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[Obo-phenotype-commits] obo/ontology/phenotype mammalian_phenotype.obo, 1.95, 1.96
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From: girlwithglasses <gir...@us...> - 2007-08-14 16:25:55
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sc8-pr-cvs3.sourceforge.net:/tmp/cvs-serv31069/obo/ontology/phenotype Modified Files: mammalian_phenotype.obo Log Message: Automated file update Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.95 retrieving revision 1.96 diff -C2 -d -r1.95 -r1.96 *** mammalian_phenotype.obo 11 Aug 2007 01:04:58 -0000 1.95 --- mammalian_phenotype.obo 14 Aug 2007 16:25:50 -0000 1.96 *************** *** 1,4 **** format-version: 1.2 ! date: 09:08:2007 16:40 saved-by: csmith auto-generated-by: OBO-Edit 1.002 --- 1,4 ---- format-version: 1.2 ! date: 13:08:2007 16:42 saved-by: csmith auto-generated-by: OBO-Edit 1.002 *************** *** 798,803 **** id: MP:0000136 name: abnormal microglial cell morphology ! def: "anomalous structure, number, or composition of the small neuroglial cells, possibly of mesodermal origin, which may become phagocytic, in areas of neural damage or inflammation" [anna:Anna V. Anagnostopoulos_Mouse Genome Informatics Curator, PMID:11567042] is_a: MP:0000952 ! abnormal CNS glia [Term] --- 798,804 ---- id: MP:0000136 name: abnormal microglial cell morphology ! def: "any strucutral anomaly of the small, migratory, phagocytic, interstitial cells derived from myeloid progenitor cells and found in the parenchyma of the central nervous system; microglia are scavengers, engulfing dead cells and other debris, and in Alzheimer's disease, microglia are found associated with dying nerve cells and amyloid plaques" [PMID:16322748] is_a: MP:0000952 ! abnormal CNS glia + is_a: MP:0002446 ! abnormal macrophage morphology [Term] *************** *** 7763,7766 **** --- 7764,7768 ---- synonym: "reduced body size" EXACT [] synonym: "runt" EXACT [] + synonym: "runted" EXACT [] synonym: "runting" EXACT [] synonym: "small body size" EXACT [] *************** *** 10305,10309 **** id: MP:0001764 name: abnormal homeostasis ! def: "anomaly in the state of equilibrium in the body with respect to various functions and to chemical composition of the fluids and tissues" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] synonym: "homeostasis abnormalities" EXACT [] is_a: MP:0005376 ! homeostasis/metabolism phenotype --- 10307,10312 ---- id: MP:0001764 name: abnormal homeostasis ! def: "anomaly in the maintenance of equilibrium in the body with respect to various functions and to chemical or protein composition of the fluids and tissues" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] ! synonym: "abnormal homeostatic process" EXACT [] synonym: "homeostasis abnormalities" EXACT [] is_a: MP:0005376 ! homeostasis/metabolism phenotype *************** *** 11228,11231 **** --- 11231,11237 ---- name: male infertility def: "inability of male to produce live offspring" [J:60409, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] + synonym: "male infertile" EXACT [] + synonym: "male sterile" EXACT [] + synonym: "male sterility" EXACT [] is_a: MP:0001924 ! infertility is_a: MP:0003698 ! abnormal male reproductive system physiology *************** *** 11235,11238 **** --- 11241,11247 ---- name: female infertility def: "inability of female to produce live offspring" [J:34193, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] + synonym: "female infertile" EXACT [] + synonym: "female sterile" EXACT [] + synonym: "female sterility" EXACT [] is_a: MP:0001924 ! infertility is_a: MP:0003699 ! abnormal female reproductive system physiology *************** *** 15843,15847 **** def: "altered ability or inability to metabolize or respond to foreign substances" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, J:55555] synonym: "abnormal metabolism of xenobiotics" EXACT [] ! is_a: MP:0002121 ! other metabolic defect [Term] --- 15852,15856 ---- def: "altered ability or inability to metabolize or respond to foreign substances" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator, cwg:Carroll-Ann W. Goldsmith_Mouse Genome Informatics Curator, J:55555] synonym: "abnormal metabolism of xenobiotics" EXACT [] ! is_a: MP:0005266 ! abnormal metabolism [Term] *************** *** 19815,19818 **** --- 19824,19828 ---- name: abnormal cellular cholesterol metabolism def: "impaired regulation of cellular cholesterol levels" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator] + is_a: MP:0005266 ! abnormal metabolism is_a: MP:0005621 ! abnormal cell physiology *************** *** 22694,22698 **** def: "altered ability or inability to metabolize or respond to substances normally present in the body" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator] synonym: "abnormal metabolism of endogenous compounds" EXACT [] ! is_a: MP:0002121 ! other metabolic defect [Term] --- 22704,22708 ---- def: "altered ability or inability to metabolize or respond to substances normally present in the body" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator] synonym: "abnormal metabolism of endogenous compounds" EXACT [] ! is_a: MP:0005266 ! abnormal metabolism [Term] *************** *** 23049,23053 **** id: MP:0003691 name: abnormal microglial cell physiology ! def: "anomalous activity of the small neuroglial cells, possibly of mesodermal origin, which may become phagocytic, in areas of neural damage or inflammation" [hdene:Howard Dene_Mouse Genome Informatics Curator] is_a: MP:0003690 ! abnormal glial cell physiology --- 23059,23064 ---- id: MP:0003691 name: abnormal microglial cell physiology ! def: "any functional anomaly of the small, migratory, phagocytic, interstitial cells derived from myeloid progenitor cells and found in the parenchyma of the central nervous system; microglia are scavengers, engulfing dead cells and other debris, and in Alzheimer's disease, microglia are found associated with dying nerve cells and amyloid plaques" [PMID:16322748] ! is_a: MP:0002451 ! abnormal macrophage physiology is_a: MP:0003690 ! abnormal glial cell physiology *************** *** 23773,23777 **** name: abnormal nucleotide metabolism def: "impaired regulation of nucleotide levels in either production or breakdown of these structural components of nucleic acids" [MeSH:National Library of Medicine_Medical Subject Headings] ! is_a: MP:0001764 ! abnormal homeostasis [Term] --- 23784,23788 ---- name: abnormal nucleotide metabolism def: "impaired regulation of nucleotide levels in either production or breakdown of these structural components of nucleic acids" [MeSH:National Library of Medicine_Medical Subject Headings] ! is_a: MP:0005266 ! abnormal metabolism [Term] *************** *** 30230,30234 **** --- 30241,30248 ---- id: MP:0004778 name: increased number of foam cells + def: "greater than normal number of a type of macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions" [CL:0000517] is_a: MP:0001547 ! abnormal lipid level + is_a: MP:0005425 ! increased macrophage cell number + is_a: MP:0008243 ! abnormal foam cell morphology [Term] *************** *** 31641,31644 **** --- 31655,31659 ---- def: "any structural anomaly of the bone resorpting cells that removes bone tissue by degrading the mineralized matrix" [csmith:Cynthia L. Smith_Mouse Genome Informatics Curator] synonym: "abnormal osteophage morphology" EXACT [] + is_a: MP:0002446 ! abnormal macrophage morphology is_a: MP:0003795 ! abnormal bone structure *************** *** 33766,33772 **** id: MP:0005266 name: abnormal metabolism ! def: "anomalous chemical and physical changes occurring in tissue " [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] synonym: "metabolic abnormalities" EXACT [] ! is_obsolete: true [Term] --- 33781,33788 ---- id: MP:0005266 name: abnormal metabolism ! def: "any anomaly in the processes that cause many of the chemical changes in living organisms, including anabolism and catabolism; metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation" [GO:0008152] ! synonym: "abnormal metabolic process" EXACT [] synonym: "metabolic abnormalities" EXACT [] ! is_a: MP:0005376 ! homeostasis/metabolism phenotype [Term] *************** *** 34154,34158 **** id: MP:0005319 name: abnormal enzyme/ coenzyme level ! def: "altered concentration of any of these proteins, or their cofactors, that act as catalysts to induce chemical changes in other substances" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] is_a: MP:0001764 ! abnormal homeostasis --- 34170,34174 ---- id: MP:0005319 name: abnormal enzyme/ coenzyme level ! def: "altered level of any of these proteins, or their cofactors, that act as catalysts to induce chemical changes in other substances" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] is_a: MP:0001764 ! abnormal homeostasis *************** *** 35899,35903 **** name: abnormal enzyme/coenzyme activity def: "altered ability of any of these proteins, or their cofactors, to act as catalysts to induce chemical changes in other substances" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] ! is_a: MP:0001764 ! abnormal homeostasis [Term] --- 35915,35919 ---- name: abnormal enzyme/coenzyme activity def: "altered ability of any of these proteins, or their cofactors, to act as catalysts to induce chemical changes in other substances" [Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] ! is_a: MP:0005266 ! abnormal metabolism [Term] *************** *** 39607,39610 **** --- 39623,39627 ---- def: "any anomaly in the process whereby new strands of DNA are synthesized" [GO:0006260] xref: GO:0006260 + is_a: MP:0005266 ! abnormal metabolism is_a: MP:0005621 ! abnormal cell physiology *************** *** 39614,39617 **** --- 39631,39635 ---- def: "any anomaly in the process of restoring DNA after damage or replication error" [GO:0006281] xref: GO:0006281 + is_a: MP:0005266 ! abnormal metabolism is_a: MP:0005621 ! abnormal cell physiology *************** *** 40847,40850 **** --- 40865,40929 ---- is_a: MP:0003204 ! decreased neuron apoptosis + [Term] + id: MP:0008237 + name: abnormal ventral coat pigmentation + def: "irregular or unusual pigmentation of ventrum hair in relation to control animals" [llw2:Linda Washburn_Mouse Genome Informatics Curator] + is_a: MP:0002075 ! abnormal coat color + + [Term] + id: MP:0008238 + name: abnormal dorsoventral coat patterning + def: "irregular or unusual pigmentation pattern of the dorsal-to-ventral axis compared to control animals" [llw2:Linda Washburn_Mouse Genome Informatics Curator] + is_a: MP:0002075 ! abnormal coat color + + [Term] + id: MP:0008239 + name: epigenetic coat coloration + def: "a range of wild-type and mutant allele coat coloration, from mouse to mouse or coat color mosaicism of an individual mouse, due to differential methylation of the mutation causing element" [llw2:Linda Washburn_Mouse Genome Informatics Curator] + is_a: MP:0005366 ! variegated coat color + + [Term] + id: MP:0008240 + name: abnormal spleen marginal zone macrophage morphology + def: "any structural anomaly of the cells present in the splenic marginal zone and are involved in the recognition and clearance of material, such as pathogen-derived material, from the splenic circulation" [PMID:16322748] + is_a: MP:0002362 ! abnormal spleen marginal zone morphology + is_a: MP:0002446 ! abnormal macrophage morphology + + [Term] + id: MP:0008241 + name: abnormal metallophilic macrophage morphology + def: "any structural anomaly of the macrophage cells that surround the white pulp of the spleen, adjacent to the marginal sinus" [PMID:16322748] + synonym: "abnormal marginal metallophilic macrophage" EXACT [] + synonym: "abnormal splenic marginal metallophilic macrophages" EXACT [] + synonym: "abnormal splenic metallophilic macrophage morphology" EXACT [] + is_a: MP:0002357 ! abnormal spleen white pulp morphology + is_a: MP:0002446 ! abnormal macrophage morphology + + [Term] + id: MP:0008242 + name: abnormal perivascular macrophage morphology + def: "any structural anomaly of macrophages that line the small blood vessels" [PMID:16322748] + is_a: MP:0001614 ! abnormal vasculature + is_a: MP:0002446 ! abnormal macrophage morphology + + [Term] + id: MP:0008243 + name: abnormal foam cell morphology + def: "any structural anomaly of a type of macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions" [CL:0000517] + is_a: MP:0002446 ! abnormal macrophage morphology + + [Term] + id: MP:0008244 + name: abnormal peritoneal macrophage morphology + def: "any structural anomaly of a mononuclear phagocyte that develops from bone marrow precursors but is resident in the peritoneum" [CL:0000581, MESH:A.11.329.372.630] + is_a: MP:0002446 ! abnormal macrophage morphology + + [Term] + id: MP:0008245 + name: abnormal alveolar macrophage morphology + def: "any structural anomaly of the round, granular, mononuclear phagocytes found in the alveoli of the lungs which ingest small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells" [CL:0000583, MESH:A.11.329.372.600] + is_a: MP:0002270 ! abnormal respiratory alveoli morphology + is_a: MP:0002446 ! abnormal macrophage morphology + [Typedef] id: is_a |