format-version: 1.2 data-version: releases/2015-01-29 date: 30:01:2015 14:21 saved-by: midori auto-generated-by: OBO-Edit 2.3.1 subsetdef: qc_do_not_annotate "Term not to be used for direct annotation" subsetdef: qc_do_not_manually_annotate "Term not to be used for direct manual annotation" default-namespace: fission_yeast_phenotype remark: svn version: $Revision: 714 $ ontology: fypo [Term] id: FYPO:0000001 name: phenotype def: "Any of the set of observable characteristics of an organism resulting from the interaction of its genotype with the environment." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast phenotype" EXACT [PomBase:mah] creation_date: 2011-03-16T03:59:25Z [Term] id: FYPO:0000002 name: cell phenotype def: "A phenotype that is observed at the level of an individual cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast cell phenotype" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype disjoint_from: FYPO:0000003 ! cell population phenotype created_by: midori creation_date: 2011-03-16T04:25:28Z [Term] id: FYPO:0000003 name: cell population phenotype def: "A phenotype that is observed at the level of a population of cells." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note: differentium is population level, and may reflect observation conditions. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast cell population phenotype" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype created_by: midori creation_date: 2011-03-16T04:26:35Z [Term] id: FYPO:0000004 name: cell viability def: "A cell phenotype that consists of the cell's disposition to survive and develop normally." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Viability is usually determined under standard laboratory conditions, i.e. a cell is generally considered viable if it can grow in rich medium under normal conditions such as temperature, pressure, oxygen level, pH, etc. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate is_a: FYPO:0000002 ! cell phenotype is_a: PATO:0000169 ! viability intersection_of: PATO:0000169 ! viability intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000005 name: abnormal cell morphology alt_id: FYPO:0000019 def: "A cell phenotype characterized by altered cell morphology, i.e. the size, shape, or structure of the cell is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cell morphology, misshapen cells" RELATED [PomBase:mah] synonym: "cellular morphology: abnormal" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: FYPO:0003037 ! abnormal cell phenotype is_a: PATO:0000051 ! morphology intersection_of: PATO:0000051 ! morphology intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000011 name: abnormal cell cycle alt_id: FYPO:0000406 def: "A cellular process phenotype in which a cell does not proceed normally through a cell cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cell-division cycle" EXACT [GO:0007049, PomBase:mah] synonym: "cell cycle defects" EXACT [PomBase:mah] synonym: "cell cycle progression: abnormal" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000628 ! abnormal cellular process is_a: FYPO:0000631 ! cell cycle phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0007049 ! cell cycle intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0007049 ! cell cycle relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000014 name: tapered cell def: "A cell morphology phenotype in which the cell tapers at one end to a diameter smaller than the other. The cell diameter at the narrow end is smaller than that of a wild-type cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "bottle-shaped cell" EXACT [PomBase:vw] synonym: "cell morphology, bottle/skittle" EXACT [PomBase:mah] synonym: "skittle-shaped cell" EXACT [PomBase:mah] is_a: FYPO:0001126 ! abnormal cell shape is_a: PATO:0002213 ! obclavate intersection_of: PATO:0002213 ! obclavate intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000015 name: branched vegetative cell def: "A cell morphology phenotype observed in the vegetative growth phase of the life cycle in which a daughter cell begins to grow at approximately a right angle to the septum or cell division site of the mother cell, resulting in the formation of a single cell that has a branch." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "branched cell" EXACT [PomBase:mah] synonym: "branched cell during vegetative growth" EXACT [PomBase:mah] synonym: "branched vegetative cell during mitotic cell cycle" RELATED [PomBase:mah] synonym: "branched, septated cell" EXACT [PomBase:jh, PomBase:mah, PomBase:vw] synonym: "branched, septated vegetative cell" EXACT [PomBase:vw] synonym: "cell morphology, branched" EXACT [PomBase:mah] is_a: FYPO:0002196 ! abnormal vegetative cell shape is_a: PATO:0000402 ! branched intersection_of: PATO:0000402 ! branched intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000017 name: elongated cell def: "A cell morphology phenotype in which cells are longer than normal, i.e. the maximum distance between the cell ends is greater than normal." [PomBase:mah, PomBase:vw] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that this term is classified as a type of abnormal cell shape, because wild-type cells are never seen with the proportions (length:width ratio) observed in elongated cells. Small cells, in contrast, have the same proportions as a subset of wild-type cells, and simply do not grow to the full length seen in wild type. subset: qc_do_not_manually_annotate synonym: "cell morphology, elongated cell" EXACT [PomBase:mah] synonym: "long cell" EXACT [PomBase:vw] is_a: FYPO:0001126 ! abnormal cell shape is_a: FYPO:0001127 ! abnormal cell size is_a: PATO:0000573 ! increased length intersection_of: PATO:0000573 ! increased length intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000020 name: pear-shaped cell def: "A cell morphology phenotype in which a cell is shaped in the form of a pear. One end is rounded, while the other resembles an end of a normal rod-shaped cell. The normally shaped end has the same diameter as a wild-type cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cell morphology, pear shaped" EXACT [PomBase:mah] synonym: "ice cream cone-shaped cell" EXACT [PMID:2236039, PomBase:vw] is_a: FYPO:0001126 ! abnormal cell shape is_a: PATO:0002240 ! teardrop-shaped intersection_of: PATO:0002240 ! teardrop-shaped intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000023 name: small cell def: "A cell morphology phenotype in which a cell has an abnormally low volume." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that this term is not classified as a type of abnormal cell shape, small cells, have the same proportions as a subset of wild-type cells, and simply do not grow to the full length seen in wild type. Elongated cells, in contrast, have proportions (length:width ratio) that are never observed in wild-type cells, and so are classified under both abnormal cell shape and abnormal cell size. subset: qc_do_not_manually_annotate synonym: "cell size: decreased" EXACT [SGD:phenotype_annotation] is_a: FYPO:0001127 ! abnormal cell size is_a: PATO:0000596 ! decreased volume intersection_of: PATO:0000596 ! decreased volume intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000025 name: swollen cell def: "A cell morphology phenotype in which a cell has a larger volume than normal. In a swollen cell, both length and diameter are greater than normal, although the cell is only considered elongated if the length:width ratio is also greater than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cell morphology, swollen cells" EXACT [PomBase:mah] synonym: "enlarged cell" RELATED [PomBase:mah] synonym: "increased cell size" RELATED [PomBase:vw] synonym: "increased cell volume" EXACT [PomBase:mah] synonym: "large cell" RELATED [PomBase:vw] is_a: FYPO:0001127 ! abnormal cell size is_a: PATO:0000595 ! increased volume intersection_of: PATO:0000595 ! increased volume intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000045 name: abnormal cell population growth def: "A cell population phenotype in which a population of cells grow abnormally." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "growth defect" RELATED [PomBase:mah] is_a: FYPO:0000139 ! cell population growth phenotype is_a: FYPO:0000300 ! biological process phenotype created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000046 name: decreased cell population growth alt_id: FYPO:0000222 def: "A cell population phenotype in which cell population growth is decreased relative to normal. Decreased growth may reflect a reduced growth rate (i.e. slower growth), growth that occurs to a lesser extent than normal, or both." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "aerobic growth defects" RELATED [PomBase:mah] synonym: "decreased aerobic cell population growth" NARROW [PomBase:mah] synonym: "decreased growth" BROAD [PomBase:mah] synonym: "reduced aerobic cell population growth" NARROW [PomBase:mah] synonym: "reduced cell population growth" EXACT [PomBase:mah] synonym: "slow aerobic cell population growth" NARROW [PomBase:mah] is_a: FYPO:0000045 ! abnormal cell population growth is_a: FYPO:0002058 ! viable cell population created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000047 name: normal cell population growth def: "A cell population phenotype in which a population of cells grow normally." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "growth normal" BROAD [PomBase:mah] is_a: FYPO:0000139 ! cell population growth phenotype is_a: FYPO:0002058 ! viable cell population relationship: has_part FYPO:0001419 ! normal cell population growth rate created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000049 name: inviable cell def: "A viability phenotype in which a cell is unable to survive under conditions in which wild type cells survive." [PomBase:mah] comment: Viability is usually determined under standard laboratory conditions, i.e. a cell is generally considered inviable if it cannot grow in rich medium under normal conditions such as temperature, pressure, oxygen level, pH, etc. Note that if you have done an experiment that assays the viability of a population of cells, such as looking at colony growth or growth in liquid culture, you should also annotate to 'inviable cell population' (FYPO:0002059) or one of its descendants. This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "essential" RELATED [PomBase:mah] synonym: "lethal" EXACT [PomBase:mah] is_a: FYPO:0000004 ! cell viability is_a: PATO:0000718 ! lethal (sensu genetics) intersection_of: PATO:0000718 ! lethal (sensu genetics) intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000054 name: abnormal microtubule cytoskeleton organization alt_id: FYPO:0000053 def: "A phenotype that affects the organization of the microtubule cytoskeleton. Microtubule cytoskeleton organization is a cellular process that results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GO:0000226, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that an abnormal microtubule cytoskeleton organization process may, but does not necessarily, result in a physically abnormal microtubule cytoskeleton. subset: qc_do_not_manually_annotate synonym: "abnormal microtubule cytoskeleton organisation" EXACT [PomBase:mah] synonym: "abnormal microtubule organisation" RELATED [PomBase:mah] synonym: "abnormal microtubule organization" RELATED [PomBase:mah] synonym: "microtubule cytoskeleton defects" EXACT [PomBase:mah] synonym: "microtubule organization defects" RELATED [PomBase:mah] is_a: FYPO:0000297 ! microtubule cytoskeleton organization phenotype is_a: FYPO:0000802 ! abnormal cytoskeleton organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0000226 ! microtubule cytoskeleton organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0000226 ! microtubule cytoskeleton organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000061 name: multinucleate vegetative cell def: "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which a cell contains more than one nucleus." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "multinucleate cells during vegetative growth" EXACT [PomBase:al] synonym: "multinucleate vegetative cell during mitotic cell cycle" RELATED [PomBase:mah] synonym: "multiple nuclei during vegetative growth" EXACT [PomBase:al] is_a: FYPO:0001322 ! abnormal subcellular component during vegetative growth is_a: FYPO:0003341 ! multinucleate intersection_of: PATO:0001908 ! multinucleate intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000063 name: abnormal DNA recombination def: "A cellular process phenotype in which DNA recombination is abnormal. DNA recombination is a process that results in reassortment of genes, producing gene combinations different from those that were present in the parents." [GO:0006310, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal recombination" EXACT [PomBase:vw] synonym: "recombination defects" EXACT [PomBase:mah] is_a: FYPO:0000293 ! DNA metabolism phenotype is_a: FYPO:0000860 ! abnormal metabolic process intersection_of: inheres_in GO:0006310 ! DNA recombination intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0006310 ! DNA recombination relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-03-29T05:53:56Z [Term] id: FYPO:0000114 name: cellular process phenotype def: "A phenotype that affects a cellular process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast cellular process phenotype" EXACT [PomBase:mah] is_a: FYPO:0000002 ! cell phenotype is_a: FYPO:0000300 ! biological process phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0044763 ! single-organism cellular process relationship: inheres_in GO:0044763 ! single-organism cellular process created_by: midori creation_date: 2011-04-12T12:00:38Z [Term] id: FYPO:0000119 name: abnormal spindle assembly alt_id: FYPO:0000285 def: "A cellular process phenotype in which spindle assembly is abnormal. Spindle assembly is the aggregation, arrangement and bonding together of a set of components to form the spindle." [GO:0051225, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000054 ! abnormal microtubule cytoskeleton organization is_a: FYPO:0000336 ! abnormal cellular component assembly is_a: FYPO:0002734 ! abnormal cell cycle process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0051225 ! spindle assembly intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0051225 ! spindle assembly relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-03-29T05:54:40Z [Term] id: FYPO:0000124 name: viable cell def: "A viability phenotype in which a cell is able to survive under the specified conditions." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000004 ! cell viability is_a: PATO:0000719 ! viable intersection_of: PATO:0000719 ! viable intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2011-03-29T05:54:40Z [Term] id: FYPO:0000136 name: cellular physical quality phenotype def: "A phenotype that affects any physical object quality, such as morphology, number, location, etc., of a cell or a cellular component." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "cellular physical object quality phenotype" EXACT [PATO:0001241] synonym: "fission yeast cellular physical object quality phenotype" EXACT [PomBase:mah] is_a: FYPO:0000002 ! cell phenotype is_a: PATO:0001241 ! physical object quality intersection_of: PATO:0001241 ! physical object quality intersection_of: inheres_in GO:0005575 ! cellular_component relationship: inheres_in GO:0005575 ! cellular_component created_by: midori creation_date: 2011-04-12T12:01:21Z [Term] id: FYPO:0000137 name: mitotic cell cycle checkpoint phenotype def: "A cell phenotype that affects any mitotic cell cycle checkpoint." [PomBase:mah] subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast mitotic cell cycle checkpoint phenotype" EXACT [PomBase:mah] is_a: FYPO:0000631 ! cell cycle phenotype is_a: FYPO:0001334 ! regulation phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0007093 ! mitotic cell cycle checkpoint relationship: inheres_in GO:0007093 ! mitotic cell cycle checkpoint created_by: midori creation_date: 2011-04-12T12:55:38Z [Term] id: FYPO:0000138 name: localization phenotype def: "A cell phenotype that affects the localization of a structure or substance in a cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast localization phenotype" EXACT [PomBase:mah] synonym: "localisation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0051641 ! cellular localization relationship: inheres_in GO:0051641 ! cellular localization created_by: midori creation_date: 2011-04-12T02:16:04Z [Term] id: FYPO:0000139 name: cell population growth phenotype def: "A cell phenotype that affects the rate or extent of cell population growth." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast cell population growth phenotype" EXACT [PomBase:mah] is_a: FYPO:0000003 ! cell population phenotype created_by: midori creation_date: 2011-04-12T02:22:51Z [Term] id: FYPO:0000140 name: cellular metabolism phenotype def: "A cellular process phenotype that affects metabolism in the cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast cellular metabolism phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0044237 ! cellular metabolic process relationship: inheres_in GO:0044237 ! cellular metabolic process created_by: midori creation_date: 2011-04-12T02:23:26Z [Term] id: FYPO:0000142 name: gene expression phenotype def: "A cellular process phenotype that affects gene expression. Gene expression includes transcription, RNA processing, and, for protein-coding genes, translation and protein maturation." [GO:0010467, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast gene expression phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0010467 ! gene expression relationship: inheres_in GO:0010467 ! gene expression created_by: midori creation_date: 2011-04-12T05:46:51Z [Term] id: FYPO:0000143 name: transcription regulation phenotype def: "A gene expression phenotype that affects the regulation of DNA-dependent transcription." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast transcription regulation phenotype" EXACT [PomBase:mah] synonym: "gene-specific transcription regulation phenotype" RELATED [GO:0006355, PomBase:mah] synonym: "transcriptional control phenotype" BROAD [GO:0006355, PomBase:mah] is_a: FYPO:0000288 ! gene expression regulation phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0006355 ! regulation of transcription, DNA-templated relationship: inheres_in GO:0006355 ! regulation of transcription, DNA-templated created_by: midori creation_date: 2011-04-12T05:47:38Z [Term] id: FYPO:0000145 name: regulation phenotype def: "A cellular process phenotype that affects the regulation of a molecular function, biological process, or biological quality." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast regulation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0065007 ! biological regulation relationship: inheres_in GO:0065007 ! biological regulation created_by: midori creation_date: 2011-04-12T06:00:44Z [Term] id: FYPO:0000149 name: transport phenotype def: "A cell process phenotype that affects a transport process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast transport phenotype" EXACT [PomBase:mah] is_a: FYPO:0000138 ! localization phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0006810 ! transport relationship: inheres_in GO:0006810 ! transport created_by: midori creation_date: 2011-04-14T05:43:20Z [Term] id: FYPO:0000162 name: abnormal cellular response to stress def: "A cellular response phenotype in which a cellular response to stress is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Use a descendant of this term if you have assayed the response to a stress at the subcellular or molecular level. If you have assayed growth of cells exposed to the stress in culture, use a descendant of 'sensitive to stress' (FYPO:0002549) or 'resistance to stress' (FYPO:0002046). subset: qc_do_not_manually_annotate is_a: FYPO:0000298 ! cellular response phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0033554 ! cellular response to stress intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0033554 ! cellular response to stress relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-13T03:34:54Z [Term] id: FYPO:0000176 name: abnormal DNA replication initiation def: "A cellular process phenotype in which the initiation of DNA replication is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal DNA-dependent DNA replication initiation" EXACT [PomBase:mah] is_a: FYPO:0000217 ! abnormal DNA replication intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0006270 ! DNA replication initiation intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0006270 ! DNA replication initiation relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-13T03:34:54Z [Term] id: FYPO:0000180 name: abnormal cellular response to oxidative stress def: "A stress response phenotype in which a cellular response to oxidative stress is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000162 ! abnormal cellular response to stress intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0034599 ! cellular response to oxidative stress intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0034599 ! cellular response to oxidative stress relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-13T03:34:54Z [Term] id: FYPO:0000186 name: abnormal cell division def: "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which cell division is abnormal." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "abnormal cell division during mitotic cell cycle" RELATED [PomBase:mah] synonym: "abnormal cell division during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0001362 ! abnormal cellular process during vegetative growth intersection_of: PATO:0000001 ! quality intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0051301 ! cell division intersection_of: qualifier PATO:0000460 ! abnormal relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0051301 ! cell division relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-13T03:41:10Z [Term] id: FYPO:0000217 name: abnormal DNA replication def: "A cellular process phenotype in which DNA replication is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal DNA-dependent DNA replication" EXACT [PomBase:mah] is_a: FYPO:0000293 ! DNA metabolism phenotype is_a: FYPO:0000860 ! abnormal metabolic process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0006261 ! DNA-dependent DNA replication intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0006261 ! DNA-dependent DNA replication relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-13T03:41:10Z [Term] id: FYPO:0000257 name: normal phenotype def: "A phenotype that shows no detectable differences from normal. In fission yeast, the characteristics of wild type cells of the sequenced strain (972 h-) or the isogenic h+ or h90 strains are regarded as normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast normal phenotype" EXACT [PomBase:mah] synonym: "no obvious phenotype" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype is_a: PATO:0000001 ! quality intersection_of: PATO:0000001 ! quality intersection_of: inheres_in FYPO:0000001 ! phenotype intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in FYPO:0000001 ! phenotype relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2011-04-19T02:59:38Z [Term] id: FYPO:0000263 name: abnormal regulation of translation in response to stress def: "A gene expression phenotype in which regulation of translation in response to stress is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "protein synthesis after stress, defective" RELATED [PomBase:mah] is_a: FYPO:0000162 ! abnormal cellular response to stress is_a: FYPO:0000289 ! translation regulation phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0043555 ! regulation of translation in response to stress intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0043555 ! regulation of translation in response to stress relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-19T02:59:38Z [Term] id: FYPO:0000287 name: abnormal subcellular component def: "A physical cellular phenotype in which the amount, distribution, or morphology of a cell part is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "abnormal subcellular component physical object quality" EXACT [PomBase:mah] synonym: "abnormal subcellular structure" RELATED [PomBase:mah] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: FYPO:0001985 ! abnormal phenotype intersection_of: PATO:0001241 ! physical object quality intersection_of: inheres_in GO:0044464 ! cell part intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0044464 ! cell part relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-04-21T11:18:18Z [Term] id: FYPO:0000288 name: gene expression regulation phenotype def: "A regulation phenotype that affects the regulation of gene expression." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast gene expression regulation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000142 ! gene expression phenotype is_a: FYPO:0000145 ! regulation phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0010468 ! regulation of gene expression relationship: inheres_in GO:0010468 ! regulation of gene expression created_by: midori creation_date: 2011-04-21T02:22:36Z [Term] id: FYPO:0000289 name: translation regulation phenotype def: "A gene expression phenotype that affects the regulation of translation." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast translation regulation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000288 ! gene expression regulation phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0006417 ! regulation of translation relationship: inheres_in GO:0006417 ! regulation of translation created_by: midori creation_date: 2011-04-21T02:25:06Z [Term] id: FYPO:0000290 name: transcription phenotype during vegetative growth def: "A cellular process phenotype that affects DNA-dependent transcription." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast transcription phenotype" EXACT [PomBase:mah] synonym: "transcription phenotype during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000142 ! gene expression phenotype is_a: FYPO:0000294 ! RNA metabolism phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0006351 ! transcription, DNA-templated relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0006351 ! transcription, DNA-templated created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000291 name: translation phenotype def: "A cellular process phenotype that affects translation." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast translation phenotype" EXACT [PomBase:mah] synonym: "translation phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "translation phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000142 ! gene expression phenotype is_a: FYPO:0001348 ! cellular metabolism phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0006412 ! translation relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0006412 ! translation created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000292 name: nucleic acid metabolism phenotype def: "A cellular process phenotype that affects any nucleic acid metabolic process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast nucleic acid metabolism phenotype" EXACT [PomBase:mah] is_a: FYPO:0000140 ! cellular metabolism phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0090304 ! nucleic acid metabolic process relationship: inheres_in GO:0090304 ! nucleic acid metabolic process created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000293 name: DNA metabolism phenotype def: "A cellular process phenotype that affects any DNA metabolic process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast DNA metabolism phenotype" EXACT [PomBase:mah] is_a: FYPO:0000292 ! nucleic acid metabolism phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0006259 ! DNA metabolic process relationship: inheres_in GO:0006259 ! DNA metabolic process created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000294 name: RNA metabolism phenotype def: "A cellular process phenotype that affects any RNA metabolic process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast RNA metabolism phenotype" EXACT [PomBase:mah] synonym: "RNA metabolism phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "RNA metabolism phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0001347 ! nucleic acid metabolism phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0016070 ! RNA metabolic process relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0016070 ! RNA metabolic process created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000295 name: cytoskeleton organization phenotype def: "A cellular process phenotype that affects cytoskeleton organization. Cytoskeleton organization results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GO:0007010, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cytoskeleton organisation phenotype" EXACT [PomBase:mah] synonym: "fission yeast cytoskeleton organization phenotype" EXACT [PomBase:mah] is_a: FYPO:0000334 ! cellular component organization phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0007010 ! cytoskeleton organization relationship: inheres_in GO:0007010 ! cytoskeleton organization created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000297 name: microtubule cytoskeleton organization phenotype def: "A cellular process phenotype that affects the organization of the microtubule cytoskeleton. Microtubule cytoskeleton organization results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and associated proteins." [GO:0000226, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast microtubule cytoskeleton organization phenotype" EXACT [PomBase:mah] synonym: "microtubule cytoskeleton organisation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000295 ! cytoskeleton organization phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0000226 ! microtubule cytoskeleton organization relationship: inheres_in GO:0000226 ! microtubule cytoskeleton organization created_by: midori creation_date: 2011-04-21T02:31:20Z [Term] id: FYPO:0000298 name: cellular response phenotype def: "A cellular process phenotype that affects a response to a stimulus." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast cellular response phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0051716 ! cellular response to stimulus relationship: inheres_in GO:0051716 ! cellular response to stimulus created_by: midori creation_date: 2011-04-21T04:47:15Z [Term] id: FYPO:0000300 name: biological process phenotype def: "A phenotype that affects a biological process." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast biological process phenotype" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0008150 ! biological_process relationship: inheres_in GO:0008150 ! biological_process created_by: midori creation_date: 2011-04-26T02:25:13Z [Term] id: FYPO:0000334 name: cellular component organization phenotype def: "A phenotype that affects a process of cellular component organization, i.e. the assembly, arrangement of constituent parts, or disassembly of a cellular component, that occurs at the cellular level." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cellular component organisation phenotype" EXACT [PomBase:mah] synonym: "cellular component organization phenotype at cellular level" EXACT [PomBase:mah] synonym: "fission yeast cellular component organization phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0016043 ! cellular component organization relationship: inheres_in GO:0016043 ! cellular component organization created_by: midori creation_date: 2011-06-03T11:55:29Z [Term] id: FYPO:0000335 name: abnormal cellular component organization def: "A cellular process phenotype in which any process of cellular component organization at the cellular level is abnormal." [GO:0016043, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular component organisation" EXACT [PomBase:mah] synonym: "abnormal cellular component organization at cellular level" EXACT [PomBase:mah] is_a: FYPO:0000334 ! cellular component organization phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0016043 ! cellular component organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0016043 ! cellular component organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-06-03T11:57:14Z [Term] id: FYPO:0000336 name: abnormal cellular component assembly def: "A cellular process phenotype in which any process of cellular component assembly at the cellular level is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular component assembly at cellular level" EXACT [PomBase:mah] is_a: FYPO:0000335 ! abnormal cellular component organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022607 ! cellular component assembly intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0022607 ! cellular component assembly relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-06-03T12:00:35Z [Term] id: FYPO:0000443 name: abnormal protein localization during vegetative growth def: "A cell phenotype that affects the localization of a protein in a cell in the vegetative growth phase of the life cycle. A protein may be observed in a place where it is not normally found, absent from a place where it is normally found, or both." [PomBase:mah] comment: We recommend using one of the more specific terms instead of annotating to this term directly, if possible. If this term is used, we recommend noting which protein(s) were used in the assay. subset: qc_do_not_manually_annotate synonym: "abnormal cellular protein localisation during vegetative growth" EXACT [PomBase:mah] synonym: "abnormal cellular protein localization during vegetative growth" EXACT [PomBase:mah] synonym: "abnormal protein localisation during vegetative growth" EXACT [PomBase:mah] synonym: "abnormal protein localization during mitotic cell cycle" RELATED [PomBase:mah] synonym: "protein/peptide distribution: abnormal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0001337 ! localization phenotype during vegetative growth is_a: FYPO:0001362 ! abnormal cellular process during vegetative growth is_a: FYPO:0001370 ! abnormal protein localization intersection_of: PATO:0000001 ! quality intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0034613 ! cellular protein localization intersection_of: qualifier PATO:0000460 ! abnormal relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0034613 ! cellular protein localization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-08-04T04:19:46Z [Term] id: FYPO:0000517 name: abnormal nucleus localization def: "A cellular process phenotype in which nucleus localization is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal nuclear localization" EXACT [PomBase:mah] synonym: "abnormal nucleus localisation" EXACT [PomBase:mah] is_a: FYPO:0000138 ! localization phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0051647 ! nucleus localization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0051647 ! nucleus localization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-08-15T11:08:30Z [Term] id: FYPO:0000623 name: abnormal positive regulation of transcription def: "A transcription regulation phenotype in which any process of positive regulation of transcription is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. There may be enough evidence to support annotation to a more specific term such as 'abnormal transcriptional response to pheromone' (FYPO:0000984); if not, it is safer to annotate to 'increased transcription during vegetative growth' (FYPO:0000780) or 'decreased transcription during vegetative growth' (FYPO:0000781) rather than explicitly claiming that an effect on regulation was observed. subset: qc_do_not_annotate synonym: "abnormal activation of gene-specific transcription" RELATED [GO:0045893, PomBase:mah] synonym: "abnormal activation of transcription, DNA-dependent" NARROW [GO:0045893, PomBase:mah] synonym: "abnormal positive regulation of cellular transcription, DNA-dependent" EXACT [GO:0045893, PomBase:mah] synonym: "abnormal positive regulation of gene-specific transcription" RELATED [GO:0045893, PomBase:mah] synonym: "abnormal positive regulation of transcription, DNA-dependent" EXACT [GO:0045893, PomBase:mah] synonym: "abnormal stimulation of gene-specific transcription" NARROW [GO:0045893, PomBase:mah] synonym: "abnormal stimulation of transcription, DNA-dependent" NARROW [GO:0045893, PomBase:mah] synonym: "abnormal up regulation of gene-specific transcription" RELATED [GO:0045893, PomBase:mah] synonym: "abnormal up regulation of transcription, DNA-dependent" EXACT [GO:0045893, PomBase:mah] synonym: "abnormal up-regulation of gene-specific transcription" RELATED [GO:0045893, PomBase:mah] synonym: "abnormal up-regulation of transcription, DNA-dependent" EXACT [GO:0045893, PomBase:mah] synonym: "abnormal upregulation of gene-specific transcription" RELATED [GO:0045893, PomBase:mah] synonym: "abnormal upregulation of transcription, DNA-dependent" EXACT [GO:0045893, PomBase:mah] is_a: FYPO:0000143 ! transcription regulation phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0045893 ! positive regulation of transcription, DNA-templated intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0045893 ! positive regulation of transcription, DNA-templated relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-08-19T03:38:05Z [Term] id: FYPO:0000624 name: abnormal negative regulation of transcription during vegetative growth def: "A transcription regulation phenotype observed in the vegetative growth phase of the life cycle in which any process of negative regulation of transcription is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. There may be enough evidence to support annotation to a more specific term such as 'abnormal chromatin silencing' (FYPO:0000144); if not, it is safer to annotate to 'increased transcription during vegetative growth' (FYPO:0000780) or 'decreased transcription during vegetative growth' (FYPO:0000781) rather than explicitly claiming that an effect on regulation was observed. subset: qc_do_not_annotate synonym: "abnormal down regulation of gene-specific transcription during vegetative growth" RELATED [GO:0045892, PomBase:mah] synonym: "abnormal down regulation of transcription, DNA-dependent, during vegetative growth" EXACT [GO:0045892, PomBase:mah] synonym: "abnormal down-regulation of gene-specific transcription during vegetative growth" RELATED [GO:0045892, PomBase:mah] synonym: "abnormal down-regulation of transcription, DNA-dependent, during vegetative growth" EXACT [GO:0045892, PomBase:mah] synonym: "abnormal downregulation of gene-specific transcription during vegetative growth" RELATED [GO:0045892, PomBase:mah] synonym: "abnormal downregulation of transcription, DNA-dependent, during vegetative growth" EXACT [GO:0045892, PomBase:mah] synonym: "abnormal inhibition of gene-specific transcription during vegetative growth" RELATED [GO:0045892, PomBase:mah] synonym: "abnormal inhibition of transcription, DNA-dependent, during vegetative growth" NARROW [GO:0045892, PomBase:mah] synonym: "abnormal negative regulation of cellular transcription, DNA-dependent, during vegetative growth" EXACT [GO:0045892, PomBase:mah] synonym: "abnormal negative regulation of gene-specific transcription during vegetative growth" RELATED [GO:0045892, PomBase:mah] synonym: "abnormal negative regulation of transcription during mitotic cell cycle" RELATED [PomBase:mah] synonym: "abnormal negative regulation of transcription, DNA-dependent, during vegetative growth" EXACT [GO:0045892, PomBase:mah] is_a: FYPO:0001335 ! transcription regulation phenotype during vegetative growth is_a: FYPO:0001362 ! abnormal cellular process during vegetative growth intersection_of: PATO:0000001 ! quality intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0045892 ! negative regulation of transcription, DNA-templated intersection_of: qualifier PATO:0000460 ! abnormal relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0045892 ! negative regulation of transcription, DNA-templated relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-08-19T03:40:47Z [Term] id: FYPO:0000627 name: normal cellular process def: "A phenotype in which a specific cellular process is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000114 ! cellular process phenotype is_a: FYPO:0000257 ! normal phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0044763 ! single-organism cellular process intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0044763 ! single-organism cellular process relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2011-08-19T04:05:16Z [Term] id: FYPO:0000628 name: abnormal cellular process def: "A phenotype in which a specific cellular process is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000114 ! cellular process phenotype is_a: FYPO:0003037 ! abnormal cell phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0044763 ! single-organism cellular process intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0044763 ! single-organism cellular process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-08-19T04:06:34Z [Term] id: FYPO:0000631 name: cell cycle phenotype def: "A cellular process phenotype that affects progression of the mitotic or meiotic cell cycle, or regulation of cell cycle progression." [PomBase:mah] subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cell-division cycle phenotype" EXACT [GO:0007049, PomBase:mah] synonym: "fission yeast cell cycle phenotype" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0007049 ! cell cycle relationship: inheres_in GO:0007049 ! cell cycle created_by: midori creation_date: 2011-08-19T04:16:04Z [Term] id: FYPO:0000641 name: abnormal chromosome organization def: "A cellular process phenotype in which any process of chromosome organization is abnormal. Chromosome organization results in the assembly, arrangement of constituent parts, or disassembly of chromosomes." [GO:0051276, PomBase:mah] comment: Consider annotating to 'abnormal chromosome morphology' (FYPO:0000848), but note that an abnormal chromosome organization process may, but does not necessarily, result in abnormal chromosome morphology. subset: qc_do_not_manually_annotate synonym: "abnormal chromosome organisation" EXACT [PomBase:mah] is_a: FYPO:0000335 ! abnormal cellular component organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0051276 ! chromosome organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0051276 ! chromosome organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-09-28T12:10:13Z [Term] id: FYPO:0000642 name: abnormal chromatin organization def: "A cellular process phenotype in which any process of chromatin organization is abnormal. Chromatin organization results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin." [GO:0006325, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal chromatin organisation" EXACT [PomBase:mah] is_a: FYPO:0000641 ! abnormal chromosome organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0006325 ! chromatin organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0006325 ! chromatin organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-09-28T12:16:57Z [Term] id: FYPO:0000652 name: molecular function phenotype def: "A phenotype that affects a molecular function such as binding or catalytic activity." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast molecular function phenotype" EXACT [PomBase:mah] synonym: "molecular function phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "molecular function phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0003674 ! molecular_function relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0003674 ! molecular_function created_by: midori creation_date: 2011-11-11T10:42:36Z [Term] id: FYPO:0000653 name: DNA binding phenotype def: "A phenotype that affects DNA binding. The affected gene product may be encoded by the mutated gene, or by a different gene." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast DNA binding phenotype" EXACT [PomBase:mah] is_a: FYPO:0001092 ! binding phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0003677 ! DNA binding relationship: inheres_in GO:0003677 ! DNA binding created_by: midori creation_date: 2011-11-11T10:43:39Z [Term] id: FYPO:0000654 name: catalytic activity phenotype def: "A phenotype that affects a catalytic activity." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "enzymatic activity phenotype" EXACT [PomBase:mah] synonym: "fission yeast catalytic activity phenotype" EXACT [PomBase:mah] is_a: FYPO:0000652 ! molecular function phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0003824 ! catalytic activity relationship: inheres_in GO:0003824 ! catalytic activity created_by: midori creation_date: 2011-11-11T10:44:09Z [Term] id: FYPO:0000672 name: normal cell morphology def: "A cell phenotype characterized by normal cell morphology (i.e. size, shape, and structure)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cellular morphology: normal" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: FYPO:0000257 ! normal phenotype is_a: PATO:0000051 ! morphology intersection_of: PATO:0000051 ! morphology intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2011-11-11T02:51:12Z [Term] id: FYPO:0000682 name: abnormal regulation of molecular function def: "A regulation phenotype observed in the vegetative growth phase of the life cycle in which regulation of a molecular function is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "abnormal regulation of molecular function during mitotic cell cycle" RELATED [PomBase:mah] synonym: "abnormal regulation of molecular function during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0001334 ! regulation phenotype during vegetative growth is_a: FYPO:0001362 ! abnormal cellular process during vegetative growth intersection_of: PATO:0000001 ! quality intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0065009 ! regulation of molecular function intersection_of: qualifier PATO:0000460 ! abnormal relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0065009 ! regulation of molecular function relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-12-01T01:43:05Z [Term] id: FYPO:0000702 name: protein binding phenotype def: "A phenotype that protein affects the binding of one protein to another. The relevant proteins may include the one encoded by the mutated gene, or may both be encoded by different genes." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast protein binding phenotype" EXACT [PomBase:mah] is_a: FYPO:0001092 ! binding phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0005515 ! protein binding relationship: inheres_in GO:0005515 ! protein binding created_by: midori creation_date: 2011-12-05T02:24:49Z [Term] id: FYPO:0000706 name: normal molecular function def: "A phenotype in which a specific molecular function is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate is_a: FYPO:0000257 ! normal phenotype is_a: FYPO:0000652 ! molecular function phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0003674 ! molecular_function intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0003674 ! molecular_function relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2011-12-05T03:06:23Z [Term] id: FYPO:0000707 name: abnormal molecular function def: "A phenotype in which a specific molecular function is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate is_a: FYPO:0000652 ! molecular function phenotype is_a: FYPO:0001985 ! abnormal phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0003674 ! molecular_function intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0003674 ! molecular_function relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-12-05T03:09:24Z [Term] id: FYPO:0000713 name: abnormal cellular response to starvation def: "A stress response phenotype in which the response to starvation for one or more nutrients is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular response to depletion" EXACT [PomBase:vw] synonym: "abnormal cellular response to deprivation" EXACT [PomBase:vw] is_a: FYPO:0000162 ! abnormal cellular response to stress intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0009267 ! cellular response to starvation intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0009267 ! cellular response to starvation relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2011-12-06T12:25:40Z [Term] id: FYPO:0000782 name: mislocalized protein during vegetative growth def: "A cell phenotype observed in the vegetative growth phase of the life cycle in which a protein is observed in a particular location where it is not normally found." [PomBase:mah] comment: The difference between this term and 'abnormal protein localization' (FYPO:0000443) is that 'mislocalized protein' describes a protein that is observed in a place where it is not normally found, whereas 'abnormal protein localization' additionally encompasses the absence of protein from a place where it is normally found. FYPO:0000782 can therefore be used in any case where a protein is in a different location in a mutant compared to wild type, whereas additional information is usually required to support annotation to FYPO:0000443 or its descendants. We recommend noting which protein(s) were used in the assay when annotating to this term. subset: qc_do_not_manually_annotate synonym: "mislocalised protein" EXACT [PomBase:mah] synonym: "mislocalized protein during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0001320 ! vegetative cell phenotype is_a: FYPO:0003452 ! mislocalized protein intersection_of: PATO:0000628 ! mislocalised intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in CHEBI:36080 ! protein relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in CHEBI:36080 ! protein relationship: output_of FYPO:0000443 ! abnormal protein localization during vegetative growth created_by: midori creation_date: 2012-02-29T12:48:27Z [Term] id: FYPO:0000802 name: abnormal cytoskeleton organization def: "A cellular process phenotype in which cytoskeleton organization is abnormal." [GO:0007010, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that an abnormal cytoskeleton organization process may, but does not necessarily, result in a physically abnormal cytoskeleton. subset: qc_do_not_manually_annotate synonym: "abnormal cytoskeleton organisation" EXACT [PomBase:mah] is_a: FYPO:0000295 ! cytoskeleton organization phenotype is_a: FYPO:0000335 ! abnormal cellular component organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0007010 ! cytoskeleton organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0007010 ! cytoskeleton organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-03-01T02:43:53Z [Term] id: FYPO:0000824 name: altered RNA level def: "A cell phenotype in which the amount of RNA measured in a cell differs from normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal RNA level" EXACT [PomBase:mah] synonym: "altered cellular mRNA level" NARROW [PomBase:vw] synonym: "altered cellular RNA level" EXACT [PomBase:mah] synonym: "RNA accumulation: abnormal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000989 ! altered level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal intersection_of: towards CHEBI:33697 ! ribonucleic acid relationship: inheres_in CL:0000000 ! cell relationship: output_of FYPO:0000142 ! gene expression phenotype relationship: qualifier PATO:0000460 ! abnormal relationship: towards CHEBI:33697 ! ribonucleic acid created_by: midori creation_date: 2012-03-08T03:02:56Z [Term] id: FYPO:0000826 name: decreased RNA level def: "A cell phenotype in which the amount of RNA measured in a cell is lower than normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. subset: qc_do_not_manually_annotate synonym: "decreased cellular mRNA level" NARROW [PomBase:vw] synonym: "decreased cellular RNA level" EXACT [PomBase:mah] synonym: "decreased RNA accumulation" RELATED [PomBase:mah] synonym: "decreased transcript level" EXACT [PomBase:vw] synonym: "reduced RNA level" EXACT [PomBase:mah] synonym: "RNA accumulation: decreased" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000824 ! altered RNA level is_a: FYPO:0000991 ! decreased level of substance in cell intersection_of: PATO:0001163 ! decreased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:33697 ! ribonucleic acid relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:33697 ! ribonucleic acid created_by: midori creation_date: 2012-03-08T03:16:30Z [Term] id: FYPO:0000834 name: altered protein level def: "A cell phenotype in which the amount of protein measured in a cell differs from normal. Total protein or a specific protein may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Consider annotating to a term describing abnormal translation or abnormal regulation of translation, but note that changes in protein levels may result from changes in protein stability or degradation as well as changes in protein synthesis. subset: qc_do_not_manually_annotate synonym: "abnormal protein level" EXACT [PomBase:mah] synonym: "altered cellular protein level" EXACT [PomBase:mah] synonym: "protein/peptide accumulation: abnormal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000989 ! altered level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal intersection_of: towards CHEBI:36080 ! protein relationship: inheres_in CL:0000000 ! cell relationship: output_of FYPO:0000142 ! gene expression phenotype relationship: qualifier PATO:0000460 ! abnormal relationship: towards CHEBI:36080 ! protein created_by: midori creation_date: 2012-03-09T03:50:50Z [Term] id: FYPO:0000835 name: decreased protein level def: "A cell phenotype in which the amount of protein measured in a cell is lower than normal. Total protein or a specific protein may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Consider annotating to a term describing abnormal translation or abnormal regulation of translation, but note that changes in protein levels may result from changes in protein stability or degradation as well as changes in protein synthesis. subset: qc_do_not_manually_annotate synonym: "decreased protein accumulation" RELATED [PomBase:mah] synonym: "protein/peptide accumulation: decreased" RELATED [SGD:phenotype_annotation] synonym: "reduced protein level" EXACT [PomBase:mah] is_a: FYPO:0000834 ! altered protein level is_a: FYPO:0000991 ! decreased level of substance in cell intersection_of: PATO:0001163 ! decreased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:36080 ! protein relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:36080 ! protein created_by: midori creation_date: 2012-03-09T03:50:57Z [Term] id: FYPO:0000836 name: increased protein level def: "A cell phenotype in which the amount of protein measured in a cell is higher than normal. Total protein or a specific protein may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Consider annotating to a term describing abnormal translation or abnormal regulation of translation, but note that changes in protein levels may result from changes in protein stability or degradation as well as changes in protein synthesis. subset: qc_do_not_manually_annotate synonym: "increased protein accumulation" RELATED [PomBase:mah] synonym: "protein/peptide accumulation: increased" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000834 ! altered protein level is_a: FYPO:0000990 ! increased level of substance in cell intersection_of: PATO:0001162 ! increased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:36080 ! protein relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:36080 ! protein created_by: midori creation_date: 2012-03-09T03:51:05Z [Term] id: FYPO:0000840 name: normal RNA level def: "A cell phenotype in which the amount of RNA measured in a cell is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "normal cellular RNA level" EXACT [PomBase:mah] synonym: "normal mRNA level" NARROW [PomBase:mah] synonym: "RNA accumulation: normal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0001076 ! normal level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000461 ! normal intersection_of: towards CHEBI:33697 ! ribonucleic acid relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000461 ! normal relationship: towards CHEBI:33697 ! ribonucleic acid created_by: midori creation_date: 2012-03-14T12:06:03Z [Term] id: FYPO:0000860 name: abnormal metabolic process def: "A cellular process phenotype in which a cellular metabolic process is abnormal. A metabolic process is any set of chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances." [GO:0044237, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular metabolic process" EXACT [GO:0044237, PomBase:mah] synonym: "abnormal metabolism" EXACT [GO:0044237, PomBase:mah] is_a: FYPO:0000140 ! cellular metabolism phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0044237 ! cellular metabolic process intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0044237 ! cellular metabolic process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-03-20T12:11:59Z [Term] id: FYPO:0000953 name: normal cellular response to chemical stimulus def: "A cellular response phenotype in which the cellular response to a chemical stimulus is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000298 ! cellular response phenotype is_a: FYPO:0000627 ! normal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0070887 ! cellular response to chemical stimulus intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0070887 ! cellular response to chemical stimulus relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2012-04-12T12:15:57Z [Term] id: FYPO:0000989 name: altered level of substance in cell def: "A cell phenotype in which the amount of a specific substance measured in a cell differs from normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal level of substance in cell" EXACT [PomBase:mah] is_a: FYPO:0003037 ! abnormal cell phenotype is_a: PATO:0001159 ! concentrated intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal intersection_of: towards CHEBI:24431 ! chemical entity relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2012-04-25T02:06:49Z [Term] id: FYPO:0000990 name: increased level of substance in cell def: "A cell phenotype in which the amount of a specific substance measured in a cell is higher than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "increased accumulation of substance in cell" RELATED [PomBase:mah] is_a: FYPO:0000989 ! altered level of substance in cell is_a: PATO:0001162 ! increased concentration intersection_of: PATO:0001162 ! increased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:24431 ! chemical entity relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2012-04-25T02:07:28Z [Term] id: FYPO:0000991 name: decreased level of substance in cell def: "A cell phenotype in which the amount of a specific substance measured in a cell is lower than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "reduced level of substance in cell" EXACT [PomBase:mah] is_a: FYPO:0000989 ! altered level of substance in cell is_a: PATO:0001163 ! decreased concentration intersection_of: PATO:0001163 ! decreased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:24431 ! chemical entity relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2012-04-25T02:08:00Z [Term] id: FYPO:0001013 name: abnormal membrane organization def: "A cellular process phenotype in which cellular membrane organization is abnormal. Cellular membrane organization results in the assembly, arrangement of constituent parts, or disassembly of a lipid bilayer membrane, such as the plasma membrane or an organelle membrane." [GO:0061024, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular membrane organization" EXACT [GO:0061024, PomBase:mah] synonym: "abnormal membrane organisation" EXACT [PomBase:mah] is_a: FYPO:0000335 ! abnormal cellular component organization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0061024 ! membrane organization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0061024 ! membrane organization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-04-26T12:57:24Z [Term] id: FYPO:0001024 name: cell cycle arrest phenotype def: "A cell cycle phenotype that affects or involves the normal or abnormal occurrence of cell cycle arrest. In cell cycle arrest, progression through the cell cycle is halted during one of the normal phases (G1, S, G2, or M)." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "fission yeast cell cycle arrest phenotype" EXACT [PomBase:mah] is_a: FYPO:0000145 ! regulation phenotype is_a: FYPO:0000631 ! cell cycle phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0007050 ! cell cycle arrest relationship: inheres_in GO:0007050 ! cell cycle arrest created_by: midori creation_date: 2012-05-09T01:15:41Z [Term] id: FYPO:0001057 name: abnormal amino acid import def: "A cellular process phenotype in which the import of one or more amino acids into the cell is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal amino acid import into cell" EXACT [PomBase:al] synonym: "abnormal amino acid uptake" EXACT [PomBase:mah] is_a: FYPO:0001720 ! abnormal transport intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1902837 ! amino acid import into cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:1902837 ! amino acid import into cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-05-11T03:54:42Z [Term] id: FYPO:0001058 name: decreased amino acid import def: "A cellular process phenotype in which the import of one or more amino acids into the cell occurs to a lower extent than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "decreased amino acid import into cell" EXACT [PomBase:al] synonym: "decreased amino acid uptake" EXACT [PomBase:mah] synonym: "reduced amino acid import" EXACT [PomBase:mah] is_a: FYPO:0001057 ! abnormal amino acid import is_a: PATO:0002052 ! decreased occurrence intersection_of: PATO:0002052 ! decreased occurrence intersection_of: inheres_in GO:1902837 ! amino acid import into cell relationship: inheres_in GO:1902837 ! amino acid import into cell created_by: midori creation_date: 2012-05-11T03:55:46Z [Term] id: FYPO:0001076 name: normal level of substance in cell def: "A cell phenotype in which the amount of a specific substance measured in a cell is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000002 ! cell phenotype is_a: FYPO:0000257 ! normal phenotype is_a: PATO:0001159 ! concentrated intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000461 ! normal intersection_of: towards CHEBI:24431 ! chemical entity relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000461 ! normal relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2012-05-31T16:27:42Z [Term] id: FYPO:0001092 name: binding phenotype def: "A phenotype that affects the binding of a gene product to another substance. The affected gene product may be encoded by the mutated gene, or by a different gene." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast binding phenotype" EXACT [PomBase:mah] is_a: FYPO:0000652 ! molecular function phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0005488 ! binding relationship: inheres_in GO:0005488 ! binding created_by: midori creation_date: 2012-06-01T14:07:32Z [Term] id: FYPO:0001126 name: abnormal cell shape def: "A cell morphology phenotype in which a cell has an abnormal shape." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "misshapen cell" RELATED [PomBase:mah] is_a: FYPO:0000005 ! abnormal cell morphology is_a: PATO:0000052 ! shape intersection_of: PATO:0000052 ! shape intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-06-07T15:28:36Z [Term] id: FYPO:0001127 name: abnormal cell size def: "A cell morphology phenotype in which a cell has a volume or dimensions that differ from normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000005 ! abnormal cell morphology is_a: PATO:0000117 ! size intersection_of: PATO:0000117 ! size intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-06-07T16:00:41Z [Term] id: FYPO:0001222 name: binucleate vegetative cell def: "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which a cell contains two nuclei." [PomBase:mah] subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "binucleate cells during vegetative growth" EXACT [PomBase:al] synonym: "binucleate during vegetative growth" EXACT [PomBase:mah] synonym: "binucleate vegetative cell during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000061 ! multinucleate vegetative cell is_a: PATO:0001406 ! binucleate intersection_of: PATO:0001406 ! binucleate intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) created_by: midori creation_date: 2012-07-12T15:37:08Z [Term] id: FYPO:0001231 name: normal cell cortex morphology def: "A physical cellular phenotype in which the size, shape, and structure of the cell cortex is normal (i.e. indistinguishable from wild type). The cell cortex is the region of a cell that lies just beneath the plasma membrane." [GO:0005938, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype: Note that an abnormal cell cortex organization process may, but does not necessarily, result in abnormal cell cortex morphology. subset: qc_do_not_manually_annotate is_a: FYPO:0001233 ! normal subcellular component is_a: PATO:0000051 ! morphology intersection_of: PATO:0000051 ! morphology intersection_of: inheres_in GO:0005938 ! cell cortex intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0005938 ! cell cortex relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2012-07-16T13:54:21Z [Term] id: FYPO:0001233 name: normal subcellular component def: "A cell phenotype in which the amount, distribution, or morphology of a cell part is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "normal subcellular structure" RELATED [PomBase:al] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: FYPO:0000257 ! normal phenotype intersection_of: PATO:0001241 ! physical object quality intersection_of: inheres_in GO:0044464 ! cell part intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0044464 ! cell part relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2012-07-16T13:59:40Z [Term] id: FYPO:0001320 name: vegetative cell phenotype def: "A phenotype that is observed at the level of an individual cell, when the cell is in the vegetative growth phase of the cell cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cell phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "fission yeast vegetative cell phenotype" EXACT [PomBase:mah] synonym: "vegetative cell phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "vegetative cell phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000002 ! cell phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase created_by: midori creation_date: 2012-08-01T13:52:18Z [Term] id: FYPO:0001321 name: cellular physical quality phenotype during vegetative growth def: "A phenotype that affects any physical object quality, such as morphology, number, location, etc., of a cell or a cellular component in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cellular physical object quality phenotype during vegetative growth" EXACT [PATO:0001241] synonym: "cellular physical quality phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "fission yeast cellular physical object quality phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: FYPO:0001320 ! vegetative cell phenotype intersection_of: PATO:0001241 ! physical object quality intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0005575 ! cellular_component relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0005575 ! cellular_component created_by: midori creation_date: 2012-08-01T14:44:55Z [Term] id: FYPO:0001322 name: abnormal subcellular component during vegetative growth def: "A physical cellular phenotype in which the amount, distribution, or morphology of a cell part is abnormal in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "abnormal subcellular component during mitotic cell cycle" RELATED [PomBase:mah] synonym: "abnormal subcellular structure during vegetative growth" RELATED [PomBase:mah] is_a: FYPO:0000287 ! abnormal subcellular component is_a: FYPO:0001321 ! cellular physical quality phenotype during vegetative growth intersection_of: PATO:0001241 ! physical object quality intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0044464 ! cell part intersection_of: qualifier PATO:0000460 ! abnormal relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0044464 ! cell part relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-08-01T14:46:27Z [Term] id: FYPO:0001331 name: cellular process phenotype during vegetative growth def: "A phenotype that affects a cellular process in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cellular process phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "fission yeast cellular process phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000114 ! cellular process phenotype is_a: FYPO:0001320 ! vegetative cell phenotype intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0044763 ! single-organism cellular process relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0044763 ! single-organism cellular process created_by: midori creation_date: 2012-08-01T16:27:01Z [Term] id: FYPO:0001333 name: gene expression regulation phenotype during vegetative growth def: "A regulation phenotype that affects the regulation of gene expression in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast gene expression regulation phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "gene expression regulation phenotype during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000288 ! gene expression regulation phenotype is_a: FYPO:0001334 ! regulation phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0010468 ! regulation of gene expression relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0010468 ! regulation of gene expression created_by: midori creation_date: 2012-08-01T16:33:19Z [Term] id: FYPO:0001334 name: regulation phenotype during vegetative growth def: "A cellular process phenotype that affects the regulation of a molecular function, biological process, or biological quality in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast regulation phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "regulation phenotype during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000145 ! regulation phenotype is_a: FYPO:0001331 ! cellular process phenotype during vegetative growth intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0065007 ! biological regulation relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0065007 ! biological regulation created_by: midori creation_date: 2012-08-01T16:33:52Z [Term] id: FYPO:0001335 name: transcription regulation phenotype during vegetative growth def: "A gene expression phenotype that affects the regulation of DNA-dependent transcription in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast transcription regulation phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "gene-specific transcription regulation phenotype during vegetative growth" RELATED [GO:0006355, PomBase:mah] synonym: "transcription regulation phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "transcriptional control phenotype during vegetative growth" BROAD [GO:0006355, PomBase:mah] is_a: FYPO:0000143 ! transcription regulation phenotype is_a: FYPO:0001333 ! gene expression regulation phenotype during vegetative growth intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0006355 ! regulation of transcription, DNA-templated relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0006355 ! regulation of transcription, DNA-templated created_by: midori creation_date: 2012-08-01T16:36:22Z [Term] id: FYPO:0001347 name: nucleic acid metabolism phenotype during vegetative growth def: "A cellular process phenotype that affects any nucleic acid metabolic process in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast nucleic acid metabolism phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "nucleic acid metabolism phenotype during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000292 ! nucleic acid metabolism phenotype is_a: FYPO:0001348 ! cellular metabolism phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0090304 ! nucleic acid metabolic process relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0090304 ! nucleic acid metabolic process created_by: midori creation_date: 2012-08-01T17:39:21Z [Term] id: FYPO:0001348 name: cellular metabolism phenotype during vegetative growth def: "A cellular process phenotype that affects metabolism in the cell in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cellular metabolism phenotype during mitotic cell cycle" RELATED [PomBase:mah] synonym: "fission yeast cellular metabolism phenotype during vegetative growth" EXACT [PomBase:mah] is_a: FYPO:0000140 ! cellular metabolism phenotype is_a: FYPO:0001331 ! cellular process phenotype during vegetative growth intersection_of: FYPO:0000002 ! cell phenotype intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0044237 ! cellular metabolic process relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0044237 ! cellular metabolic process created_by: midori creation_date: 2012-08-01T17:40:24Z [Term] id: FYPO:0001356 name: abnormal vegetative cell population growth def: "A cellular process phenotype in which vegetative cell population growth is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that cell growth terms refer to growth under aerobic conditions unless stated otherwise. subset: qc_do_not_manually_annotate synonym: "vegetative growth defect" RELATED [PomBase:mah] is_a: FYPO:0000045 ! abnormal cell population growth is_a: FYPO:0001358 ! vegetative cell population growth phenotype is_a: PATO:0000001 ! quality intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0072690 ! single-celled organism vegetative growth phase intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0072690 ! single-celled organism vegetative growth phase relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-08-01T18:17:46Z [Term] id: FYPO:0001358 name: vegetative cell population growth phenotype def: "A cell phenotype that affects the rate or extent of cell population growth in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "cell population growth phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "fission yeast cell population growth phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "vegetative cell population growth phenotype during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000139 ! cell population growth phenotype is_a: FYPO:0000300 ! biological process phenotype intersection_of: FYPO:0000139 ! cell population growth phenotype intersection_of: inheres_in GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0072690 ! single-celled organism vegetative growth phase created_by: midori creation_date: 2012-08-01T18:21:02Z [Term] id: FYPO:0001362 name: abnormal cellular process during vegetative growth def: "A phenotype in which a specific cellular process is abnormal in the vegetative growth phase of the life cycle." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "abnormal cellular process during mitotic cell cycle" RELATED [PomBase:mah] is_a: FYPO:0000628 ! abnormal cellular process is_a: FYPO:0001331 ! cellular process phenotype during vegetative growth intersection_of: PATO:0000001 ! quality intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0044763 ! single-organism cellular process intersection_of: qualifier PATO:0000460 ! abnormal relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0044763 ! single-organism cellular process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-08-02T14:55:51Z [Term] id: FYPO:0001370 name: abnormal protein localization def: "A cell phenotype in which the localization of a protein in a cell is abnormal. A protein may be observed in a place where it is not normally found, absent from a place where it is normally found, or both." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal cellular protein localisation" EXACT [PomBase:mah] synonym: "abnormal cellular protein localization" EXACT [PomBase:mah] synonym: "abnormal protein localisation" EXACT [PomBase:mah] synonym: "protein/peptide distribution: abnormal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000628 ! abnormal cellular process is_a: FYPO:0002333 ! protein localization phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0034613 ! cellular protein localization intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0034613 ! cellular protein localization relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-08-07T13:40:05Z [Term] id: FYPO:0001373 name: abnormal protein localization to medial cortex def: "A cell phenotype in which the localization of a protein to the medial cortex is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Encompasses both presence of proteins not normally found at the medial cortex and decreased levels or absence of proteins normally found there, and describes defects in a localization process. We recommend noting which protein(s) were used in the assay when annotating to this term. subset: qc_do_not_manually_annotate synonym: "abnormal protein localisation to medial cortex" EXACT [GO:0071574, PomBase:mah] synonym: "abnormal protein localization to medial ring" EXACT [GO:0031097, GO:0071574] is_a: FYPO:0001370 ! abnormal protein localization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0071574 ! protein localization to medial cortex intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0071574 ! protein localization to medial cortex relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-08-07T13:49:11Z [Term] id: FYPO:0001375 name: protein localization abolished def: "A cell phenotype in which a protein does not localize to, and is therefore absent from, a place where it is normally found." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. If this term is used, we recommend noting which protein(s) were used in the assay. subset: qc_do_not_manually_annotate synonym: "abolished protein localization" EXACT [PomBase:mah] synonym: "protein absent from specific location in cell" RELATED [PomBase:mah] is_a: FYPO:0001370 ! abnormal protein localization is_a: PATO:0001558 ! lacking processual parts intersection_of: PATO:0001558 ! lacking processual parts intersection_of: towards GO:0034613 ! cellular protein localization relationship: towards GO:0034613 ! cellular protein localization created_by: midori creation_date: 2012-08-07T13:56:37Z [Term] id: FYPO:0001419 name: normal cell population growth rate def: "A cell population phenotype in which a population of cells grows at the same rate as wild type." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "normal growth rate" BROAD [PomBase:mah] is_a: FYPO:0002058 ! viable cell population created_by: midori creation_date: 2012-08-22T13:05:17Z [Term] id: FYPO:0001575 name: abolished vegetative cell population growth def: "A cellular process phenotype in which vegetative cell population growth does not occur, although cells remain viable." [PomBase:mah] comment: This term's primary purpose is to organize terms beneath it in the ontology, and we recommend that it not be used for direct annotations. Please consider using one of the more specific terms, which mention carbon or nitrogen sources, to annotate each phenotype, as cells that do not grow on any media would be considered inviable. subset: qc_do_not_annotate synonym: "abolished growth of population of viable vegetative cells" EXACT [PomBase:mah] synonym: "abolished vegetative cell population growth, viable cells" EXACT [PomBase:vw] synonym: "vegetative cell population growth abolished" EXACT [PomBase:mah] synonym: "vegetative population growth abolished" EXACT [PomBase:mah] is_a: FYPO:0001355 ! decreased vegetative cell population growth is_a: PATO:0001558 ! lacking processual parts intersection_of: PATO:0001558 ! lacking processual parts intersection_of: towards GO:0072690 ! single-celled organism vegetative growth phase relationship: towards GO:0072690 ! single-celled organism vegetative growth phase created_by: midori creation_date: 2012-09-20T14:52:12Z [Term] id: FYPO:0001646 name: abnormal glutamate import def: "A cellular process phenotype in which the import of glutamate into the cell is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal glutamate import into cell" EXACT [PomBase:al] synonym: "abnormal glutamate uptake" EXACT [PomBase:mah] synonym: "abnormal L-glutamate import" EXACT [PomBase:mah] is_a: FYPO:0001057 ! abnormal amino acid import intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1990123 ! L-glutamate import into cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:1990123 ! L-glutamate import into cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-09-27T15:50:49Z [Term] id: FYPO:0001649 name: decreased glutamate import def: "A cellular process phenotype in which the import of glutamate into the cell occurs to a lower extent than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "decreased glutamate import into cell" EXACT [PomBase:al] synonym: "decreased glutamate uptake" EXACT [PomBase:mah] synonym: "decreased L-glutamate import" EXACT [PomBase:mah] synonym: "reduced glutamate import" EXACT [PomBase:mah] is_a: FYPO:0001058 ! decreased amino acid import is_a: FYPO:0001646 ! abnormal glutamate import intersection_of: PATO:0002052 ! decreased occurrence intersection_of: inheres_in GO:1990123 ! L-glutamate import into cell relationship: inheres_in GO:1990123 ! L-glutamate import into cell created_by: midori creation_date: 2012-09-27T15:56:47Z [Term] id: FYPO:0001650 name: decreased lysine import def: "A cellular process phenotype in which the import of lysine into the cell occurs to a lower extent than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "decreased L-lysine import" EXACT [PomBase:mah] synonym: "decreased lysine import into cell" EXACT [PomBase:al] synonym: "decreased lysine uptake" EXACT [PomBase:mah] synonym: "reduced lysine import" EXACT [PomBase:mah] is_a: FYPO:0001058 ! decreased amino acid import is_a: FYPO:0001651 ! abnormal lysine import intersection_of: PATO:0002052 ! decreased occurrence intersection_of: inheres_in GO:1903410 ! L-lysine import into cell relationship: inheres_in GO:1903410 ! L-lysine import into cell created_by: midori creation_date: 2012-09-27T15:59:41Z [Term] id: FYPO:0001651 name: abnormal lysine import def: "A cellular process phenotype in which the import of lysine into the cell is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal L-lysine import" EXACT [PomBase:mah] synonym: "abnormal lysine import into cell" EXACT [PomBase:al] synonym: "abnormal lysine uptake" EXACT [PomBase:mah] is_a: FYPO:0001057 ! abnormal amino acid import intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1903410 ! L-lysine import into cell intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:1903410 ! L-lysine import into cell relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-09-27T16:06:07Z [Term] id: FYPO:0001673 name: normal nuclear morphology def: "A physical cellular phenotype in which the size, shape, or structure of the nucleus is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0001233 ! normal subcellular component is_a: PATO:0000051 ! morphology intersection_of: PATO:0000051 ! morphology intersection_of: inheres_in GO:0005634 ! nucleus intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0005634 ! nucleus relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2012-10-09T10:53:23Z [Term] id: FYPO:0001678 name: abolished protein localization to chromatin def: "A cell phenotype in which the localization of a protein to chromatin is abolished." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abolished protein localisation to chromatin" EXACT [PomBase:mah] synonym: "protein localization to chromatin abolished" EXACT [PomBase:mah] is_a: FYPO:0001375 ! protein localization abolished is_a: FYPO:0001679 ! abnormal protein localization to chromatin intersection_of: PATO:0001558 ! lacking processual parts intersection_of: towards GO:0071168 ! protein localization to chromatin relationship: towards GO:0071168 ! protein localization to chromatin created_by: midori creation_date: 2012-10-30T15:29:03Z [Term] id: FYPO:0001679 name: abnormal protein localization to chromatin def: "A cell phenotype in which the localization of a protein to chromatin is abnormal." [PomBase:mah] comment: Encompasses both presence of proteins not normally found associated with chromatin and decreased levels or absence of proteins normally found there, and describes defects in a localization process. We recommend noting which protein(s) were used in the assay when annotating to this term. subset: qc_do_not_manually_annotate synonym: "abnormal protein localisation to chromatin" EXACT [GO:0071168, PomBase:mah] is_a: FYPO:0001370 ! abnormal protein localization intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0071168 ! protein localization to chromatin intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0071168 ! protein localization to chromatin relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-10-30T15:39:19Z [Term] id: FYPO:0001703 name: normal mitotic cell cycle checkpoint def: "A cell cycle phenotype in which a specific mitotic cell cycle checkpoint is normal (i.e. indistinguishable from wild type). A cell cycle checkpoint controls cell cycle progression by monitoring the timing and integrity of specific cell cycle events." [GO:0000075, GO:0007093, PomBase:mah] subset: qc_do_not_manually_annotate synonym: "normal cell cycle checkpoint activation" EXACT [PomBase:mah] is_a: FYPO:0000137 ! mitotic cell cycle checkpoint phenotype is_a: FYPO:0001928 ! normal regulation of mitotic cell cycle is_a: FYPO:0002741 ! normal mitotic cell cycle process intersection_of: PATO:0000001 ! quality intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0007093 ! mitotic cell cycle checkpoint intersection_of: qualifier PATO:0000461 ! normal relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0007093 ! mitotic cell cycle checkpoint relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2012-11-07T16:00:24Z [Term] id: FYPO:0001704 name: abnormal mitotic cell cycle checkpoint def: "A cell cycle phenotype in which a specific mitotic cell cycle checkpoint is abnormal. A cell cycle checkpoint normally controls cell cycle progression by monitoring the timing and integrity of specific cell cycle events. In a mutant, the checkpoint may fail to activate under appropriate conditions, or may occur to a greater or lesser extent than wild type under any specified set of conditions." [GO:0000075, GO:0007093, PomBase:mah] subset: qc_do_not_manually_annotate synonym: "abnormal mitotic cell cycle checkpoint activation" EXACT [PomBase:mah] is_a: FYPO:0000137 ! mitotic cell cycle checkpoint phenotype is_a: FYPO:0000148 ! abnormal regulation of mitotic cell cycle is_a: FYPO:0002737 ! abnormal mitotic cell cycle process intersection_of: PATO:0000001 ! quality intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0007093 ! mitotic cell cycle checkpoint intersection_of: qualifier PATO:0000460 ! abnormal relationship: during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0007093 ! mitotic cell cycle checkpoint relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-11-07T16:03:57Z [Term] id: FYPO:0001720 name: abnormal transport def: "A phenotype in which a specific transport process is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000149 ! transport phenotype is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0006810 ! transport intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0006810 ! transport relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2012-11-08T14:01:10Z [Term] id: FYPO:0001859 name: increased minichromosome loss def: "A cell phenotype in which minichromosomes are lost at a higher frequency than normal. Minichromosome loss occurs when one or both daughter cells do not inherit copies of a minichromosome from the mother cell, and may result from failure of minichromosome replication or segregation." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that in budding yeast, increased plasmid loss is often called a minichromosome maintenance defect, because "minichromosome" is roughly synonymous with an autonomously replicated and segregated plasmid in that organism. In fission yeast, a minichromosome is a large portion of a chromosome, usually about half of chromosome 3, that replicates and segregates autonomously. For smaller autonomously replicating and segregating constructs, consider 'increased plasmid loss' (FYPO:0000786). subset: qc_do_not_manually_annotate synonym: "minichromosome maintenance defect" RELATED [PomBase:mah] is_a: FYPO:0003037 ! abnormal cell phenotype created_by: midori creation_date: 2012-12-18T14:36:26Z [Term] id: FYPO:0001872 name: abnormal cell adhesion def: "A cellular process phenotype in which adhesion of a cell to a substrate or another cell is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "adhesion defects" EXACT [PomBase:mah] is_a: FYPO:0000628 ! abnormal cellular process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0007155 ! cell adhesion intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0007155 ! cell adhesion relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-01-09T15:42:54Z [Term] id: FYPO:0001879 name: thin cell def: "A cell morphology phenotype in which a cell has an abnormally low thickness or diameter." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0001126 ! abnormal cell shape is_a: FYPO:0001127 ! abnormal cell size is_a: PATO:0000592 ! decreased thickness intersection_of: PATO:0000592 ! decreased thickness intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2013-01-30T12:06:48Z [Term] id: FYPO:0001888 name: substance absent from cell def: "A cell phenotype in which the amount of a specific substance measured in a cell is too low to detect." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000991 ! decreased level of substance in cell is_a: PATO:0002000 ! lacks all parts of type is_a: PATO:0002001 ! has fewer parts of type intersection_of: PATO:0002000 ! lacks all parts of type intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:24431 ! chemical entity relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2013-01-30T15:19:23Z [Term] id: FYPO:0001890 name: increased RNA level def: "A cell phenotype in which the amount of RNA measured in a cell is higher than normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term. subset: qc_do_not_manually_annotate synonym: "increased cellular mRNA level" NARROW [PomBase:vw] synonym: "increased cellular RNA level" EXACT [PomBase:mah] synonym: "increased RNA accumulation" RELATED [PomBase:mah] synonym: "increased transcript level" EXACT [PomBase:vw] synonym: "RNA accumulation: increased" RELATED [SGD:phenotype_annotation] is_a: FYPO:0000824 ! altered RNA level is_a: FYPO:0000990 ! increased level of substance in cell intersection_of: PATO:0001162 ! increased concentration intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:47600 ! purvalanol A relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:47600 ! purvalanol A created_by: midori creation_date: 2013-01-30T15:36:51Z [Term] id: FYPO:0001898 name: P-bodies present in decreased numbers def: "A physical cellular phenotype in which cells contain fewer cytoplasmic mRNA processing bodies (P-bodies) than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cytoplasmic mRNA processing bodies present in decreased numbers" EXACT [GO:0000932] synonym: "decreased P-body formation" RELATED [PomBase:al] synonym: "fewer P-bodies present" EXACT [PomBase:mah] synonym: "P bodies present in decreased numbers" EXACT [GO:0000932] synonym: "P-bodies present in reduced numbers" EXACT [PomBase:mah] is_a: FYPO:0000287 ! abnormal subcellular component is_a: PATO:0002001 ! has fewer parts of type intersection_of: PATO:0002001 ! has fewer parts of type intersection_of: towards GO:0000932 ! cytoplasmic mRNA processing body relationship: towards GO:0000932 ! cytoplasmic mRNA processing body created_by: midori creation_date: 2013-01-30T16:59:23Z [Term] id: FYPO:0001900 name: small P-bodies def: "A physical cellular phenotype in which cytoplasmic mRNA processing bodies (P-bodies) are smaller than normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "decreased P-body formation" RELATED [PomBase:al] synonym: "small cytoplasmic mRNA processing bodies" EXACT [GO:0000932] synonym: "small P bodies" EXACT [GO:0000932] is_a: FYPO:0000287 ! abnormal subcellular component is_a: PATO:0000596 ! decreased volume intersection_of: PATO:0000596 ! decreased volume intersection_of: inheres_in GO:0000932 ! cytoplasmic mRNA processing body relationship: inheres_in GO:0000932 ! cytoplasmic mRNA processing body created_by: midori creation_date: 2013-01-30T17:07:32Z [Term] id: FYPO:0001955 name: spheroid cell def: "A cell morphology phenotype in which a cell is shaped in the form of a spheroid. In spheroid cells, there is much less difference between the long and short axes of the cell than in wild type. Spheroid cells may shorter than normal, with approximately the same diameter as normal, or they may be enlarged." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "cell morphology, round cells" RELATED [PomBase:mah] synonym: "cell morphology, rounded cells" RELATED [PomBase:mah] synonym: "rounded cell" EXACT [PomBase:vw] is_a: FYPO:0001126 ! abnormal cell shape is_a: PATO:0001865 ! spheroid intersection_of: PATO:0001865 ! spheroid intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2013-02-07T13:58:40Z [Term] id: FYPO:0001956 name: spherical cell def: "A cell morphology phenotype in which a cell is formed in the shape of a sphere." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "orb" EXACT [PomBase:jh, PomBase:vw] is_a: FYPO:0001955 ! spheroid cell is_a: PATO:0001499 ! spherical intersection_of: PATO:0001499 ! spherical intersection_of: inheres_in CL:0000000 ! cell relationship: inheres_in CL:0000000 ! cell created_by: midori creation_date: 2013-02-07T13:58:48Z [Term] id: FYPO:0001981 name: decreased rate of DNA replication def: "A cellular process phenotype in which the rate, or speed, of DNA replication is decreased." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "reduced rate of DNA replication" EXACT [PomBase:mah] is_a: FYPO:0000217 ! abnormal DNA replication is_a: PATO:0000911 ! decreased rate intersection_of: PATO:0000911 ! decreased rate intersection_of: inheres_in GO:0006261 ! DNA-dependent DNA replication relationship: inheres_in GO:0006261 ! DNA-dependent DNA replication created_by: midori creation_date: 2013-02-13T14:54:35Z [Term] id: FYPO:0001983 name: protein absent from cell def: "A cell phenotype in which the amount of protein measured in a cell is too low to detect. Total protein or a specific protein may be affected." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "undetectable cellular protein level" EXACT [PomBase:al] is_a: FYPO:0000835 ! decreased protein level is_a: FYPO:0001888 ! substance absent from cell intersection_of: PATO:0002000 ! lacks all parts of type intersection_of: inheres_in CL:0000000 ! cell intersection_of: towards CHEBI:36080 ! protein relationship: inheres_in CL:0000000 ! cell relationship: towards CHEBI:36080 ! protein created_by: midori creation_date: 2013-02-13T15:06:40Z [Term] id: FYPO:0001985 name: abnormal phenotype def: "A phenotype that shows detectable differences from normal. In fission yeast, the characteristics of wild type cells of the sequenced strain (972 h-) or the isogenic h+ or h90 strains are regarded as normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast abnormal phenotype" EXACT [PomBase:mah] is_a: FYPO:0000001 ! phenotype is_a: PATO:0000001 ! quality intersection_of: PATO:0000001 ! quality intersection_of: inheres_in FYPO:0000001 ! phenotype intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in FYPO:0000001 ! phenotype relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-02-13T15:39:55Z [Term] id: FYPO:0002045 name: resistance to heat shock def: "A cell phenotype in which cells show decreased sensitivity to heat shock. Heat shock is a form of heat stress in which cells are briefly exposed to a very high temperature." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "resistant to heat shock" EXACT [PomBase:mah] is_a: FYPO:0002046 ! resistance to stress created_by: midori creation_date: 2013-03-14T15:54:13Z [Term] id: FYPO:0002046 name: resistance to stress def: "A phenotype in which cells in a population show decreased sensitivity to a stress. Typically, a cell population are deemed resistant to a stress if cells in the population grow and divide when exposed to the stress at an intensity at which wild-type cells stop growing (and may die)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Use a descendant of this term if you have assayed growth of cells exposed to a stress in culture. If you have assayed the response to the stress at the subcellular or molecular level, consider annotating to a descendant of 'abnormal cellular response to stress' (FYPO:0000162). subset: qc_do_not_manually_annotate synonym: "resistant to stress" EXACT [PomBase:mah] synonym: "stress resistance: increased" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000139 ! cell population growth phenotype created_by: midori creation_date: 2013-03-14T15:56:42Z [Term] id: FYPO:0002057 name: cell population viability def: "A cell population phenotype that reflects the proportion of the population that survive and develop normally." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate is_a: FYPO:0000003 ! cell population phenotype created_by: midori creation_date: 2013-04-04T13:48:22Z [Term] id: FYPO:0002058 name: viable cell population def: "A cell population phenotype in which cells in the population are viable." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Note that a viable population may contain individual cells that are inviable. Usually it is difficult to detect inviable cells within an otherwise viable population, especially if population growth is simply assayed by OD increase in liquid culture or by colony formation on plates. If you have done an experiment that detects individual inviable cells, consider using the term 'mixed population including viable and inviable cells' (FYPO:0000908). subset: qc_do_not_manually_annotate is_a: FYPO:0002057 ! cell population viability relationship: includes_cells_with_phenotype FYPO:0000124 ! viable cell created_by: midori creation_date: 2013-04-04T13:51:27Z [Term] id: FYPO:0002059 name: inviable cell population def: "A cell population phenotype in which none of the cells in the population are viable." [PomBase:mah] subset: qc_do_not_manually_annotate is_a: FYPO:0002057 ! cell population viability relationship: comprises_cells_with_phenotype FYPO:0000049 ! inviable cell created_by: midori creation_date: 2013-04-04T13:54:32Z [Term] id: FYPO:0002069 name: mislocalized nucleus def: "A physical cellular phenotype in which a cell has a nucleus in an abnormal location. The normal location is at the midpoint of the long axis of the cell." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "abnormal nucleus location" EXACT [PomBase:mah] synonym: "abnormal nucleus position" EXACT [PomBase:mah] synonym: "displaced nucleus" EXACT [PomBase:vw] synonym: "mislocalised nucleus" EXACT [PomBase:mah] synonym: "misplaced nuclei" EXACT [PomBase:vw] synonym: "misplaced nucleus" EXACT [PomBase:vw] synonym: "nuclear position: abnormal" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000136 ! cellular physical quality phenotype is_a: PATO:0000628 ! mislocalised intersection_of: PATO:0000628 ! mislocalised intersection_of: inheres_in GO:0005634 ! nucleus relationship: inheres_in GO:0005634 ! nucleus relationship: output_of FYPO:0000517 ! abnormal nucleus localization created_by: midori creation_date: 2013-04-17T16:12:37Z [Term] id: FYPO:0002071 name: mislocalized nucleus during vegetative growth def: "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which a cell has a nucleus in an abnormal location. The normal location of a single nucleus is at the midpoint of the long axis of the cell (during mitotic telophase, daughter nuclei normally move away from the cell division site)." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "abnormal nucleus location during vegetative growth" EXACT [PomBase:mah] synonym: "abnormal nucleus position during vegetative growth" EXACT [PomBase:mah] synonym: "displaced nucleus during vegetative growth" EXACT [PomBase:vw] synonym: "mislocalised nucleus during vegetative growth" EXACT [PomBase:mah] synonym: "mislocalized nucleus during mitotic cell cycle" RELATED [PomBase:mah] synonym: "mislocalized nucleus during vegetative growth" EXACT [PomBase:mah] synonym: "misplaced nuclei during vegetative growth" EXACT [PomBase:vw] synonym: "misplaced nucleus during vegetative growth" EXACT [PomBase:vw] is_a: FYPO:0001321 ! cellular physical quality phenotype during vegetative growth is_a: FYPO:0002069 ! mislocalized nucleus intersection_of: PATO:0000628 ! mislocalised intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase intersection_of: inheres_in GO:0005634 ! nucleus relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase relationship: inheres_in GO:0005634 ! nucleus relationship: output_of FYPO:0001338 ! abnormal nucleus localization during vegetative growth created_by: midori creation_date: 2013-04-17T16:20:51Z [Term] id: FYPO:0002114 name: transporter activity phenotype def: "A phenotype that affects a transporter activity." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast transporter activity phenotype" EXACT [PomBase:mah] is_a: FYPO:0000652 ! molecular function phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0005215 ! transporter activity relationship: inheres_in GO:0005215 ! transporter activity created_by: midori creation_date: 2013-05-07T13:25:10Z [Term] id: FYPO:0002115 name: normal transporter activity def: "A molecular function phenotype in which the observed rate of a specified transporter activity is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000706 ! normal molecular function is_a: FYPO:0002114 ! transporter activity phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0005215 ! transporter activity intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0005215 ! transporter activity relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2013-05-07T13:26:31Z [Term] id: FYPO:0002116 name: abnormal transporter activity def: "A molecular function phenotype in which the observed rate of a specified transporter activity is abnormal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000707 ! abnormal molecular function is_a: FYPO:0002114 ! transporter activity phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0005215 ! transporter activity intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0005215 ! transporter activity relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-05-07T13:27:14Z [Term] id: FYPO:0002117 name: abolished transporter activity def: "A molecular function phenotype in which a specified transporter activity is absent." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "catalytic activity abolished" EXACT [PomBase:mah] is_a: FYPO:0002116 ! abnormal transporter activity is_a: PATO:0001558 ! lacking processual parts intersection_of: PATO:0001558 ! lacking processual parts intersection_of: towards GO:0005215 ! transporter activity relationship: towards GO:0005215 ! transporter activity created_by: midori creation_date: 2013-05-07T13:27:44Z [Term] id: FYPO:0002118 name: decreased transporter activity def: "A molecular function phenotype in which the observed rate of a specified transporter activity is decreased." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "reduced transporter activity" EXACT [PomBase:mah] is_a: FYPO:0002116 ! abnormal transporter activity is_a: PATO:0002052 ! decreased occurrence intersection_of: PATO:0002052 ! decreased occurrence intersection_of: inheres_in GO:0005215 ! transporter activity relationship: inheres_in GO:0005215 ! transporter activity created_by: midori creation_date: 2013-05-07T13:28:05Z [Term] id: FYPO:0002119 name: increased transporter activity def: "A molecular function phenotype in which the observed rate of a specified transporter activity is increased." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0002116 ! abnormal transporter activity is_a: PATO:0002051 ! increased occurrence intersection_of: PATO:0002051 ! increased occurrence intersection_of: inheres_in GO:0005215 ! transporter activity relationship: inheres_in GO:0005215 ! transporter activity created_by: midori creation_date: 2013-05-07T13:28:21Z [Term] id: FYPO:0002131 name: RNA binding phenotype def: "A phenotype that affects RNA binding. The relevant gene product may be encoded by the mutated gene, or by a different gene." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "fission yeast DNA binding phenotype" EXACT [PomBase:mah] is_a: FYPO:0001092 ! binding phenotype intersection_of: FYPO:0000001 ! phenotype intersection_of: inheres_in GO:0003723 ! RNA binding relationship: inheres_in GO:0003723 ! RNA binding created_by: midori creation_date: 2013-05-07T16:56:35Z [Term] id: FYPO:0002333 name: protein localization phenotype def: "A cell phenotype that affects the localization of a protein in a cell." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "cellular protein localization phenotype" EXACT [GO:0034613] synonym: "fission yeast protein localization phenotype" EXACT [PomBase:mah] synonym: "protein localisation phenotype" EXACT [PomBase:mah] is_a: FYPO:0000138 ! localization phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0034613 ! cellular protein localization relationship: inheres_in GO:0034613 ! cellular protein localization created_by: midori creation_date: 2013-07-05T15:59:48Z [Term] id: FYPO:0002549 name: sensitive to stress def: "A phenotype in which cells in a population show increased sensitivity to a stress. Typically, a cell population are deemed sensitive to a stress if cells in the population stop growing (and may die) when exposed to the stress at an intensity that allows a population of wild type cells to grow and divide." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. Use a descendant of this term if you have assayed growth of cells exposed to a stress in culture. If you have assayed the response to the stress at the subcellular or molecular level, consider annotating to a descendant of 'abnormal cellular response to stress' (FYPO:0000162). subset: qc_do_not_manually_annotate synonym: "hypersensitive to stress" EXACT [PomBase:mah] synonym: "stress resistance: decreased" EXACT [SGD:phenotype_annotation] is_a: FYPO:0000139 ! cell population growth phenotype created_by: midori creation_date: 2013-08-27T15:46:35Z [Term] id: FYPO:0002734 name: abnormal cell cycle process def: "A cellular process phenotype in which a cell does not execute a cell cycle process normally. A cell cycle process is any of the processes that form part of the cell cycle, and thereby ensures successive accurate and complete genome replication and chromosome segregation." [GO:0022402, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000011 ! abnormal cell cycle intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022402 ! cell cycle process intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0022402 ! cell cycle process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:08:57Z [Term] id: FYPO:0002735 name: abnormal cell cycle phase def: "A cellular process phenotype in which a cell does not proceed normally through a specific cell cycle phase. A cell cycle phase is any of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GO:0022403, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000011 ! abnormal cell cycle intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022403 ! cell cycle phase intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0022403 ! cell cycle phase relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:09:18Z [Term] id: FYPO:0002736 name: abnormal mitotic cell cycle phase def: "A cellular process phenotype in which a cell does not proceed normally through a specific mitotic cell cycle phase. A mitotic cell cycle phase is any of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GO:0022403, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000059 ! abnormal mitotic cell cycle is_a: FYPO:0002735 ! abnormal cell cycle phase intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022403 ! cell cycle phase intersection_of: part_of GO:0000278 ! mitotic cell cycle intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0022403 ! cell cycle phase relationship: part_of GO:0000278 ! mitotic cell cycle relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:14:48Z [Term] id: FYPO:0002737 name: abnormal mitotic cell cycle process def: "A cellular process phenotype in which a cell does not execute a mitotic cell cycle process normally. A mitotic cell cycle process is any of the processes that form part of the mitotic cell cycle, and thereby ensures successive accurate and complete genome replication and chromosome segregation during the vegetative growth phase of the life cycle." [GO:0022402, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000059 ! abnormal mitotic cell cycle is_a: FYPO:0002734 ! abnormal cell cycle process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1903047 ! mitotic cell cycle process intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:1903047 ! mitotic cell cycle process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:15:09Z [Term] id: FYPO:0002738 name: abnormal meiotic cell cycle phase def: "A cellular process phenotype in which a cell does not proceed normally through a specific meiotic cell cycle phase. A meiotic cell cycle phase is any of the distinct periods or stages into which the meiotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GO:0022403, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000052 ! abnormal meiotic cell cycle is_a: FYPO:0002735 ! abnormal cell cycle phase intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022403 ! cell cycle phase intersection_of: part_of GO:0051321 ! meiotic cell cycle intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:0022403 ! cell cycle phase relationship: part_of GO:0051321 ! meiotic cell cycle relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:16:12Z [Term] id: FYPO:0002739 name: abnormal meiotic cell cycle process def: "A cellular process phenotype in which a cell does not execute a meiotic cell cycle process normally. A meiotic cell cycle process is any of the processes that form part of the meiotic cell cycle, and thereby ensures successive accurate and complete genome replication and meiotic chromosome segregation." [GO:0022402, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000052 ! abnormal meiotic cell cycle is_a: FYPO:0002734 ! abnormal cell cycle process intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1903046 ! meiotic cell cycle process intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in GO:1903046 ! meiotic cell cycle process relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2013-10-01T15:17:46Z [Term] id: FYPO:0002740 name: normal mitotic cell cycle phase def: "A cellular process phenotype in which a cell proceeds normally through a specific mitotic cell cycle phase. A mitotic cell cycle phase is any of the distinct periods or stages into which the mitotic cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GO:0022403, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000411 ! normal mitotic cell cycle is_a: FYPO:0003833 ! normal cell cycle phase intersection_of: PATO:0000001 ! quality intersection_of: during GO:0000278 ! mitotic cell cycle intersection_of: inheres_in GO:0022403 ! cell cycle phase intersection_of: qualifier PATO:0000461 ! normal relationship: during GO:0000278 ! mitotic cell cycle relationship: inheres_in GO:0022403 ! cell cycle phase relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2013-10-01T16:02:38Z [Term] id: FYPO:0002741 name: normal mitotic cell cycle process def: "A cellular process phenotype in which a cell executes a mitotic cell cycle process normally. A mitotic cell cycle process is any of the processes that form part of the mitotic cell cycle, and thereby ensures successive accurate and complete genome replication and chromosome segregation." [GO:1903047, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0000411 ! normal mitotic cell cycle intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:1903047 ! mitotic cell cycle process intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:1903047 ! mitotic cell cycle process relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2013-10-01T16:03:12Z [Term] id: FYPO:0003037 name: abnormal cell phenotype def: "A phenotype that shows detectable differences from normal at the level of an individual cell. In fission yeast, the characteristics of wild type cells of the sequenced strain (972 h-) or the isogenic h+ or h90 strains are regarded as normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "abnormal fission yeast cell phenotype" EXACT [PomBase:mah] is_a: FYPO:0000002 ! cell phenotype is_a: FYPO:0001985 ! abnormal phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in FYPO:0000002 ! cell phenotype intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in FYPO:0000002 ! cell phenotype relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2014-01-17T15:10:08Z [Term] id: FYPO:0003341 name: multinucleate def: "A physical cellular phenotype in which a cell contains more than one nucleus." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "multinucleate cells" EXACT [PomBase:al] synonym: "multiple nuclei" EXACT [PomBase:al] is_a: FYPO:0000287 ! abnormal subcellular component is_a: PATO:0001908 ! multinucleate intersection_of: PATO:0001908 ! multinucleate intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) created_by: midori creation_date: 2014-05-07T15:45:12Z [Term] id: FYPO:0003478 name: signal transduction phenotype def: "A cellular process phenotype that affects signal transduction. Signal transduction is the process in which a signal is conveyed to trigger a change in the activity or state of a cell. It begins with reception of a signal and ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. A phenotype may affect one or more steps in one or more signal transduction pathways." [GO:0007165, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate synonym: "fission yeast signal transduction phenotype" EXACT [PomBase:mah] is_a: FYPO:0000145 ! regulation phenotype intersection_of: FYPO:0000002 ! cell phenotype intersection_of: inheres_in GO:0007165 ! signal transduction relationship: inheres_in GO:0007165 ! signal transduction created_by: midori creation_date: 2014-07-01T12:26:39Z [Term] id: FYPO:0003558 name: increased repeat element RNA level def: "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from repeat elements, such as LTRs, retrotransposons, or wtf elements, measured in a cell is higher than normal." [PMID:24957674, PomBase:mah] comment: Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. subset: qc_do_not_manually_annotate synonym: "increased repeat element RNA accumulation" RELATED [PomBase:mah] synonym: "increased repeat element RNA level during mitotic cell cycle" RELATED [PomBase:mah] synonym: "increased repeat element RNA level during vegetative growth" EXACT [PomBase:mah] synonym: "increased repeat element transcript level" EXACT [PomBase:vw] is_a: FYPO:0000825 ! increased RNA level during vegetative growth created_by: midori creation_date: 2014-07-17T11:26:36Z [Term] id: FYPO:0003627 name: normal protein localization def: "A cell phenotype in which the localization of a protein in a cell is normal (i.e. indistinguishable from wild type)." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "normal cellular protein localisation" EXACT [PomBase:mah] synonym: "normal cellular protein localization" EXACT [PomBase:mah] synonym: "normal protein localisation" EXACT [PomBase:mah] is_a: FYPO:0000627 ! normal cellular process is_a: FYPO:0002333 ! protein localization phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0034613 ! cellular protein localization intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0034613 ! cellular protein localization relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2014-08-06T14:23:40Z [Term] id: FYPO:0003755 name: abnormal vegetative cell phenotype def: "A phenotype that shows detectable differences from normal at the level of an individual cell, when the cell is in the vegetative growth phase of the cell cycle. In fission yeast, the characteristics of wild type cells of the sequenced strain (972 h-) or the isogenic h+ or h90 strains are regarded as normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "abnormal cell phenotype during vegetative growth" EXACT [PomBase:mah] synonym: "abnormal vegetative fission yeast cell phenotype" EXACT [PomBase:mah] is_a: FYPO:0001320 ! vegetative cell phenotype is_a: FYPO:0003037 ! abnormal cell phenotype intersection_of: PATO:0000001 ! quality intersection_of: inheres_in FYPO:0001320 ! vegetative cell phenotype intersection_of: qualifier PATO:0000460 ! abnormal relationship: inheres_in FYPO:0001320 ! vegetative cell phenotype relationship: qualifier PATO:0000460 ! abnormal created_by: midori creation_date: 2014-09-01T17:20:24Z [Term] id: FYPO:0003833 name: normal cell cycle phase def: "A cellular process phenotype in which a cell proceeds normally through a specific cell cycle phase. A cell cycle phase is any of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GO:0022403, PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate is_a: FYPO:0003832 ! normal cell cycle intersection_of: PATO:0000001 ! quality intersection_of: inheres_in GO:0022403 ! cell cycle phase intersection_of: qualifier PATO:0000461 ! normal relationship: inheres_in GO:0022403 ! cell cycle phase relationship: qualifier PATO:0000461 ! normal created_by: midori creation_date: 2014-10-15T11:04:03Z [Term] id: FYPO:0003937 name: increased cell population growth def: "A cell population phenotype in which cell population growth is increased relative to normal. Increased growth may reflect a reduced growth rate (i.e. faster growth), growth that occurs to a greater extent than normal, or both." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "fast aerobic cell population growth" NARROW [PomBase:mah] synonym: "increased aerobic cell population growth" NARROW [PomBase:mah] synonym: "increased growth" BROAD [PomBase:mah] is_a: FYPO:0000045 ! abnormal cell population growth is_a: FYPO:0002058 ! viable cell population created_by: midori creation_date: 2014-10-29T11:58:04Z [Term] id: FYPO:0004044 name: elongated tetranucleate vegetative cell def: "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which a cell contains four nuclei and is longer than normal." [PomBase:mah] subset: qc_do_not_annotate subset: qc_do_not_manually_annotate synonym: "elongated tetranucleate cells during vegetative growth" EXACT [PomBase:al] synonym: "elongated tetranucleate vegetative cell during mitotic cell cycle" RELATED [PomBase:mah] synonym: "long tetranucleate vegetative cell" EXACT [PomBase:mah] is_a: FYPO:0000133 ! elongated multinucleate vegetative cell is_a: FYPO:0004043 ! tetranucleate vegetative cell intersection_of: FYPO:0000002 ! cell phenotype intersection_of: has_part FYPO:0001122 ! elongated vegetative cell intersection_of: has_part FYPO:0004043 ! tetranucleate vegetative cell relationship: has_part FYPO:0001122 ! elongated vegetative cell relationship: has_part FYPO:0004043 ! tetranucleate vegetative cell created_by: midori creation_date: 2014-11-25T11:59:21Z [Term] id: FYPO:0004083 name: normal protein level def: "A cell phenotype in which the amount of protein measured in a cell is normal (i.e. indistinguishable from wild type). Total protein or a specific protein may be affected." [PomBase:mah] subset: qc_do_not_manually_annotate synonym: "protein/peptide accumulation: normal" RELATED [SGD:phenotype_annotation] is_a: FYPO:0001076 ! normal level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) intersection_of: qualifier PATO:0000461 ! normal intersection_of: towards CHEBI:36080 ! protein relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi) relationship: qualifier PATO:0000461 ! normal relationship: towards CHEBI:36080 ! protein created_by: midori creation_date: 2014-11-27T15:14:06Z [Term] id: FYPO:0004139 name: altered level of substance in cell during nitrogen starvation def: "A cell phenotype in which the amount of a specific substance measured in a cell that is subject to nitrogen starvation differs from normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal level of substance in cell during nitrogen starvation" EXACT [PomBase:mah] is_a: FYPO:0000989 ! altered level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: exists_during GO:0006995 ! cellular response to nitrogen starvation intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal intersection_of: towards CHEBI:24431 ! chemical entity relationship: exists_during GO:0006995 ! cellular response to nitrogen starvation relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal relationship: towards CHEBI:24431 ! chemical entity created_by: midori creation_date: 2014-12-09T12:14:06Z [Term] id: FYPO:0004320 name: altered DNA level def: "A cell phenotype in which the amount of DNA measured in a cell differs from normal." [PomBase:mah] comment: This is a high-level term whose primary purpose is to organize terms beneath it in the ontology, and we expect that it will not be used for direct annotations. Please consider using a more specific term to annotate each phenotype. subset: qc_do_not_manually_annotate synonym: "abnormal DNA content" EXACT [PomBase:mah] synonym: "abnormal DNA level" EXACT [PomBase:mah] synonym: "altered cellular DNA level" EXACT [PomBase:mah] is_a: FYPO:0000989 ! altered level of substance in cell intersection_of: PATO:0001159 ! concentrated intersection_of: inheres_in CL:0000000 ! cell intersection_of: qualifier PATO:0000460 ! abnormal intersection_of: towards CHEBI:16991 ! deoxyribonucleic acid relationship: inheres_in CL:0000000 ! cell relationship: qualifier PATO:0000460 ! abnormal relationship: towards CHEBI:16991 ! deoxyribonucleic acid created_by: midori creation_date: 2015-01-21T13:48:16Z