zeco-full.obo

format-version: 1.2
data-version: zeco/releases/2022-02-14/zeco-full.owl
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
subsetdef: ZECO:0000267 ""
default-namespace: zebrafish_experimental_conditions_ontology
ontology: zeco/zeco-full
property_value: http://purl.org/dc/elements/1.1/description "Ontology of Zebrafish Experimental Conditions" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Experimental Conditions Ontology" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/
property_value: owl:versionInfo "2022-02-14" xsd:string

[Term]
id: BFO:0000002
name: continuant
def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." []
disjoint_from: BFO:0000003 ! occurrent
relationship: BFO:0000050 BFO:0000002 ! part of continuant

[Term]
id: BFO:0000003
name: occurrent
def: "An entity that has temporal parts and that happens, unfolds or develops through time." []
relationship: BFO:0000050 BFO:0000003 ! part of occurrent

[Term]
id: BFO:0000004
name: independent continuant
def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." []
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000004 ! part of independent continuant

[Term]
id: BFO:0000015
name: process
def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." []
is_a: BFO:0000003 ! occurrent

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role

[Term]
id: BFO:0000017
name: realizable entity
def: "A specifically dependent continuant  that inheres in continuant  entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." []
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
relationship: BFO:0000050 BFO:0000017 ! part of realizable entity

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
relationship: BFO:0000050 BFO:0000019 ! part of quality

[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." []
is_a: BFO:0000002 ! continuant
relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant

[Term]
id: BFO:0000023
name: role
def: "A realizable entity  the manifestation of which brings about some result or end that is not essential to a continuant  in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant  in some kinds of natural, social or institutional contexts." []
is_a: BFO:0000017 ! realizable entity

[Term]
id: BFO:0000034
name: function
is_a: BFO:0000016 ! disposition

[Term]
id: BFO:0000040
name: material entity
def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." []
is_a: BFO:0000004 ! independent continuant

[Term]
id: CARO:0000000
name: anatomical entity
is_a: CARO:0030000 ! biological entity
property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl

[Term]
id: CARO:0030000
name: biological entity
is_a: BFO:0000004 ! independent continuant

[Term]
id: GO:0003674
name: molecular_function
is_a: BFO:0000015 ! process
property_value: IAO:0000589 "molecular process" xsd:string

[Term]
id: GO:0003824
name: catalytic activity
is_a: GO:0003674 ! molecular_function

[Term]
id: GO:0008150
name: biological_process
is_a: BFO:0000015 ! process

[Term]
id: GO:0016301
name: kinase activity
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups

[Term]
id: GO:0016740
name: transferase activity
is_a: GO:0003824 ! catalytic activity

[Term]
id: GO:0016772
name: transferase activity, transferring phosphorus-containing groups
is_a: GO:0016740 ! transferase activity

[Term]
id: PATO:0000001
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000589 "quality (PATO)" xsd:string

[Term]
id: ZECO:0000100
name: conditions
def: "The state in which an organism exists. " []

[Term]
id: ZECO:0000101
name: control conditions
def: "Condition which serves as a standard against which experimental conditions can be compared." []
subset: ZECO:0000267
is_a: ZECO:0000100 ! conditions

[Term]
id: ZECO:0000102
name: generic control
def: "Control condition in which the conditions of the organism in the control experiment are not standard but are being used as the condition against which the experimental condition is compared." []
synonym: "innocuous condition" EXACT []
is_a: ZECO:0000101 ! control conditions

[Term]
id: ZECO:0000103
name: standard conditions
def: "Experimental condition that is the standard environment for zebrafish husbandry, as described in ‘The Zebrafish Book’. In general the standard environment utilizes contaminant free tank water, heated to 28.5 degrees C, with the fish fed a normal contaminant free diet, with standard osmolarity, pH, and normal light cycle of 14hr light/10hr dark." []
subset: ZECO:0000267
is_a: ZECO:0000100 ! conditions

[Term]
id: ZECO:0000104
name: experimental conditions
def: "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition." []
subset: ZECO:0000267
is_a: ZECO:0000100 ! conditions

[Term]
id: ZECO:0000105
name: biological treatment
def: "Experimental condition in which the organism is treated with a microorganism." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000106
name: bacterial treatment
def: "Biological treatment in which fish have been infected with bacteria. This infection can be done by addition of bacteria in the water or by injection of bacteria, (for example in the brain ventricle, in the caudal vein, in the yolk sac), or ingestion, or other means." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000107
name: fungal treatment
def: "Biological treatment in which fish have been infected with a fungus." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000108
name: germ free
def: "Biological treatment in which fish were raised in the absence of bacteria." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000109
name: protozoan treatment
def: "Biological treatment in which fish have been infected with protozoa." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000110
name: viral treatment
def: "Biological treatment in which fish have been infected with a virus." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000111
name: chemical treatment
def: "Experimental condition in which the fish is treated with a chemical substance. This treatment could be administered by adding the chemical substance to the tank water, injections, or by consumption." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000112
name: diet
def: "Experimental condition where the food of the zebrafish is manipulated in some way." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000113
name: food availability
def: "Experimental condition in which the availability of food is manipulated." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000114
name: fasting
def: "Limited food availability condition in which there is no food provided." []
is_a: ZECO:0000115 ! limited food availability

[Term]
id: ZECO:0000115
name: limited food availability
def: "Food availability condition in which food is provided in limited supply." []
is_a: ZECO:0000113 ! food availability

[Term]
id: ZECO:0000116
name: unlimited food availability
def: "Food availability condition in which food is available in unlimited supply." []
is_a: ZECO:0000247 ! increased food availability

[Term]
id: ZECO:0000117
name: food content
def: "Diet condition in which the contents of the food is manipulated." []
is_a: ZECO:0000112 ! diet

[Term]
id: ZECO:0000118
name: cholesterol content
def: "Food content condition in which the amount of cholesterol in the diet is manipulated." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000119
name: high cholesterol
def: "Cholesterol content condition in which the amount of cholesterol in the diet is elevated." []
is_a: ZECO:0000118 ! cholesterol content

[Term]
id: ZECO:0000120
name: low cholesterol
def: "Cholesterol content condition in which the amount of cholesterol in the diet is reduced." []
is_a: ZECO:0000118 ! cholesterol content

[Term]
id: ZECO:0000121
name: fat content
def: "Food content condition in which the amount of fat in the diet is manipulated." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000122
name: high fat
def: "Fat content condition in which the amount of fat in the diet is elevated." []
is_a: ZECO:0000121 ! fat content
is_a: ZECO:0000251 ! nutrient increased

[Term]
id: ZECO:0000123
name: high saturated fat
def: "High fat condition in which the amount of saturated fat in the diet is elevated." []
is_a: ZECO:0000122 ! high fat

[Term]
id: ZECO:0000124
name: high monounsaturated fat
def: "High fat condition in which the amount of monounsaturated fat in the diet is elevated." []
is_a: ZECO:0000122 ! high fat

[Term]
id: ZECO:0000125
name: low fat
def: "Fat content condition in which the amount of fat in the diet is reduced." []
is_a: ZECO:0000121 ! fat content
is_a: ZECO:0000250 ! nutrient decreased

[Term]
id: ZECO:0000126
name: low trans fat
def: "Low fat condition in which the amount of trans fat in the diet is reduced." []
is_a: ZECO:0000125 ! low fat

[Term]
id: ZECO:0000127
name: low polyunsaturated fat
def: "Low fat condition in which the amount of polyunsaturated fat in the diet is reduced." []
is_a: ZECO:0000125 ! low fat

[Term]
id: ZECO:0000128
name: protein content
def: "Food content condition in which the amount of protein in the diet is manipulated." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000129
name: high protein
def: "Protein content condition in which the protein in the diet is elevated." []
is_a: ZECO:0000128 ! protein content
is_a: ZECO:0000251 ! nutrient increased

[Term]
id: ZECO:0000130
name: low protein
def: "Protein content condition in which the protein in the diet is reduced." []
is_a: ZECO:0000128 ! protein content
is_a: ZECO:0000250 ! nutrient decreased

[Term]
id: ZECO:0000131
name: stress
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000132
name: high sugar
def: "High carbohydrate conditions in which the amount of sugar in the diet is elevated." []
is_a: ZECO:0000241 ! high carbohydrate

[Term]
id: ZECO:0000133
name: high fructose
def: "High sugar condition in which the amount of fructose in the diet is elevated." []
is_a: ZECO:0000132 ! high sugar

[Term]
id: ZECO:0000134
name: high glucose
def: "High sugar condition in which the amount of glucose in the diet is elevated." []
is_a: ZECO:0000132 ! high sugar

[Term]
id: ZECO:0000135
name: high sucrose
def: "High sugar condition in which the amount of sucrose in the diet is elevated." []
is_a: ZECO:0000132 ! high sugar

[Term]
id: ZECO:0000136
name: low sugar
def: "High carbohydrate conditions in which the amount of sugar in the diet is reduced." []
is_a: ZECO:0000242 ! low carbohydrate

[Term]
id: ZECO:0000137
name: low sucrose
def: "Low sugar condition in which the amount of sucrose in the diet is reduced." []
is_a: ZECO:0000136 ! low sugar

[Term]
id: ZECO:0000138
name: low fructose
def: "Low sugar condition in which the amount of fructose in the diet is reduced." []
is_a: ZECO:0000136 ! low sugar

[Term]
id: ZECO:0000139
name: low glucose
def: "Low sugar condition in which the amount of glucose in the diet is reduced." []
is_a: ZECO:0000136 ! low sugar

[Term]
id: ZECO:0000140
name: housing conditions
def: "Experimental condition that manipulates the enclosure of the fish." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000141
name: open roofed
def: "Housing condition in which the roof of the enclosure if open." []
is_a: ZECO:0000140 ! housing conditions

[Term]
id: ZECO:0000142
name: overcrowding
def: "Housing condition in which the enclosure of the fish is overcrowded, containing an excess of fish that reduces the available space of the enclosure." []
synonym: "high density" EXACT []
is_a: ZECO:0000140 ! housing conditions

[Term]
id: ZECO:0000143
name: in vitro culture
def: "Experimental condition in which components of the fish have been removed and are maintained separately." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000144
name: organ culture
def: "In vitro culture condition in which an organ is dissected/isolated/collected from the fish and placed in culture. The analysis of the experiment is done on this organ in culture." []
is_a: ZECO:0000143 ! in vitro culture

[Term]
id: ZECO:0000145
name: primary cell culture
def: "In vitro culture condition in which an embryo or adult fish is dissociated to a single cell suspension. The analysis is made on this cell culture." []
is_a: ZECO:0000143 ! in vitro culture

[Term]
id: ZECO:0000146
name: lighting conditions
def: "Experimental condition in which the intensity, wavelength, and/or duration of illumination is (are) different from the one in controlled conditions." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000147
name: light duration
is_a: ZECO:0000146 ! lighting conditions

[Term]
id: ZECO:0000148
name: altered light dark cycle
is_a: ZECO:0000147 ! light duration

[Term]
id: ZECO:0000149
name: constant dark
is_a: ZECO:0000147 ! light duration

[Term]
id: ZECO:0000150
name: constant light
is_a: ZECO:0000147 ! light duration

[Term]
id: ZECO:0000151
name: light intensity
is_a: ZECO:0000146 ! lighting conditions

[Term]
id: ZECO:0000152
name: high light intensity
is_a: ZECO:0000151 ! light intensity

[Term]
id: ZECO:0000153
name: low light intensity
is_a: ZECO:0000151 ! light intensity

[Term]
id: ZECO:0000154
name: gravity
def: "Experimental condition in which gravity forces are manipulated. For zebrafish, this can be in the form of centrifugal forces or trips to outerspace." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000155
name: mechanical stress
def: "Experimental condition in which an external mechanical force is applied to the fish or part of the fish." []
is_a: ZECO:0000131 ! stress

[Term]
id: ZECO:0000156
name: vibration
is_a: ZECO:0000155 ! mechanical stress

[Term]
id: ZECO:0000157
name: water flow
is_a: ZECO:0000155 ! mechanical stress

[Term]
id: ZECO:0000158
name: circular flow
is_a: ZECO:0000157 ! water flow

[Term]
id: ZECO:0000159
name: through flow
is_a: ZECO:0000157 ! water flow

[Term]
id: ZECO:0000160
name: temperature exposure
def: "Experimental condition in which the zebrafish is exposed to an increased or decreased temperature." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000161
name: stable temperature exposure
def: "Temperature exposure condition in which fish are raised in temperature different (lower or higher) than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000160 ! temperature exposure

[Term]
id: ZECO:0000162
name: cold exposure
def: "Temperature exposure condition in which fish are raised in temperature that is lower than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000161 ! stable temperature exposure

[Term]
id: ZECO:0000163
name: heat exposure
def: "Temperature exposure condition in which fish are raised in temperature that is higher than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000161 ! stable temperature exposure

[Term]
id: ZECO:0000164
name: temperature shock
def: "Temperature exposure condition in which fish are subjected for a short period of time to temperature that is lower or higher than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000160 ! temperature exposure

[Term]
id: ZECO:0000165
name: cold shock
def: "Temperature shock condition in which fish are subjected for a short period of time to temperature lower than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000164 ! temperature shock

[Term]
id: ZECO:0000166
name: heat shock
def: "Temperature shock condition in which fish are subjected for a short period of time to temperature higher than the controlled temperature. The standard controlled temperature (according to the zebrafish book) is 28.5 degrees C." []
is_a: ZECO:0000164 ! temperature shock

[Term]
id: ZECO:0000168
name: ablation
def: "Targeted destruction of an anatomical structure." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000169
name: chemical ablation
def: "Experimental condition which uses a chemical to ablate an anatomical structure or cell." []
is_a: ZECO:0000168 ! ablation

[Term]
id: ZECO:0000170
name: light ablation
def: "Experimental condition which uses focused light to ablate an anatomical structure or cell." []
is_a: ZECO:0000168 ! ablation
is_a: ZECO:0000245 ! light damage

[Term]
id: ZECO:0000171
name: resection
def: "Surgical manipulation in which a particular organ, appendage, or part of an organism is removed." []
is_a: ZECO:0000176 ! surgical manipulation

[Term]
id: ZECO:0000172
name: amputation
def: "Resection condtion in which all or part of an extremity such as the fin or tail are removed." []
is_a: ZECO:0000171 ! resection

[Term]
id: ZECO:0000173
name: vaccine treatment
def: "Biological treatment in which the organism is treated with a substance to stimulate the production of antibodies and provide immunity against one or several diseases." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000174
name: laceration
def: "Experimental condition in which there is a deep cut or tear of the flesh." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000176
name: surgical manipulation
def: "Experimental condition that involves  manual or instrumental techniques to alter anatomical structures." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000177
name: xenotransplantation
def: "Experimental condition in which living cells or tissues from one species are transplanted into another." []
is_a: ZECO:0000105 ! biological treatment

[Term]
id: ZECO:0000178
name: perforation
def: "Experimental condition in which a hole or break in the membranes of an organ or structure of the body is created." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000179
name: abrasion
def: "Experimental condition that results in superficial damage of tissue such that it is scraped or worn away." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000180
name: contusion
def: "Experimental condition that results in hematoma of tissue in which capillaries and sometimes venules are damaged by trauma, allowing blood to seep, hemorrhage, or extravasate into the surrounding interstitial tissues. (https://en.wikipedia.org/wiki/Bruise)" []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000181
name: transection
def: "Cutting transversly of an organ or tissue. Type of cutting often used to divide the spinal cord to investigate neural regeneration in zebrafish." []
is_a: ZECO:0000176 ! surgical manipulation

[Term]
id: ZECO:0000182
name: water quality
def: "Experimental condition in which a chemical or physical characteristic of water is altered." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000183
name: gas composition
comment: Water quality condition that alters the concentration of atmospheric gases in water.
is_a: ZECO:0000182 ! water quality

[Term]
id: ZECO:0000184
name: carbon dioxide content
def: "A gas composition condition that alters the concentraion of carbion dioxide." []
is_a: ZECO:0000183 ! gas composition

[Term]
id: ZECO:0000185
name: hypercapnia
is_a: ZECO:0000184 ! carbon dioxide content

[Term]
id: ZECO:0000186
name: hypocapnia
is_a: ZECO:0000184 ! carbon dioxide content

[Term]
id: ZECO:0000187
name: oxygen content
def: "A gas composition condition that alters the concentraion of oxygen." []
is_a: ZECO:0000183 ! gas composition

[Term]
id: ZECO:0000188
name: hyperoxia
def: "An oxygen content with high concentration of oxygen." []
is_a: ZECO:0000187 ! oxygen content

[Term]
id: ZECO:0000189
name: hypoxia
def: "An oxygen content with low concentration of oxygen." []
is_a: ZECO:0000187 ! oxygen content

[Term]
id: ZECO:0000190
name: ion composition
is_a: ZECO:0000182 ! water quality

[Term]
id: ZECO:0000191
name: modified calcium composition
is_a: ZECO:0000190 ! ion composition

[Term]
id: ZECO:0000192
name: high calcium
is_a: ZECO:0000191 ! modified calcium composition

[Term]
id: ZECO:0000193
name: low calcium
is_a: ZECO:0000191 ! modified calcium composition

[Term]
id: ZECO:0000194
name: modified potassium composition
is_a: ZECO:0000190 ! ion composition

[Term]
id: ZECO:0000195
name: high potassium
is_a: ZECO:0000194 ! modified potassium composition

[Term]
id: ZECO:0000196
name: low potassium
is_a: ZECO:0000194 ! modified potassium composition

[Term]
id: ZECO:0000197
name: modified sodium composition
is_a: ZECO:0000190 ! ion composition

[Term]
id: ZECO:0000198
name: high sodium
is_a: ZECO:0000197 ! modified sodium composition

[Term]
id: ZECO:0000199
name: low sodium
is_a: ZECO:0000197 ! modified sodium composition

[Term]
id: ZECO:0000200
name: pH
is_a: ZECO:0000190 ! ion composition

[Term]
id: ZECO:0000201
name: acidic
def: "Experimental condition in which the pH of the water is lower than the pH of the controlled conditions." []
is_a: ZECO:0000200 ! pH

[Term]
id: ZECO:0000202
name: basic
def: "Experimental condition in which the pH of the water is higher than the pH of the controlled conditions." []
is_a: ZECO:0000200 ! pH

[Term]
id: ZECO:0000203
name: water salinity
is_a: ZECO:0000182 ! water quality

[Term]
id: ZECO:0000204
name: hypertonic
def: "Experimental condition in which the salt concentration is higher than the one in controlled conditions." []
is_a: ZECO:0000203 ! water salinity

[Term]
id: ZECO:0000205
name: hypotonic
def: "Experimental condition in which the salt concentration is lower than the one in controlled conditions." []
is_a: ZECO:0000203 ! water salinity

[Term]
id: ZECO:0000206
name: isotonic
is_a: ZECO:0000203 ! water salinity

[Term]
id: ZECO:0000207
name: stable
is_a: ZECO:0000203 ! water salinity

[Term]
id: ZECO:0000208
name: radiation
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000209
name: electromagnetic radiation
is_a: ZECO:0000208 ! radiation

[Term]
id: ZECO:0000210
name: radio waves
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000211
name: microwaves
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000212
name: infared
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000213
name: visible light
def: "Electromagnetic radiation with a wavelength from 400 nm to 700 nm. Visible light referes to the light which is visible to the human eye and is responsible fo the sense of sight." [https://en.wikipedia.org/wiki/Light]
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000214
name: ultraviolet light
def: "Electromagnetic radiation with a wavelength from 10 nm to 400nm. Long-wavelength ultraviolet radiation can cause chemical reactions and causes many substances to glow or fluoresce." [https://en.wikipedia.org/wiki/Ultraviolet]
synonym: "UV" EXACT []
synonym: "UV light" EXACT []
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000215
name: x-ray
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000216
name: gamma ray
is_a: ZECO:0000209 ! electromagnetic radiation

[Term]
id: ZECO:0000217
name: particle radiation
is_a: ZECO:0000208 ! radiation

[Term]
id: ZECO:0000218
name: proton
is_a: ZECO:0000217 ! particle radiation

[Term]
id: ZECO:0000219
name: neutron
is_a: ZECO:0000217 ! particle radiation

[Term]
id: ZECO:0000220
name: acoustic radiation
is_a: ZECO:0000208 ! radiation

[Term]
id: ZECO:0000221
name: alpha particle
is_a: ZECO:0000217 ! particle radiation

[Term]
id: ZECO:0000222
name: electromagnetic field
def: "Experimental condition in which the fish is exposed to a physical field that is produced by electrically charged objects." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000223
name: electric field
def: "Experimental condition where the fish is exposed to materials that produce an electric field." []
is_a: ZECO:0000222 ! electromagnetic field

[Term]
id: ZECO:0000224
name: magnetic field
def: "Experimental condition where the fish is exposed to magnetic materials." []
is_a: ZECO:0000222 ! electromagnetic field

[Term]
id: ZECO:0000225
name: high polysunsaturated fat
def: "High fat condition in which the amount of polyunsaturated fat in the diet is elevated." []
is_a: ZECO:0000122 ! high fat

[Term]
id: ZECO:0000226
name: high trans fat
def: "High fat condition in which the amount of trans fat in the diet is elevated." []
is_a: ZECO:0000122 ! high fat

[Term]
id: ZECO:0000227
name: low saturated fat
def: "Low fat condition in which the amount of saturated fat in the diet is reduced." []
is_a: ZECO:0000125 ! low fat

[Term]
id: ZECO:0000228
name: low monounsaturated fat
def: "Low fat condition in which the amount of monounsaturated fat in the diet is reduced." []
is_a: ZECO:0000125 ! low fat

[Term]
id: ZECO:0000229
name: physical alteration
def: "Experimental condition in which an anatomical structure, cell, or organ has sustained targeted physical change, usually through the use of an instrument." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000230
name: bacterial treatment by injection
def: "Bacterial treatment where the bacteria are injected into the fish." []
is_a: ZECO:0000106 ! bacterial treatment

[Term]
id: ZECO:0000231
name: bacterial treatment by exposure to environment
def: "Bacterial treatment where the bacteria are introduced via the environment. For zebrafish this is the tank water." []
is_a: ZECO:0000106 ! bacterial treatment

[Term]
id: ZECO:0000232
name: fungal treatment by injection
def: "Fungal treatment where the fungus is injected into the fish." []
is_a: ZECO:0000107 ! fungal treatment

[Term]
id: ZECO:0000233
name: fungal treatment by exposure to environment
def: "Fungal treatment where the fungus is introduced via the environment. For zebrafish this is the tank water." []
is_a: ZECO:0000107 ! fungal treatment

[Term]
id: ZECO:0000234
name: viral treatment by exposure to environment
def: "Viral treatment where the virus is introduced via the environment. For zebrafish this is the tank water." []
is_a: ZECO:0000110 ! viral treatment

[Term]
id: ZECO:0000235
name: viral treatment by injection
def: "Viral treatment where the virus is injected into the fish." []
is_a: ZECO:0000110 ! viral treatment

[Term]
id: ZECO:0000236
name: cancer xenotransplantation
def: "Xenotransplantation condition in which cancer cells are injected or grafted into the zebrafish." []
is_a: ZECO:0000177 ! xenotransplantation

[Term]
id: ZECO:0000237
name: chemical treatment by injection
def: "Chemical treatment in which the chemical is injected into the zebrafish." []
is_a: ZECO:0000111 ! chemical treatment

[Term]
id: ZECO:0000238
name: chemical treatment by environment
def: "Chemical treatment condition in which the chemical is introduced through the environment. For zebrafish this is the tank water." []
is_a: ZECO:0000111 ! chemical treatment

[Term]
id: ZECO:0000239
name: chemical treatment by diet
def: "Chemical treatment condition in which the chemical is introduced through the diet." []
is_a: ZECO:0000111 ! chemical treatment
is_a: ZECO:0000112 ! diet

[Term]
id: ZECO:0000240
name: carbohydrate content
def: "Food content condition in which the amount of carbohydrate in the diet is manipulated." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000241
name: high carbohydrate
def: "Food content condtion in which the amount of carbohydrate in the diet is elevated." []
is_a: ZECO:0000240 ! carbohydrate content
is_a: ZECO:0000251 ! nutrient increased

[Term]
id: ZECO:0000242
name: low carbohydrate
def: "Food content condtion in which the amount of carbohydrate in the diet is reduced." []
is_a: ZECO:0000240 ! carbohydrate content
is_a: ZECO:0000250 ! nutrient decreased

[Term]
id: ZECO:0000243
name: stress by handling
is_a: ZECO:0000131 ! stress

[Term]
id: ZECO:0000244
name: ultrasound
def: "Mechanical stress condition where the organism is subjected to vibrations having an ultrasonic frequency." []
is_a: ZECO:0000156 ! vibration

[Term]
id: ZECO:0000245
name: light damage
def: "Physical alteration which uses light to damage the anatomical structure, cell, or organ." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000246
name: undercrowding
def: "Housing condition in which the enclosure of the fish is undercrowded,containing a low amount of fish that increases the available space of the enclosure." []
synonym: "low density" EXACT []
is_a: ZECO:0000140 ! housing conditions

[Term]
id: ZECO:0000247
name: increased food availability
def: "Food availability condition in which food is provided in increased supply." []
synonym: "overfeeding" EXACT []
is_a: ZECO:0000113 ! food availability

[Term]
id: ZECO:0000248
name: cold damage
def: "Physical alteration which uses cold to damage an anatomical structure, cell, or organ" []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000249
name: cryoablation
def: "Experimental condition which uses a cold instrument to ablate an anatomical structure or cell." []
is_a: ZECO:0000168 ! ablation
is_a: ZECO:0000248 ! cold damage

[Term]
id: ZECO:0000250
name: nutrient decreased
def: "Food content condition in which levels of a nutrient are decreased relative to standard diet." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000251
name: nutrient increased
def: "Food content condition in which levels of a nutrient are increased relative to standard diet." []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000252
name: feeding regime
def: "Experimental condition that manipulates the frequency or way an organism is fed." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

[Term]
id: ZECO:0000253
name: gavage
def: "Feeding regime in which food, drugs, or other substances are administered by force, typically through a tube leading down the throat to the stomach." []
is_a: ZECO:0000252 ! feeding regime

[Term]
id: ZECO:0000254
name: bacterial treatment by gavage
def: "Bacterial treatment condition where bacteria are introduced to the organism by gavage." []
is_a: ZECO:0000106 ! bacterial treatment
is_a: ZECO:0000253 ! gavage

[Term]
id: ZECO:0000255
name: chemical treatment by gavage
def: "Chemical treatment condition where the chemical is introduced to the organism by gavage." []
is_a: ZECO:0000111 ! chemical treatment
is_a: ZECO:0000253 ! gavage

[Term]
id: ZECO:0000256
name: bacterial treatment by diet
def: "Bacterial treatment where bacteria are introduced via the diet." []
is_a: ZECO:0000106 ! bacterial treatment

[Term]
id: ZECO:0000259
name: cauterization
def: "Condition that uses a cold or hot insturment, electrical current, or chemical to burn or dissolve an anatomical structure to remove or close it off." []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000260
name: thermal cauterization
def: "Cauterization of a tissue using a heated instrument." []
is_a: ZECO:0000259 ! cauterization

[Term]
id: ZECO:0000261
name: compression injury
def: "An injury that occurs because of pressure from a heavy object onto a body part. A compression injury may also arise from squeezing of a body part between two objects. https://www.medicinenet.com/crush_injury/definition.htm" []
synonym: "crush injury" EXACT []
is_a: ZECO:0000229 ! physical alteration

[Term]
id: ZECO:0000262
name: probiotic content
def: "Food content condition in which the amount of probiotics in the diet is manipulated" []
is_a: ZECO:0000117 ! food content

[Term]
id: ZECO:0000263
name: microgravity
def: "Experimental condition in which gravity forces are smaller than in control conditions. An example of a microgravity condition would be trips to outerspace." []
is_a: ZECO:0000154 ! gravity

[Term]
id: ZECO:0000264
name: increased gravity
def: "Experimental condition in which gravity forces are greater than in control conditions. An example of an increased gravity condition would be the application of centrifugal forces." []
is_a: ZECO:0000154 ! gravity

[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000002
property_value: RO:0040042 BFO:0000003
property_value: RO:0040042 BFO:0000004
property_value: RO:0040042 BFO:0000017
property_value: RO:0040042 BFO:0000019
property_value: RO:0040042 BFO:0000020
property_value: RO:0040042 BFO:0000031
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part

[Typedef]
id: BFO:0000051
name: has part
def: "a core relation that holds between a whole and its part" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: RO:0002131 ! overlaps

[Typedef]
id: BFO:0000062
name: preceded by
def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000062
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes

[Typedef]
id: BFO:0000063
name: precedes
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
holds_over_chain: BFO:0000050 BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020 ! specifically dependent continuant
is_inverse_functional: true

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000003 ! occurrent
inverse_of: RO:0000057 ! has participant

[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000002 ! continuant
holds_over_chain: BFO:0000051 RO:0000057

[Typedef]
id: RO:0000079
name: function of
def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string
property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "function_of" xsd:string
property_value: IAO:0000118 "is function of" xsd:string
domain: BFO:0000034 ! function
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000085 ! has function

[Typedef]
id: RO:0000080
name: quality of
def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string
property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string
property_value: IAO:0000118 "is quality of" xsd:string
property_value: IAO:0000118 "quality_of" xsd:string
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000086 ! has quality

[Typedef]
id: RO:0000081
name: role of
def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string
property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string
property_value: IAO:0000118 "is role of" xsd:string
property_value: IAO:0000118 "role_of" xsd:string
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000087 ! has role

[Typedef]
id: RO:0000085
name: has function
def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string
property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "has_function" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000034 ! function
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string
range: BFO:0000019 ! quality
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000087
name: has role
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string
property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string
property_value: IAO:0000118 "has_role" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000023 ! role
is_a: RO:0000053 ! has characteristic

[Typedef]
id: RO:0000091
name: has disposition
def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
domain: BFO:0000004 ! independent continuant
range: BFO:0000016 ! disposition
is_a: RO:0000053 ! has characteristic
inverse_of: RO:0000092 ! disposition of

[Typedef]
id: RO:0000092
name: disposition of
def: "inverse of has disposition" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
subset: RO:0002259
is_a: RO:0000052 ! characteristic of

[Typedef]
id: RO:0002013
name: has regulatory component activity
def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." []
is_a: RO:0002017 ! has component activity
is_a: RO:0002334 ! regulated by
created_by: dos
creation_date: 2017-05-24T09:30:46Z

[Typedef]
id: RO:0002014
name: has negative regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function.  Internal regulatory functions are treated as components.  For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002335 ! negatively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:01Z

[Typedef]
id: RO:0002015
name: has positive regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components.  So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002336 ! positively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:17Z

[Typedef]
id: RO:0002017
name: has component activity
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
is_a: RO:0002018 ! has component process
created_by: dos
creation_date: 2017-05-24T09:44:33Z

[Typedef]
id: RO:0002018
name: has component process
def: "w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_a: RO:0002180 ! has component
created_by: dos
creation_date: 2017-05-24T09:49:21Z

[Typedef]
id: RO:0002022
name: directly regulated by
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"}
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates
created_by: dos
creation_date: 2017-09-17T13:52:24Z

[Typedef]
id: RO:0002023
name: directly negatively regulated by
def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates
created_by: dos
creation_date: 2017-09-17T13:52:38Z

[Typedef]
id: RO:0002024
name: directly positively regulated by
def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates
created_by: dos
creation_date: 2017-09-17T13:52:47Z

[Typedef]
id: RO:0002025
name: has effector activity
def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674),  A 'has component activity' B and B is the effector (output function) of B.  Each compound function has only one effector activity." [GOC:dos]
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
is_functional: true
is_a: RO:0002017 ! has component activity
created_by: dos
creation_date: 2017-09-22T14:14:36Z

[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002087
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes

[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
is_a: BFO:0000063 ! precedes

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: BFO:0000051 RO:0002131
is_a: RO:0002323 ! mereotopologically related to
transitive_over: BFO:0000050 ! part of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []

[Typedef]
id: RO:0002180
name: has component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002202
name: develops from
def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" []
comment: This is the transitive form of the develops from relation
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Melissa Haendel" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000004 ! independent continuant
is_transitive: true
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002203 ! develops into

[Typedef]
id: RO:0002203
name: develops into
def: "inverse of develops from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
is_transitive: true
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002387 ! has potential to develop into
is_a: RO:0002388 ! has potential to directly develop into

[Typedef]
id: RO:0002211
name: regulates
def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
holds_over_chain: RO:0002578 RO:0002578
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by
transitive_over: RO:0002025 ! has effector activity

[Typedef]
id: RO:0002212
name: negatively regulates
def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by

[Typedef]
id: RO:0002213
name: positively regulates
def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by

[Typedef]
id: RO:0002215
name: capable of
def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " []
subset: ro-eco
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string
domain: BFO:0000004 ! independent continuant
range: BFO:0000015 ! process
is_a: RO:0002216 ! capable of part of

[Typedef]
id: RO:0002216
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent

[Typedef]
id: RO:0002233
name: has input
def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
domain: BFO:0000015 ! process
is_a: RO:0000057 ! has participant
inverse_of: RO:0002352 ! input of

[Typedef]
id: RO:0002254
name: has developmental contribution from
def: "x has developmental contribution from y iff x has some part z such that z develops from y" []
property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: CARO:0000000 ! anatomical entity
range: CARO:0000000 ! anatomical entity
holds_over_chain: BFO:0000051 RO:0002202
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002255 ! developmentally contributes to

[Typedef]
id: RO:0002255
name: developmentally contributes to
def: "inverse of has developmental contribution from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002203 BFO:0000050
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002385 ! has potential to developmentally contribute to

[Typedef]
id: RO:0002258
name: developmentally preceded by
def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" []
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "false" xsd:boolean
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002324 ! developmentally related to
inverse_of: RO:0002286 ! developmentally succeeded by

[Typedef]
id: RO:0002263
name: acts upstream of
def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
holds_over_chain: RO:0002327 RO:0002411
is_a: RO:0002264 ! acts upstream of or within

[Typedef]
id: RO:0002264
name: acts upstream of or within
def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
synonym: "affects" RELATED []
property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within
holds_over_chain: RO:0002327 RO:0002418
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002286
name: developmentally succeeded by
def: "Inverse of developmentally preceded by" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: RO:0002304
name: causally upstream of, positive effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004049 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004047 ! causally upstream of or within, positive effect

[Typedef]
id: RO:0002305
name: causally upstream of, negative effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004050 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect

[Typedef]
id: RO:0002314
name: characteristic of part of
def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." []
property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "inheres in part of" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002502 ! depends on
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: RO:0002324
name: developmentally related to
def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string

[Typedef]
id: RO:0002327
name: enables
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
is_a: RO:0002215 ! capable of
inverse_of: RO:0002333 ! enabled by
transitive_over: BFO:0000051 ! has part
transitive_over: RO:0002017 ! has component activity

[Typedef]
id: RO:0002328
name: functionally related to
def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string

[Typedef]
id: RO:0002329
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002331
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: seeAlso Involved:in
holds_over_chain: RO:0002327 BFO:0000050
is_a: RO:0000056 ! participates in
is_a: RO:0002431 ! involved in or involved in regulation of
transitive_over: BFO:0000050 ! part of

[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000057 ! has participant
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
domain: BFO:0000015 ! process
range: BFO:0000015 ! process
is_transitive: true
is_a: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002335
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002384
name: has developmental potential involving
def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
domain: CARO:0000000 ! anatomical entity
range: CARO:0000000 ! anatomical entity
is_a: RO:0002324 ! developmentally related to

[Typedef]
id: RO:0002385
name: has potential to developmentally contribute to
def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: RO:0002387
name: has potential to develop into
def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: RO:0002388
name: has potential to directly develop into
def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002387 ! has potential to develop into

[Typedef]
id: RO:0002404
name: causally downstream of
def: "inverse of upstream of" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: BFO:0000062 ! preceded by
is_a: RO:0002427 ! causally downstream of or within
inverse_of: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002405
name: immediately causally downstream of
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002087 ! immediately preceded by
is_a: RO:0002404 ! causally downstream of
inverse_of: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002410
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string

[Typedef]
id: RO:0002411
name: causally upstream of
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: BFO:0000063 ! precedes
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002412
name: immediately causally upstream of
def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p  must be an input of q." []
property_value: IAO:0000114 IAO:0000428
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002411
is_a: RO:0002090 ! immediately precedes
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002418
name: causally upstream of or within
def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." []
synonym: "affects" RELATED []
property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
is_transitive: true
is_a: RO:0002501 ! causal relation between processes
inverse_of: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002427
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_transitive: true
is_a: RO:0002501 ! causal relation between processes

[Typedef]
id: RO:0002428
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002327 RO:0002211
holds_over_chain: RO:0002331 RO:0002211
is_a: RO:0002263 ! acts upstream of
is_a: RO:0002431 ! involved in or involved in regulation of

[Typedef]
id: RO:0002429
name: involved in positive regulation of
def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004049 RO:0002428
holds_over_chain: RO:0002327 RO:0002213
holds_over_chain: RO:0002331 RO:0002213
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002430
name: involved in negative regulation of
def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004050 RO:0002428
holds_over_chain: RO:0002327 RO:0002212
holds_over_chain: RO:0002331 RO:0002212
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002431
name: involved in or involved in regulation of
def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" []
property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or reguates" xsd:string
is_a: RO:0002264 ! acts upstream of or within
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002434
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_symmetric: true

[Typedef]
id: RO:0002436
name: molecularly interacts with
def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." []
property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: seeAlso ECO:0000353
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002447
name: phosphorylates
property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string
is_a: RO:0002436 ! molecularly interacts with

[Typedef]
id: RO:0002448
name: directly regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." []
synonym: "molecularly controls" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002436 ! molecularly interacts with
is_a: RO:0011002 ! regulates activity of

[Typedef]
id: RO:0002449
name: directly negatively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." []
synonym: "molecularly decreases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly inhibits" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002450
name: directly positively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." []
synonym: "molecularly increases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly activates" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002464
name: helper property (not for use in curation)
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string

[Typedef]
id: RO:0002481
name: is kinase activity
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002564 ! molecular interaction relation helper property

[Typedef]
id: RO:0002500
name: causal agent in process
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002595 ! causal relation between material entity and a process
inverse_of: RO:0002608 ! process has causal agent

[Typedef]
id: RO:0002501
name: causal relation between processes
def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
domain: BFO:0000003 ! occurrent
range: BFO:0000003 ! occurrent
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002502
name: depends on
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso BFO:0000169

[Typedef]
id: RO:0002506
name: causal relation between entities
property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002559
name: causally influenced by
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string
is_a: RO:0002506 ! causal relation between entities
inverse_of: RO:0002566 ! causally influences

[Typedef]
id: RO:0002563
name: interaction relation helper property
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI
is_a: RO:0002464 ! helper property (not for use in curation)

[Typedef]
id: RO:0002564
name: molecular interaction relation helper property
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002563 ! interaction relation helper property

[Typedef]
id: RO:0002566
name: causally influences
def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string
domain: BFO:0000002 ! continuant
range: BFO:0000002 ! continuant
is_a: RO:0002506 ! causal relation between entities

[Typedef]
id: RO:0002578
name: directly regulates
def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: RO:0002575 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002584
name: has part structure that is capable of
def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" []
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: BFO:0000051 RO:0002215
is_a: RO:0002328 ! functionally related to
is_a: RO:0002595 ! causal relation between material entity and a process

[Typedef]
id: RO:0002595
name: causal relation between material entity and a process
def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." []
property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
domain: BFO:0000040 ! material entity
range: BFO:0000015 ! process
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002596
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002211
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002597
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002212
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002598
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002213
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002608
name: process has causal agent
def: "Inverse of 'causal agent in process'" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002629
name: directly positively regulates
def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002578
is_a: RO:0002213 ! positively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002630
name: directly negatively regulates
def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002578
is_a: RO:0002212 ! negatively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0004031
name: enables subfunction
def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." []
holds_over_chain: RO:0002327 BFO:0000051
is_a: RO:0002328 ! functionally related to
created_by: cjm
creation_date: 2018-01-25T23:20:13Z

[Typedef]
id: RO:0004032
name: acts upstream of or within, positive effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004049 RO:0002264
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect
holds_over_chain: RO:0002327 RO:0004047
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:30Z

[Typedef]
id: RO:0004033
name: acts upstream of or within, negative effect
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004050 RO:0002264
holds_over_chain: RO:0002327 RO:0004046
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:51Z

[Typedef]
id: RO:0004034
name: acts upstream of, positive effect
def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004049 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect
holds_over_chain: RO:0002327 RO:0002304
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004032 ! acts upstream of or within, positive effect
created_by: cjm
creation_date: 2018-01-26T23:53:14Z

[Typedef]
id: RO:0004035
name: acts upstream of, negative effect
def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: RO:0004050 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect
holds_over_chain: RO:0002327 RO:0002305
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004033 ! acts upstream of or within, negative effect
created_by: cjm
creation_date: 2018-01-26T23:53:22Z

[Typedef]
id: RO:0004046
name: causally upstream of or within, negative effect
property_value: RO:0004050 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:05Z

[Typedef]
id: RO:0004047
name: causally upstream of or within, positive effect
property_value: RO:0004049 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:19Z

[Typedef]
id: RO:0011002
name: regulates activity of
def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." []
property_value: IAO:0000117 "Vasundra Touré" xsd:string
domain: BFO:0000040 ! material entity
range: BFO:0000040 ! material entity
is_a: RO:0002566 ! causally influences

[Typedef]
id: RO:0017001
name: utilizes
def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." []
property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string
property_value: IAO:0000117 "Asiyah Lin" xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string
property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string
property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string
holds_over_chain: RO:0002215 RO:0002233
creation_date: 2021-11-08

[Typedef]
id: RO:0019000
name: regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599
domain: BFO:0000015 ! process
range: PATO:0000001 ! quality
holds_over_chain: RO:0002211 RO:0019000
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0019001
name: positively regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599
holds_over_chain: RO:0002213 RO:0019001
is_a: RO:0019000 ! regulates characteristic

[Typedef]
id: RO:0019002
name: negatively regulates characteristic
def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." []
property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599
holds_over_chain: RO:0002212 RO:0019001
holds_over_chain: RO:0002213 RO:0019002
is_a: RO:0019000 ! regulates characteristic