format-version: 1.2
data-version: releases/2015-11-20
date: 20:11:2015 14:25
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
subset: qc_do_not_manually_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
subset: qc_do_not_manually_annotate
synonym: "fission yeast cell phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000001 ! phenotype
intersection_of: FYPO:0000001 ! phenotype
intersection_of: inheres_in_part_of GO:0005575 ! cellular_component
disjoint_from: FYPO:0000003 ! cell population phenotype
relationship: inheres_in_part_of GO:0005575 ! cellular_component
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:0000136 ! cellular physical quality 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:0003037 ! abnormal cell phenotype
is_a: FYPO:0004638 ! abnormal cellular physical quality 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_annotate
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_part_of GO:0007049 ! cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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 from the lateral portion of the long axis of the cell, and at an 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]
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: "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: "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_annotate
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
is_a: FYPO:0001985 ! abnormal 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_annotate
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 (i.e. indistinguishably 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: "growth normal" BROAD [PomBase:mah]
is_a: FYPO:0000139 ! cell population growth phenotype
is_a: FYPO:0000257 ! normal phenotype
is_a: FYPO:0002058 ! viable cell population
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:0000052
name: abnormal meiotic cell cycle
def: "A cellular process phenotype in which a cell does not proceed normally through a meiotic 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: "meiotic cell cycle defects" EXACT [PomBase:mah]
is_a: FYPO:0000011 ! abnormal cell cycle
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0051321 ! meiotic cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0051321 ! meiotic cell cycle
relationship: qualifier PATO:0000460 ! abnormal
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_part_of GO:0000226 ! microtubule cytoskeleton organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0000226 ! microtubule cytoskeleton organization
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2011-03-29T05:53:56Z

[Term]
id: FYPO:0000059
name: abnormal mitotic cell cycle
def: "A cellular process phenotype in which a cell does not proceed normally through a mitotic 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: "mitotic cell cycle defects" EXACT [PomBase:mah]
synonym: "mitotic cell cycle: abnormal" EXACT [SGD:phenotype_annotation]
is_a: FYPO:0000011 ! abnormal cell cycle
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0000278 ! mitotic cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0000278 ! mitotic cell cycle
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_annotate
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_part_of GO:0006310 ! DNA recombination
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0044763 ! single-organism cellular process
relationship: inheres_in_part_of 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_part_of GO:0051225 ! spindle assembly
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0005575 ! cellular_component
relationship: inheres_in_part_of 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]
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 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_part_of GO:0007093 ! mitotic cell cycle checkpoint
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0051641 ! cellular localization
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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
subset: qc_do_not_manually_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_part_of GO:0044237 ! cellular metabolic process
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0010467 ! gene expression
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0006355 ! regulation of transcription, DNA-templated
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0065007 ! biological regulation
relationship: inheres_in_part_of GO:0065007 ! biological regulation
created_by: midori
creation_date: 2011-04-12T06:00:44Z

[Term]
id: FYPO:0000148
name: abnormal regulation of mitotic cell cycle
def: "A regulation phenotype in which regulation of the mitotic cell cycle 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:0000059 ! abnormal mitotic cell cycle
is_a: FYPO:0001334 ! regulation phenotype during vegetative growth
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0007346 ! regulation of mitotic cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0007346 ! regulation of mitotic cell cycle
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2011-04-13T03:34:54Z

[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
subset: qc_do_not_manually_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_part_of GO:0006810 ! transport
relationship: inheres_in_part_of 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_part_of GO:0033554 ! cellular response to stress
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0006270 ! DNA replication initiation
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0034599 ! cellular response to oxidative stress
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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]
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 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_part_of GO:0051301 ! cell division
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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_part_of GO:0006261 ! DNA-dependent DNA replication
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0043555 ! regulation of translation in response to stress
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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, composition 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
subset: qc_do_not_manually_annotate
synonym: "abnormal subcellular component physical object quality" EXACT [PomBase:mah]
synonym: "abnormal subcellular structure" RELATED [PomBase:mah]
is_a: FYPO:0004638 ! abnormal cellular physical quality phenotype
intersection_of: PATO:0001241 ! physical object quality
intersection_of: inheres_in_part_of GO:0044464 ! cell part
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0010468 ! regulation of gene expression
relationship: inheres_in_part_of 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_part_of GO:0006417 ! regulation of translation
relationship: inheres_in_part_of 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 observed in the vegetative growth phase of the life cycle 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
subset: qc_do_not_manually_annotate
synonym: "transcription phenotype during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0004847 ! transcription phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in_part_of GO:0006351 ! transcription, DNA-templated
relationship: during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0006412 ! translation
relationship: during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0090304 ! nucleic acid metabolic process
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0006259 ! DNA metabolic process
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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:0000292 ! nucleic acid metabolism phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: inheres_in_part_of GO:0016070 ! RNA metabolic process
relationship: inheres_in_part_of 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_part_of GO:0007010 ! cytoskeleton organization
relationship: inheres_in_part_of 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_part_of GO:0000226 ! microtubule cytoskeleton organization
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0051716 ! cellular response to stimulus
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_annotate
synonym: "fission yeast biological process phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000001 ! phenotype
intersection_of: FYPO:0000001 ! phenotype
intersection_of: inheres_in_part_of GO:0008150 ! biological_process
relationship: inheres_in_part_of GO:0008150 ! biological_process
created_by: midori
creation_date: 2011-04-26T02:25:13Z

[Term]
id: FYPO:0000329
name: abnormal protein modification during vegetative growth
def: "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which protein modification is abnormal. All modifications may be affected, or only modifications of a certain type, or on specific proteins, or even specific sites within specific proteins." [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 protein modification during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "abnormal protein/peptide modification during vegetative growth" EXACT [PomBase:mah]
is_a: FYPO:0000328 ! abnormal protein metabolic process during vegetative growth
is_a: FYPO:0002494 ! abnormal protein modification
intersection_of: PATO:0000001 ! quality
intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in_part_of GO:0006464 ! cellular protein modification process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0006464 ! cellular protein modification process
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2011-05-11T03:40:46Z

[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_part_of GO:0016043 ! cellular component organization
relationship: inheres_in_part_of 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_part_of GO:0016043 ! cellular component organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0022607 ! cellular component assembly
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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: 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: "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_part_of 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_part_of GO:0034613 ! cellular protein localization
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2011-08-04T04:19:46Z

[Term]
id: FYPO:0000445
name: cell cycle arrest in mitotic G1 phase
def: "A cellular process phenotype in which progression through the mitotic cell cycle is arrested in G1 phase." [PomBase:mah]
comment: For phenotypes affecting the G1 cell cycle that normally occurs in response to mating pheromone, see 'abnormal cell cycle arrest in response to pheromone' (FYPO:0000530) and its child terms.
subset: qc_do_not_manually_annotate
synonym: "cell cycle arrest in mitotic G1 phase during vegetative growth" EXACT [PomBase:mah]
synonym: "mitotic cell cycle arrest in G1 phase" EXACT [PomBase:mah]
synonym: "mitotic cell cycle progression in G1 phase: arrested" EXACT [SGD:phenotype_annotation]
synonym: "mitotic G1 phase arrest" EXACT [PomBase:mah]
is_a: FYPO:0000837 ! cell cycle arrest in mitotic interphase
intersection_of: during GO:0000080 ! mitotic G1 phase
intersection_of: inheres_in GO:0071850 ! mitotic cell cycle arrest
intersection_of: qualifier PATO:0000467 ! present
relationship: during GO:0000080 ! mitotic G1 phase
relationship: inheres_in GO:0071850 ! mitotic cell cycle arrest
relationship: qualifier PATO:0000467 ! present
created_by: midori
creation_date: 2011-08-12T02:07:59Z

[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_part_of GO:0051647 ! nucleus localization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0045893 ! positive regulation of transcription, DNA-templated
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of 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_part_of 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_annotate
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_part_of GO:0044763 ! single-organism cellular process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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]
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-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_part_of GO:0007049 ! cell cycle
relationship: inheres_in_part_of 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: 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 chromosome organisation" EXACT [PomBase:mah]
is_a: FYPO:0000335 ! abnormal cellular component organization
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0051276 ! chromosome organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0006325 ! chromatin organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_annotate
synonym: "fission yeast molecular function phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000001 ! phenotype
intersection_of: FYPO:0000001 ! phenotype
intersection_of: inheres_in GO:0003674 ! molecular_function
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
subset: qc_do_not_manually_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_part_of 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_part_of 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_part_of GO:0009267 ! cellular response to starvation
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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: 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. 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:0003452 ! mislocalized protein
is_a: FYPO:0004639 ! abnormal cellular physical quality phenotype during vegetative growth
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_part_of GO:0007010 ! cytoskeleton organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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:0000837
name: cell cycle arrest in mitotic interphase
def: "A cellular process phenotype in which progression through the mitotic cell cycle is arrested in any part of interphase. Includes normal and abnormal occurrences of arrest." [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 cycle arrest in mitotic interphase during vegetative growth" EXACT [PomBase:mah]
synonym: "interphase block" RELATED [PomBase:vw]
synonym: "mitotic cell cycle arrest in interphase" EXACT [PomBase:mah]
synonym: "mitotic interphase cell cycle arrest" EXACT [PomBase:mah]
is_a: FYPO:0004040 ! mitotic cell cycle arrest phenotype
intersection_of: FYPO:0001024 ! cell cycle arrest phenotype
intersection_of: during GO:0051329 ! mitotic interphase
intersection_of: during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in GO:0071850 ! mitotic cell cycle arrest
intersection_of: qualifier PATO:0000467 ! present
relationship: during GO:0051329 ! mitotic interphase
relationship: during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in GO:0071850 ! mitotic cell cycle arrest
relationship: qualifier PATO:0000467 ! present
created_by: midori
creation_date: 2012-03-09T04:18:58Z

[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_part_of GO:0044237 ! cellular metabolic process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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: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: FYPO:0004638 ! abnormal cellular physical quality 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_part_of GO:0061024 ! membrane organization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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]
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 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_part_of GO:0007050 ! cell cycle arrest
relationship: inheres_in_part_of 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_part_of GO:1902837 ! amino acid import into cell
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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:0000136 ! cellular physical quality 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, composition 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:0001312
name: normal vegetative phenotype
def: "A normal phenotype that is observed when cells are 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_manually_annotate
synonym: "fission yeast normal vegetative phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000257 ! normal phenotype
created_by: midori
creation_date: 2012-08-01T11:18:45Z

[Term]
id: FYPO:0001313
name: normal subcellular component during vegetative growth
def: "A cell phenotype in which the amount, distribution, or morphology of a cell part is normal (i.e. indistinguishable from wild type) when the cell is 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_manually_annotate
synonym: "normal subcellular component during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "normal subcellular structure during vegetative growth" RELATED [PomBase:mah]
is_a: FYPO:0001233 ! normal 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:0000461 ! normal
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in GO:0044464 ! cell part
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2012-08-01T12:32:26Z

[Term]
id: FYPO:0001319
name: normal cellular process during vegetative growth
def: "A phenotype in which a specific cellular process is normal (i.e. indistinguishable from wild type) 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_manually_annotate
synonym: "normal cellular process during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0000627 ! normal cellular process
is_a: FYPO:0001312 ! normal vegetative phenotype
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:0000461 ! normal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in GO:0044763 ! single-organism cellular process
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2012-08-01T13:42:47Z

[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_part_of GO:0005575 ! cellular_component
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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, morphology, or other physical characteristic 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:0004639 ! abnormal 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:0001323
name: altered level of substance in cell during vegetative growth
def: "A cell phenotype in which the amount of a specific substance measured in a cell differs from normal when the cell is 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_manually_annotate
synonym: "abnormal level of substance in cell during vegetative growth" EXACT [PomBase:mah]
synonym: "altered level of substance in cell during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0000989 ! altered level of substance in cell
is_a: FYPO:0004639 ! abnormal cellular physical quality phenotype during vegetative growth
intersection_of: PATO:0001159 ! concentrated
intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
intersection_of: qualifier PATO:0000460 ! abnormal
intersection_of: towards CHEBI:24431 ! chemical entity
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
relationship: qualifier PATO:0000460 ! abnormal
relationship: towards CHEBI:24431 ! chemical entity
created_by: midori
creation_date: 2012-08-01T14:57:41Z

[Term]
id: FYPO:0001326
name: altered RNA level during vegetative growth
def: "A cell phenotype in which the amount of RNA measured in a cell differs from normal when the cell is in the vegetative growth phase of the life cycle. 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. Also, 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 or its descendants.
subset: qc_do_not_manually_annotate
synonym: "abnormal RNA level during vegetative growth" EXACT [PomBase:mah]
synonym: "altered cellular RNA level during vegetative growth" EXACT [PomBase:mah]
synonym: "altered RNA level during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "altered transcript level during vegetative growth" EXACT [PomBase:vw]
is_a: FYPO:0000824 ! altered RNA level
is_a: FYPO:0001323 ! altered level of substance in cell during vegetative growth
intersection_of: PATO:0001159 ! concentrated
intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
intersection_of: qualifier PATO:0000460 ! abnormal
intersection_of: towards CHEBI:33697 ! ribonucleic acid
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
relationship: qualifier PATO:0000460 ! abnormal
relationship: towards CHEBI:33697 ! ribonucleic acid
created_by: midori
creation_date: 2012-08-01T15:11:33Z

[Term]
id: FYPO:0001330
name: increased level of substance in cell during vegetative growth
def: "A cell phenotype in which the amount of a specific substance measured in a cell is higher than normal when the cell is 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_manually_annotate
synonym: "increased accumulation of substance in cell during vegetative growth" RELATED [PomBase:mah]
synonym: "increased level of substance in cell during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0000990 ! increased level of substance in cell
is_a: FYPO:0001323 ! altered level of substance in cell during vegetative growth
intersection_of: PATO:0001162 ! increased concentration
intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
intersection_of: towards CHEBI:24431 ! chemical entity
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in CL:0000334 ! vegetative cell (sensu Fungi)
relationship: towards CHEBI:24431 ! chemical entity
created_by: midori
creation_date: 2012-08-01T16:24:14Z

[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_part_of GO:0044763 ! single-organism cellular process
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0010468 ! regulation of gene expression
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_part_of GO:0065007 ! biological regulation
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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_part_of GO:0006355 ! regulation of transcription, DNA-templated
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0006355 ! regulation of transcription, DNA-templated
created_by: midori
creation_date: 2012-08-01T16:36:22Z

[Term]
id: FYPO:0001337
name: localization phenotype during vegetative growth
def: "A cell phenotype that affects the localization of a structure or substance in a 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: "fission yeast localization phenotype during vegetative growth" EXACT [PomBase:mah]
synonym: "localisation phenotype during vegetative growth" EXACT [PomBase:mah]
synonym: "localization phenotype during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0000138 ! localization phenotype
is_a: FYPO:0001331 ! cellular process 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_part_of GO:0051641 ! cellular localization
relationship: during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0051641 ! cellular localization
created_by: midori
creation_date: 2012-08-01T16:55:18Z

[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_part_of GO:0090304 ! nucleic acid metabolic process
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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_part_of GO:0044237 ! cellular metabolic process
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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_annotate
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
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_part_of GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of 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_part_of 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_part_of 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_part_of GO:0034613 ! cellular protein localization
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0071574 ! protein localization to medial cortex
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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]
synonym: "protein localisation abolished" EXACT [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
subset: qc_do_not_manually_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_part_of GO:1990123 ! L-glutamate import into cell
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:1903410 ! L-lysine import into cell
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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: 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 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 or its descendants.
subset: qc_do_not_manually_annotate
synonym: "abnormal protein localisation to chromatin" EXACT [GO:0071168, PomBase:mah]
is_a: FYPO:0004996 ! abnormal protein localization to chromosome
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0071168 ! protein localization to chromatin
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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]
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 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]
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 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_part_of 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_part_of 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_part_of GO:0006810 ! transport
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0007155 ! cell adhesion
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
subset: qc_do_not_manually_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_annotate
subset: qc_do_not_manually_annotate
is_a: FYPO:0002057 ! cell population viability
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]
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:0002057 ! cell population viability
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]
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 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
subset: qc_do_not_manually_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_part_of GO:0034613 ! cellular protein localization
relationship: inheres_in_part_of GO:0034613 ! cellular protein localization
created_by: midori
creation_date: 2013-07-05T15:59:48Z

[Term]
id: FYPO:0002494
name: abnormal protein modification
def: "A cellular process phenotype in which protein modification is abnormal. All modifications may be affected, or only modifications of a certain type, or on specific proteins, or even specific sites within specific proteins." [GO:0030163, 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:0002274 ! abnormal protein metabolic process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0006464 ! cellular protein modification process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0006464 ! cellular protein modification process
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2013-08-08T15:45:44Z

[Term]
id: FYPO:0002496
name: normal metabolic process
def: "A cellular process phenotype in which a cellular metabolic process is normal (i.e. indistinguishable from wild type). 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: "normal cellular metabolic process" EXACT [GO:0044237, PomBase:mah]
synonym: "normal metabolism" EXACT [GO:0044237, PomBase:mah]
is_a: FYPO:0000627 ! normal cellular process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in GO:0044237 ! cellular metabolic process
intersection_of: qualifier PATO:0000461 ! normal
relationship: inheres_in GO:0044237 ! cellular metabolic process
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2013-08-08T15:51:57Z

[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:0002677
name: abnormal protein phosphorylation
def: "A cellular process phenotype in which the phosphorylation of one or more specific proteins 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. If this term is used, we recommend noting which protein(s) were used in the assay.
subset: qc_do_not_manually_annotate
is_a: FYPO:0002494 ! abnormal protein modification
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0006468 ! protein phosphorylation
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0006468 ! protein phosphorylation
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2013-09-19T11:41:10Z

[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_part_of GO:0022402 ! cell cycle process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0022403 ! cell cycle phase
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0022403 ! cell cycle phase
intersection_of: part_of GO:0000278 ! mitotic cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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
synonym: "abnormal mitotic cell cycle process during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "abnormal mitotic cell cycle process during vegetative growth" EXACT [PomBase:mah]
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_part_of GO:1903047 ! mitotic cell cycle process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:0022403 ! cell cycle phase
intersection_of: part_of GO:0051321 ! meiotic cell cycle
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_part_of GO:1903046 ! meiotic cell cycle process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of 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_annotate
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:0003452
name: mislocalized protein
def: "A cell phenotype in which a protein is observed in a particular location where it is not 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. 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:0003452 and its descendants 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]
is_a: FYPO:0003037 ! abnormal cell phenotype
is_a: FYPO:0004638 ! abnormal cellular physical quality phenotype
is_a: PATO:0000628 ! mislocalised
intersection_of: PATO:0000628 ! mislocalised
intersection_of: inheres_in CHEBI:36080 ! protein
relationship: inheres_in CHEBI:36080 ! protein
relationship: output_of FYPO:0001370 ! abnormal protein localization
created_by: midori
creation_date: 2014-06-24T12:20:58Z

[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
subset: qc_do_not_manually_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_part_of GO:0007165 ! signal transduction
relationship: inheres_in_part_of 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. Also consider using a more specific term to annotate each phenotype.
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:0003832
name: normal cell cycle
def: "A cellular process phenotype in which cell cycle progression 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: "cell cycle progression: normal" EXACT [SGD:phenotype_annotation]
synonym: "normal cell cycle progression" EXACT [PomBase:mah]
synonym: "normal cell-division cycle" EXACT [GO:0007049, PomBase:mah]
is_a: FYPO:0001319 ! normal 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:0007049 ! cell cycle
intersection_of: qualifier PATO:0000461 ! normal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in GO:0007049 ! cell cycle
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2014-10-15T11:01:20Z

[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:0004040
name: mitotic cell cycle arrest phenotype
def: "A cell cycle phenotype that affects or involves the normal or abnormal occurrence of mitotic cell cycle arrest. In mitotic cell cycle arrest, progression through the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, or M)." [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 cycle arrest phenotype during mitotic cell cycle" EXACT [PomBase:mah]
synonym: "cell cycle arrest phenotype during vegetative growth" EXACT [PomBase:mah]
synonym: "fission yeast mitotic cell cycle arrest phenotype" EXACT [PomBase:mah]
is_a: FYPO:0001024 ! cell cycle arrest phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: inheres_in GO:0071850 ! mitotic cell cycle arrest
relationship: inheres_in GO:0071850 ! mitotic cell cycle arrest
created_by: midori
creation_date: 2014-11-27T12:18:23Z

[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]
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/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

[Term]
id: FYPO:0004593
name: abnormal vegetative cell phenotype following normal mitosis
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, and after it has undergone a normal mitotic nuclear division and passed through the subsequent mitotic interphase." [PomBase:mah]
comment: This term groups phenotypes that affect the second round of mitosis to take place after a mutation exerts its effect. For example, if a conditional mutant is shifted to restrictive conditions in G1 or S phase and the first mitosis thereafter is normal, but an abnormality arises in the second (even if cells are returned to permissive conditions in the second G1 or S phase), a descendant of this term is applicable. 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 phenotype following normal mitosis during vegetative growth" EXACT [PomBase:mah]
synonym: "abnormal vegetative cell phenotype following normal mitosis and interphase" EXACT [PomBase:mah]
synonym: "abnormal vegetative cell phenotype following normal mitosis and passage through mitotic G1 phase" EXACT [PomBase:vw]
synonym: "abnormal vegetative cell phenotype following normal mitotic nuclear division" EXACT [GO:0007067]
synonym: "abnormal vegetative cell phenotype following normal nuclear division during mitotic cell cycle" EXACT [PomBase:mah]
is_a: FYPO:0003755 ! abnormal vegetative cell phenotype
created_by: midori
creation_date: 2015-04-29T15:59:40Z

[Term]
id: FYPO:0004620
name: abnormal spindle disassembly
def: "A cellular process phenotype in which spindle disassembly is abnormal. Spindle disassembly is the controlled breakdown of the spindle." [GO:0051230, 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:0002734 ! abnormal cell cycle process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0051230 ! spindle disassembly
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: has_output FYPO:0004438 ! long mitotic spindle during anaphase
relationship: inheres_in_part_of GO:0051230 ! spindle disassembly
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-05-05T15:09:51Z

[Term]
id: FYPO:0004638
name: abnormal cellular physical quality phenotype
def: "A phenotype in which any physical object quality, such as morphology, number, location, etc., of a cell or a cellular component 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
synonym: "abnormal cellular physical object quality" EXACT [PATO:0001241]
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_part_of GO:0005575 ! cellular_component
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0005575 ! cellular_component
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-05-08T14:33:25Z

[Term]
id: FYPO:0004639
name: abnormal cellular physical quality phenotype during vegetative growth
def: "A phenotype observed in the vegetative growth phase of the life cycle in which any physical object quality, such as morphology, number, location, etc., of a cell or a cellular component 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
synonym: "abnormal cellular physical object quality during vegetative growth" EXACT [PomBase:mah]
synonym: "abnormal cellular physical quality phenotype during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0001321 ! cellular physical quality phenotype during vegetative growth
is_a: FYPO:0004638 ! abnormal cellular physical quality phenotype
intersection_of: PATO:0001241 ! physical object quality
intersection_of: exists_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in_part_of GO:0005575 ! cellular_component
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0005575 ! cellular_component
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-05-08T15:13:46Z

[Term]
id: FYPO:0004847
name: transcription phenotype
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
subset: qc_do_not_manually_annotate
synonym: "fission yeast transcription phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000142 ! gene expression phenotype
is_a: FYPO:0000294 ! RNA metabolism phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: inheres_in_part_of GO:0006351 ! transcription, DNA-templated
relationship: inheres_in_part_of GO:0006351 ! transcription, DNA-templated
created_by: midori
creation_date: 2015-08-26T14:59:27Z

[Term]
id: FYPO:0004849
name: normal protein metabolic process
def: "A cellular process phenotype in which a protein metabolic process is normal (i.e. indistinguishable from wild type). A protein metabolic process is a series of chemical reactions and pathways involving a specific protein." [GO:0019538, 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 metabolic process" EXACT [PomBase:mah]
synonym: "normal protein metabolism" EXACT [GO:0019538]
is_a: FYPO:0000140 ! cellular metabolism phenotype
is_a: FYPO:0002496 ! normal metabolic process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0044267 ! cellular protein metabolic process
intersection_of: qualifier PATO:0000461 ! normal
relationship: inheres_in_part_of GO:0044267 ! cellular protein metabolic process
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2015-08-26T15:36:24Z

[Term]
id: FYPO:0004850
name: normal RNA metabolic process
def: "A cellular process phenotype in which a protein metabolic process is normal (i.e. indistinguishable from wild type). An RNA metabolic process is a series of chemical reactions and pathways involving any type of RNA." [GO:0016070, 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 RNA metabolism" EXACT [GO:0016070]
is_a: FYPO:0000294 ! RNA metabolism phenotype
is_a: FYPO:0002496 ! normal metabolic process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0016070 ! RNA metabolic process
intersection_of: qualifier PATO:0000461 ! normal
relationship: inheres_in_part_of GO:0016070 ! RNA metabolic process
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2015-08-26T15:49:11Z

[Term]
id: FYPO:0004851
name: abnormal RNA metabolic process
def: "A cellular process phenotype in which a protein metabolic process is abnormal. An RNA metabolic process is a series of chemical reactions and pathways involving any type of RNA." [GO:0016070, 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 metabolism" EXACT [GO:0016070]
is_a: FYPO:0000294 ! RNA metabolism phenotype
is_a: FYPO:0000860 ! abnormal metabolic process
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0016070 ! RNA metabolic process
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0016070 ! RNA metabolic process
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-08-26T15:50:46Z

[Term]
id: FYPO:0004852
name: RNA transport phenotype
def: "A cell process phenotype that affects an RNA 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
subset: qc_do_not_manually_annotate
is_a: FYPO:0000149 ! transport phenotype
is_a: FYPO:0004853 ! RNA localization phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: inheres_in_part_of GO:0050658 ! RNA transport
relationship: inheres_in_part_of GO:0050658 ! RNA transport
created_by: midori
creation_date: 2015-08-26T15:52:33Z

[Term]
id: FYPO:0004853
name: RNA localization phenotype
def: "A cell phenotype that affects the localization of an RNA 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
subset: qc_do_not_manually_annotate
synonym: "fission yeast RNA localization phenotype" EXACT [PomBase:mah]
synonym: "RNA localisation phenotype" EXACT [PomBase:mah]
is_a: FYPO:0000138 ! localization phenotype
intersection_of: FYPO:0000002 ! cell phenotype
intersection_of: inheres_in_part_of GO:0006403 ! RNA localization
relationship: inheres_in_part_of GO:0006403 ! RNA localization
created_by: midori
creation_date: 2015-08-26T15:54:27Z

[Term]
id: FYPO:0004916
name: abnormal regulation of catalytic activity
def: "A regulation phenotype observed in the vegetative growth phase of the life cycle in which regulation of a catalytic 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_annotate
subset: qc_do_not_manually_annotate
synonym: "abnormal regulation of catalytic activity during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "abnormal regulation of catalytic activity during vegetative growth" EXACT [PomBase:mah]
is_a: FYPO:0000682 ! abnormal regulation of molecular function
intersection_of: PATO:0000001 ! quality
intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in_part_of GO:0050790 ! regulation of catalytic activity
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0050790 ! regulation of catalytic activity
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-10-07T14:45:40Z

[Term]
id: FYPO:0004919
name: normal 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 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
synonym: "normal regulation of molecular function during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "normal regulation of molecular function during vegetative growth" EXACT [PomBase:mah]
is_a: FYPO:0000257 ! normal phenotype
is_a: FYPO:0001334 ! regulation 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_part_of GO:0065009 ! regulation of molecular function
intersection_of: qualifier PATO:0000461 ! normal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0065009 ! regulation of molecular function
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2015-10-07T14:50:58Z

[Term]
id: FYPO:0004920
name: normal regulation of catalytic activity
def: "A regulation phenotype observed in the vegetative growth phase of the life cycle in which regulation of a catalytic 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_annotate
subset: qc_do_not_manually_annotate
synonym: "normal regulation of catalytic activity during mitotic cell cycle" RELATED [PomBase:mah]
synonym: "normal regulation of catalytic activity during vegetative growth" EXACT [PomBase:mah]
is_a: FYPO:0004919 ! normal regulation of molecular function
intersection_of: PATO:0000001 ! quality
intersection_of: happens_during GO:0072690 ! single-celled organism vegetative growth phase
intersection_of: inheres_in GO:0050790 ! regulation of catalytic activity
intersection_of: qualifier PATO:0000461 ! normal
relationship: happens_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in GO:0050790 ! regulation of catalytic activity
relationship: qualifier PATO:0000461 ! normal
created_by: midori
creation_date: 2015-10-07T14:51:58Z

[Term]
id: FYPO:0004996
name: abnormal protein localization to chromosome
def: "A cell phenotype in which the localization of a protein to a specific location on a chromosome 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 all or part of a chromosome 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 chromosome" EXACT [PomBase:mah]
is_a: FYPO:0001370 ! abnormal protein localization
intersection_of: PATO:0000001 ! quality
intersection_of: inheres_in_part_of GO:0034502 ! protein localization to chromosome
intersection_of: qualifier PATO:0000460 ! abnormal
relationship: inheres_in_part_of GO:0034502 ! protein localization to chromosome
relationship: qualifier PATO:0000460 ! abnormal
created_by: midori
creation_date: 2015-10-28T11:52:12Z

[Term]
id: FYPO:0005044
name: translation regulation phenotype during vegetative growth
def: "A gene expression phenotype that affects the regulation of translation 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 translation regulation phenotype during vegetative growth" EXACT [PomBase:mah]
synonym: "translation regulation phenotype during mitotic cell cycle" RELATED [PomBase:mah]
is_a: FYPO:0000289 ! translation 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_part_of GO:0006417 ! regulation of translation
relationship: exists_during GO:0072690 ! single-celled organism vegetative growth phase
relationship: inheres_in_part_of GO:0006417 ! regulation of translation
created_by: midori
creation_date: 2015-11-10T12:14:24Z