal hair growth *************** *** 9941,9945 **** id: MP:0001664 name: abnormal digestion ! def: "altered ability of the mechanical, chemical, and enzymatic processes of the body to convert ingested food into material suitable for assimilation for synthesis of tissues or liberation of energy " [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] synonym: "abnormal digestive function" EXACT [] is_a: MP:0001663 ! abnormal digestive system physiology --- 9941,9945 ---- id: MP:0001664 name: abnormal digestion ! def: "altered ability of the mechanical, chemical, and enzymatic processes of the body to convert ingested food into material suitable for assimilation for synthesis of tissues or liberation of energy" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] synonym: "abnormal digestive function" EXACT [] is_a: MP:0001663 ! abnormal digestive system physiology *************** *** 9954,9958 **** id: MP:0001666 name: abnormal nutrient absorption ! def: "anomalous ability of the body to take in constituents of food necessary for normal physiologic function" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] is_a: MP:0001663 ! abnormal digestive system physiology --- 9954,9958 ---- id: MP:0001666 name: abnormal nutrient absorption ! def: "anomaly in the ability of the body to take in constituents of food necessary for normal physiological function" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition"] is_a: MP:0001663 ! abnormal digestive system physiology *************** *** 19496,19500 **** name: abnormal cell migration def: "defect in the movement of cells during developmental or chemotactic processes" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] ! is_a: MP:0005384 ! cellular phenotype [Term] --- 19496,19500 ---- name: abnormal cell migration def: "defect in the movement of cells during developmental or chemotactic processes" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] ! is_a: MP:0005621 ! abnormal cell physiology [Term] *************** *** 25713,25719 **** name: chromosome breakage alt_id: MP:0002008 ! def: "chromosome instability in the from of increased frequency of spontaneous breakage with or without rearrangements" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! synonym: "chromosomal instability" EXACT [] ! is_a: MP:0003111 ! abnormal nucleus morphology [Term] --- 25713,25718 ---- name: chromosome breakage alt_id: MP:0002008 ! def: "chromosome instability in the form of increased frequency of spontaneous breakage with or without rearrangements" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] ! is_a: MP:0008866 ! chromosomal instability [Term] *************** *** 48047,48051 **** id: MP:0008847 name: abnormal suprachiasmatic nucleus morphology ! def: "any structural anomaly of an ovoid densely packed collection of small cells of the anterior hypothalamus lying close to the midline in a shallow impression of the optic chiasm; it recieves input from the retina and influences neuroendocrine function" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MESH:A08.186.211.730.317.357.342.625] is_a: MP:0000837 ! abnormal hypothalamus morphology --- 48046,48050 ---- id: MP:0008847 name: abnormal suprachiasmatic nucleus morphology ! def: "any structural anomaly of an ovoid densely packed collection of small cells of the anterior hypothalamus lying close to the midline in a shallow impression of the optic chiasm; it receives input from the retina and influences neuroendocrine function" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MESH:A08.186.211.730.317.357.342.625] is_a: MP:0000837 ! abnormal hypothalamus morphology *************** *** 48091,48094 **** --- 48090,48174 ---- is_a: MP:0000013 ! abnormal adipose tissue distribution + [Term] + id: MP:0008854 + name: bleb + def: "presence of a blister-like, nearly hemispherical structure formed during embryonic development filled with air, serous fluid or blood" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + synonym: "blistering" BROAD [] + synonym: "bulla" EXACT [] + is_a: MP:0001191 ! abnormal skin condition + + [Term] + id: MP:0008855 + name: eye bleb + def: "presence of blister-like structures formed in the eye during embryonic development that are usually filled with blood" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0001286 ! abnormal eye development + + [Term] + id: MP:0008856 + name: fetal bleb + def: "presence of subepidermal blister-like structures on the skin, often on the head, formed during embryonic development and usually filled with blood" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0003941 ! abnormal skin development + + [Term] + id: MP:0008857 + name: myelencephalic blebs + def: "presence of blister-like structures formed on the posterior portion of the embryonic hindbrain that are usually filled with blood" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0006108 ! abnormal hindbrain development + + [Term] + id: MP:0008858 + name: abnormal hair cycle anagen phase + def: "anomaly in the growth phase of the hair cycle" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0000427 ! abnormal hair cycle + + [Term] + id: MP:0008859 + name: abnormal hair cycle catagen phase + def: "anomaly in the phase of the hair growth cycle during which cell proliferation ceases, the hair follicle shortens, and an anchored hair is produced" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0000427 ! abnormal hair cycle + + [Term] + id: MP:0008860 + name: abnormal hair cycle telogen phase + def: "anomaly in the resting or quiescent phase of the hair growth cycle which follows cessation of proliferation (catagen) and preceeds hair loss" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0000427 ! abnormal hair cycle + + [Term] + id: MP:0008861 + name: abnormal hair shedding + def: "anomaly in the hair cycle changes the timing of the hair loss that normally follows the anagen phase" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] + is_a: MP:0000427 ! abnormal hair cycle + + [Term] + id: MP:0008862 + name: asymmetric snout + def: "presence of a snout that lacks mirrored identity on either side of the median plane" [MGI:mberry "Melissa Berry, Genetics Resources Curator"] + synonym: "snout asymmetry" EXACT [] + is_a: MP:0000443 ! abnormal snout morphology + + [Term] + id: MP:0008863 + name: craniofacial asymmetry + def: "head or facila features that lack mirrored identity on either side of the median plane" [MGI:mberry "Melissa Berry, Genetics Resources Curator"] + is_a: MP:0003935 ! abnormal craniofacial development + + [Term] + id: MP:0008864 + name: abnormal intestinal secretion + def: "any anomaly in the quantity or rate of any substance transported from intestinal cells into the lumen of the intestine" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + is_a: MP:0000501 ! abnormal digestive secretion + + [Term] + id: MP:0008865 + name: abnormal intestinal absorption + def: "any anomaly in the quantity or rate of any substance taken up by intestinal cells from the lumen of the intestine" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] + is_a: MP:0001664 ! abnormal digestion + + [Term] + id: MP:0008866 + name: chromosomal instability + def: "increase in the probability that whole chromosomes or large fractions of chromosomes are gained or lost during cell division, resulting in an imbalance in the number of chromosomes per cell (aneuploidy) and an enhanced rate of loss of heterozygosity" [PMID:12446840] + is_a: MP:0005621 ! abnormal cell physiology + [Typedef] id: part_of |
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From: Seth C. <sjc...@us...> - 2008-07-19 07:02:01
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv14272/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-18 07:01:59
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv6504/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-17 07:01:51
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv29867/phenotype Modified Files: mammalian_phenotype.obo mosquito_insecticide_resistance.obo Log Message: Automated file update Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.185 retrieving revision 1.186 diff -C2 -d -r1.185 -r1.186 *** mammalian_phenotype.obo 4 Jul 2008 07:01:51 -0000 1.185 --- mammalian_phenotype.obo 17 Jul 2008 07:01:54 -0000 1.186 *************** *** 1,4 **** format-version: 1.2 ! date: 03:07:2008 15:16 saved-by: csmith auto-generated-by: OBO-Edit 1.101 --- 1,4 ---- format-version: 1.2 ! date: 16:07:2008 16:46 saved-by: csmith auto-generated-by: OBO-Edit 1.101 *************** *** 53,57 **** name: loss of subcutaneous adipose tissue def: "reduction in amount or absence of adipose tissue beneath the skin" [PMID:8941642] ! is_a: MP:0000013 ! abnormal adipose tissue distribution [Term] --- 53,58 ---- name: loss of subcutaneous adipose tissue def: "reduction in amount or absence of adipose tissue beneath the skin" [PMID:8941642] ! comment: Obsolete. Use instead the terms decreased subcutaneous adipose tissue amount (MP:0008844) or absent subcutaneous adipose tissue (MP:0008843). ! is_obsolete: true [Term] *************** *** 8164,8169 **** name: eyelids open at birth alt_id: MP:0001342 ! def: "widely open eyes instead of closed at perinatal stage" [J:51966] comment: In mouse, eyelids normally fuse about 5 days prior to birth and reopen about 19 days later. is_a: MP:0003153 ! early eyelid opening --- 8165,8171 ---- name: eyelids open at birth alt_id: MP:0001342 ! def: "widely open eyes instead of closed at perinatal stage; the upper and lower thin folds of skin and muscle that cover the exposed portion of the eye do not fuse together during development and an individual is born with the eye uncovered" [MGI:llw2 "Linda Washburn, Mouse Genome Informatics Curator"] comment: In mouse, eyelids normally fuse about 5 days prior to birth and reopen about 19 days later. + synonym: "open eyelids" EXACT [] is_a: MP:0003153 ! early eyelid opening *************** *** 9356,9359 **** --- 9358,9362 ---- name: impaired swimming def: "reduced ability or inability to swim" [J:39081, J:45446] + synonym: "impaired ability to orient in water" NARROW [] is_a: MP:0001516 ! abnormal motor coordination/ balance is_a: MP:0003312 ! abnormal locomotor coordination *************** *** 19492,19496 **** id: MP:0003091 name: abnormal cell migration ! def: "defect in the movement of cells during developmental processes" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0005384 ! cellular phenotype --- 19495,19499 ---- id: MP:0003091 name: abnormal cell migration ! def: "defect in the movement of cells during developmental or chemotactic processes" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0005384 ! cellular phenotype *************** *** 21622,21626 **** id: MP:0003410 name: abnormal artery development ! def: "anomaly in the process of forming the blood vessels that carry blood away from the heart" [J:94740, MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0000260 ! abnormal angiogenesis is_a: MP:0002191 ! abnormal artery morphology --- 21625,21629 ---- id: MP:0003410 name: abnormal artery development ! def: "anomaly in the process of forming the blood vessels that carry blood away from the heart" [MESH:A07.231.114, MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"] is_a: MP:0000260 ! abnormal angiogenesis is_a: MP:0002191 ! abnormal artery morphology *************** *** 23617,23622 **** [Term] id: MP:0003711 ! name: abnormal pathological neovascularization ! def: "the proliferation of blood vessels in abnormal tissues or in abnormal positions" [MESH:National Library of Medicine_Medical Subject Headings] is_a: MP:0000260 ! abnormal angiogenesis --- 23620,23628 ---- [Term] id: MP:0003711 ! name: pathological neovascularization ! def: "the proliferation of blood vessels in abnormal tissues or in abnormal positions" [MESH:C23.550.589.500] ! synonym: "pathologic angiogenesis" EXACT [] ! synonym: "pathologic neovascularization" EXACT [] ! synonym: "pathological angiogenesis" EXACT [] is_a: MP:0000260 ! abnormal angiogenesis *************** *** 23664,23668 **** id: MP:0003718 name: maternal effect ! def: "expression of a phenotypic trait in an female animal's offspring that is dependent on the maternal genotype" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] is_a: MP:0005395 ! other phenotype --- 23670,23674 ---- id: MP:0003718 name: maternal effect ! def: "expression of a phenotypic trait in a female animal's offspring that is dependent on the maternal genotype" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] is_a: MP:0005395 ! other phenotype *************** *** 24483,24487 **** id: MP:0003845 name: abnormal decidualization ! def: "disrupted proliferation, differentiation or transformation of endometrial stromal cells into decidual cells in the maternal uterus following embryo implantation" [J:43609, J:48920, MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] synonym: "defective decidualization" EXACT [] is_a: MP:0004014 ! abnormal uterine environment --- 24489,24493 ---- id: MP:0003845 name: abnormal decidualization ! def: "disrupted proliferation, differentiation or transformation of endometrial stromal cells into decidual cells in the maternal uterus during embryo implantation" [J:43609, J:48920, MGI:anna "Anna V. Anagnostopoulos, Mouse Genome Informatics Curator"] synonym: "defective decidualization" EXACT [] is_a: MP:0004014 ! abnormal uterine environment *************** *** 36604,36608 **** name: choroidal neovascularization def: "new, abnormal, vessel development of the thin, highly vascularized membrane covering most of the posterior of the eye between the retina and the sclera" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] ! is_a: MP:0003711 ! abnormal pathological neovascularization is_a: MP:0006237 ! abnormal choroid vasculature --- 36610,36614 ---- name: choroidal neovascularization def: "new, abnormal, vessel development of the thin, highly vascularized membrane covering most of the posterior of the eye between the retina and the sclera" [ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator"] ! is_a: MP:0003711 ! pathological neovascularization is_a: MP:0006237 ! abnormal choroid vasculature *************** *** 48072,48075 **** --- 48078,48094 ---- is_a: MP:0008849 ! abnormal hemoglobin concentration distribution width + [Term] + id: MP:0008852 + name: retinal neovascularization + def: "formation of new blood vessels originating from the retinal veins and extending along the inner (vitreal) surface of the retina" [MESH:C11.768.725] + is_a: MP:0003711 ! pathological neovascularization + + [Term] + id: MP:0008853 + name: decreased abdominal adipose tissue amount + def: "reduction in amount of adipose tissue associated with internal organs" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"] + synonym: "reduced abdominal adipose tissue amount" EXACT [] + is_a: MP:0000013 ! abnormal adipose tissue distribution + [Typedef] id: part_of |
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From: Seth C. <sjc...@us...> - 2008-07-16 07:01:45
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv17758/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-15 07:01:49
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv30384/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-11 07:02:06
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv31920/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-10 07:01:44
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv24025/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-09 07:01:57
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv4140/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Seth C. <sjc...@us...> - 2008-07-08 07:01:46
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv28876/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Mike C. <goc...@us...> - 2008-07-07 17:04:54
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv13709 Modified Files: yeast_phenotype.obo Log Message: Updates from SGD for new phenotype qualifiers Index: yeast_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/yeast_phenotype.obo,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** yeast_phenotype.obo 28 Jan 2008 18:04:22 -0000 1.3 --- yeast_phenotype.obo 7 Jul 2008 17:04:56 -0000 1.4 *************** *** 1,7 **** format-version: 1.0 ! date: 22:01:2008 17:03 saved-by: nash auto-generated-by: OBO-Edit 1.100 default-namespace: yeast_phenotype_ontology [Term] --- 1,8 ---- format-version: 1.0 ! date: 27:06:2008 16:05 [...1221 lines suppressed...] ! id: YPO:0000266 ! name: cell cycle progression in S phase ! namespace: observable ! def: "Progression of cells through S phase, the part of the mitotic cell cycle where DNA synthesis occurs." [SGD:RSN] ! is_a: YPO:0000253 ! cell cycle progression ! ! [Term] ! id: YPO:0000267 ! name: entry into G0 (stationary phase) ! namespace: observable ! def: "Entry of cells into the G0 or stationary phase of the mitotic cell cycle, where they enter a quiescent state." [SGD:RSN] ! is_a: YPO:0000072 ! mitotic cell cycle ! ! [Term] ! id: YPO:0000268 ! name: exit from G0 (stationary phase) ! namespace: observable ! def: "Exit of cells from the G0 or stationary phase of the mitotic cell cycle, where they move from a quiescent state to one where growth and division resumes in the G1 phase of the mitotic cell cycle." [SGD:RSN] ! is_a: YPO:0000072 ! mitotic cell cycle |
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From: Seth C. <sjc...@us...> - 2008-07-07 07:01:38
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv21125/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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From: Georgios V. G. <gk...@us...> - 2008-07-06 12:46:30
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv22721 Modified Files: quality.obo Log Message: update Index: quality.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/quality.obo,v retrieving revision 1.114 retrieving revision 1.115 diff -C2 -d -r1.114 -r1.115 *** quality.obo 13 Jun 2008 08:36:34 -0000 1.114 --- quality.obo 6 Jul 2008 12:46:34 -0000 1.115 *************** *** 1,4 **** format-version: 1.0 ! date: 13:06:2008 09:27 saved-by: George Gkoutos auto-generated-by: OBO-Edit 1.100 --- 1,4 ---- format-version: 1.0 ! date: 06:07:2008 13:42 saved-by: George Gkoutos auto-generated-by: OBO-Edit 1.100 *************** *** 2639,2642 **** --- 2639,2643 ---- id: PATO:0000462 name: absent + def: "Not existent; lacking." [thefreedictionary.:thefreedictionary. "http://www.thefreedictionary.com/"] subset: absent_slim subset: value_slim *************** *** 2646,2649 **** --- 2647,2651 ---- id: PATO:0000463 name: conspicuous + def: "A quality inhering in a bearer by virtue of being clearly visible." [thefreedictionary:thefreedictionary "http://www.thefreedictionary.com"] subset: value_slim is_a: PATO:0000070 ! presence *************** *** 2652,2655 **** --- 2654,2658 ---- id: PATO:0000464 name: inconspicuous + def: "A quality inhering in a bearer by virtue of not being clearly visible." [thefreedictionary:thefreedictionary "http://www.thefreedictionary.com"] subset: value_slim is_a: PATO:0000070 ! presence *************** *** 2674,2680 **** [Term] id: PATO:0000468 ! name: decreased def: "An amount which ir relative low." [PATOC:GVG] subset: value_slim related_synonym: "reduced" [] is_a: PATO:0000071 ! amount --- 2677,2684 ---- [Term] id: PATO:0000468 ! name: decreased amount def: "An amount which ir relative low." [PATOC:GVG] subset: value_slim + related_synonym: "decreased" [] related_synonym: "reduced" [] is_a: PATO:0000071 ! amount *************** *** 2687,2693 **** [Term] id: PATO:0000470 ! name: increased def: "An amount which ir relative high." [PATOC:GVG] subset: value_slim is_a: PATO:0000071 ! amount --- 2691,2698 ---- [Term] id: PATO:0000470 ! name: increased amount def: "An amount which ir relative high." [PATOC:GVG] subset: value_slim + related_synonym: "increased" [] is_a: PATO:0000071 ! amount *************** *** 11702,11705 **** --- 11707,11711 ---- subset: value_slim related_synonym: "tubular" [] + exact_synonym: "tubulate" [] is_a: PATO:0000052 ! shape *************** *** 11895,11898 **** --- 11901,11905 ---- name: lumenized def: "Structure which has a lumen." [PATOC:ceri] + comment: See GO term: GO:0031974 membrane-enclosed lumen [DEF:"The enclosed volume within a sealed membrane or between two sealed membranes."]. subset: value_slim exact_synonym: "tubulate" [] *************** *** 12491,12494 **** --- 12498,12521 ---- is_a: PATO:0000052 ! shape + [Term] + id: PATO:0001985 + name: frozen + def: "A quality inhering in a bearer by virtue of being kept below its freezing point." [OBI:OBI] + subset: value_slim + is_a: PATO:0000146 ! temperature + + [Term] + id: PATO:0001986 + name: dissolved + def: "A quality inhering in an bearing by virtue of passing into solution." [PATOC:GVG] + subset: value_slim + is_a: PATO:0001537 ! soluble in + + [Term] + id: PATO:0001987 + name: saccular + def: "A sac like structure." [answers.com:answers.com "http://www.answers.com/"] + is_a: PATO:0000141 ! structure + [Typedef] id: is_magnitude_of |
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From: Seth C. <sjc...@us...> - 2008-07-06 07:01:46
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv25758/phenotype Modified Files: mosquito_insecticide_resistance.obo Log Message: Automated file update |
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