Ontology of Zebrafish Experimental Conditions
Zebrafish Experimental Conditions Ontology
term replaced by
ZECO_AGR_slim
abstract upper-level terms not directly useful for analysis
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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/
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.) A 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'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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.) A 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'.
has_part
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.
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
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
conditions
Condition which serves as a standard against which experimental conditions can be compared.
control conditions
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.
generic control
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.
standard conditions
Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.
experimental conditions
Experimental condition in which the organism is treated with a microorganism.
biological treatment
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.
bacterial treatment
Biological treatment in which fish have been infected with a fungus.
fungal treatment
Biological treatment in which fish were raised in the absence of bacteria.
germ free
Biological treatment in which fish have been infected with protozoa.
protozoan treatment
Biological treatment in which fish have been infected with a virus.
viral treatment
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.
chemical treatment
Experimental condition where the food of the zebrafish is manipulated in some way.
diet
Experimental condition in which the availability of food is manipulated.
food availability
Limited food availability condition in which there is no food provided.
fasting
Food availability condition in which food is provided in limited supply.
limited food availability
Food availability condition in which food is available in unlimited supply.
unlimited food availability
Diet condition in which the contents of the food is manipulated.
food content
Food content condition in which the amount of cholesterol in the diet is manipulated.
cholesterol content
Cholesterol content condition in which the amount of cholesterol in the diet is elevated.
high cholesterol
Cholesterol content condition in which the amount of cholesterol in the diet is reduced.
low cholesterol
Food content condition in which the amount of fat in the diet is manipulated.
fat content
Fat content condition in which the amount of fat in the diet is elevated.
high fat
High fat condition in which the amount of saturated fat in the diet is elevated.
high saturated fat
High fat condition in which the amount of monounsaturated fat in the diet is elevated.
high monounsaturated fat
Fat content condition in which the amount of fat in the diet is reduced.
low fat
Low fat condition in which the amount of trans fat in the diet is reduced.
low trans fat
Low fat condition in which the amount of polyunsaturated fat in the diet is reduced.
low polyunsaturated fat
Food content condition in which the amount of protein in the diet is manipulated.
protein content
Protein content condition in which the protein in the diet is elevated.
high protein
Protein content condition in which the protein in the diet is reduced.
low protein
stress
High carbohydrate conditions in which the amount of sugar in the diet is elevated.
high sugar
High sugar condition in which the amount of fructose in the diet is elevated.
high fructose
High sugar condition in which the amount of glucose in the diet is elevated.
high glucose
High sugar condition in which the amount of sucrose in the diet is elevated.
high sucrose
High carbohydrate conditions in which the amount of sugar in the diet is reduced.
low sugar
Low sugar condition in which the amount of sucrose in the diet is reduced.
low sucrose
Low sugar condition in which the amount of fructose in the diet is reduced.
low fructose
Low sugar condition in which the amount of glucose in the diet is reduced.
low glucose
Experimental condition that manipulates the enclosure of the fish.
housing conditions
Housing condition in which the roof of the enclosure if open.
open roofed
Housing condition in which the enclosure of the fish is overcrowded, containing an excess of fish that reduces the available space of the enclosure.
overcrowding
Experimental condition in which components of the fish have been removed and are maintained separately.
in vitro culture
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.
organ culture
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.
primary cell culture
Experimental condition in which the intensity, wavelength, and/or duration of illumination is (are) different from the one in controlled conditions.
lighting conditions
light duration
altered light dark cycle
constant dark
constant light
light intensity
high light intensity
low light intensity
Experimental condition in which gravity forces are manipulated. For zebrafish, this can be in the form of centrifugal forces or trips to outerspace.
gravity
Experimental condition in which an external mechanical force is applied to the fish or part of the fish.
mechanical stress
vibration
water flow
circular flow
through flow
Experimental condition in which the zebrafish is exposed to an increased or decreased temperature.
temperature exposure
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.
stable temperature exposure
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.
cold exposure
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.
heat exposure
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.
temperature shock
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.
cold shock
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.
heat shock
Targeted destruction of an anatomical structure.
ablation
Experimental condition which uses a chemical to ablate an anatomical structure or cell.
chemical ablation
Experimental condition which uses focused light to ablate an anatomical structure or cell.
light ablation
Surgical manipulation in which a particular organ, appendage, or part of an organism is removed.
resection
Resection condtion in which all or part of an extremity such as the fin or tail are removed.
amputation
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.
vaccine treatment
Experimental condition in which there is a deep cut or tear of the flesh.
laceration
Experimental condition that involves manual or instrumental techniques to alter anatomical structures.
surgical manipulation
Experimental condition in which living cells or tissues from one species are transplanted into another.
xenotransplantation
Experimental condition in which a hole or break in the membranes of an organ or structure of the body is created.
perforation
Experimental condition that results in superficial damage of tissue such that it is scraped or worn away.
abrasion
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)
contusion
Cutting transversly of an organ or tissue. Type of cutting often used to divide the spinal cord to investigate neural regeneration in zebrafish.
transection
Experimental condition in which a chemical or physical characteristic of water is altered.
water quality
Water quality condition that alters the concentration of atmospheric gases in water.
gas composition
A gas composition condition that alters the concentraion of carbion dioxide.
carbon dioxide content
hypercapnia
hypocapnia
A gas composition condition that alters the concentraion of oxygen.
oxygen content
An oxygen content with high concentration of oxygen.
hyperoxia
An oxygen content with low concentration of oxygen.
hypoxia
ion composition
modified calcium composition
high calcium
low calcium
modified potassium composition
high potassium
low potassium
modified sodium composition
high sodium
low sodium
Experimental condition in which the pH of the water is lower than the pH of the controlled conditions.
acidic
Experimental condition in which the pH of the water is higher than the pH of the controlled conditions.
basic
water salinity
Experimental condition in which the salt concentration is higher than the one in controlled conditions.
hypertonic
Experimental condition in which the salt concentration is lower than the one in controlled conditions.
hypotonic
isotonic
stable
radiation
electromagnetic radiation
radio waves
microwaves
infared
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.
visible light
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.
x-ray
particle radiation
proton
neutron
acoustic radiation
alpha particle
Experimental condition in which the fish is exposed to a physical field that is produced by electrically charged objects.
electromagnetic field
Experimental condition where the fish is exposed to materials that produce an electric field.
electric field
Experimental condition where the fish is exposed to magnetic materials.
magnetic field
High fat condition in which the amount of polyunsaturated fat in the diet is elevated.
high polysunsaturated fat
High fat condition in which the amount of trans fat in the diet is elevated.
high trans fat
Low fat condition in which the amount of saturated fat in the diet is reduced.
low saturated fat
Low fat condition in which the amount of monounsaturated fat in the diet is reduced.
low monounsaturated fat
Experimental condition in which an anatomical structure, cell, or organ has sustained targeted physical change, usually through the use of an instrument.
physical alteration
Bacterial treatment where the bacteria are injected into the fish.
bacterial treatment by injection
Bacterial treatment where the bacteria are introduced via the environment. For zebrafish this is the tank water.
bacterial treatment by exposure to environment
Fungal treatment where the fungus is injected into the fish.
fungal treatment by injection
Fungal treatment where the fungus is introduced via the environment. For zebrafish this is the tank water.
fungal treatment by exposure to environment
Viral treatment where the virus is introduced via the environment. For zebrafish this is the tank water.
viral treatment by exposure to environment
Viral treatment where the virus is injected into the fish.
viral treatment by injection
Xenotransplantation condition in which cancer cells are injected or grafted into the zebrafish.
cancer xenotransplantation
Chemical treatment in which the chemical is injected into the zebrafish.
chemical treatment by injection
Chemical treatment condition in which the chemical is introduced through the environment. For zebrafish this is the tank water.
chemical treatment by environment
Chemical treatment condition in which the chemical is introduced through the diet.
chemical treatment by diet
Food content condition in which the amount of carbohydrate in the diet is manipulated.
carbohydrate content
Food content condtion in which the amount of carbohydrate in the diet is elevated.
high carbohydrate
Food content condtion in which the amount of carbohydrate in the diet is reduced.
low carbohydrate
stress by handling
Mechanical stress condition where the organism is subjected to vibrations having an ultrasonic frequency.
ultrasound
Physical alteration which uses light to damage the anatomical structure, cell, or organ.
light damage
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.
undercrowding
Food availability condition in which food is provided in increased supply.
increased food availability
Physical alteration which uses cold to damage an anatomical structure, cell, or organ
cold damage
Experimental condition which uses a cold instrument to ablate an anatomical structure or cell.
cryoablation
Food content condition in which levels of a nutrient are decreased relative to standard diet.
nutrient decreased
Food content condition in which levels of a nutrient are increased relative to standard diet.
nutrient increased
Experimental condition that manipulates the frequency or way an organism is fed.
feeding regime
Feeding regime in which food, drugs, or other substances are administered by force, typically through a tube leading down the throat to the stomach.
gavage
Bacterial treatment condition where bacteria are introduced to the organism by gavage.
bacterial treatment by gavage
Chemical treatment condition where the chemical is introduced to the organism by gavage.
chemical treatment by gavage
Bacterial treatment where bacteria are introduced via the diet.
bacterial treatment by diet
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.
cauterization
Cauterization of a tissue using a heated instrument.
thermal cauterization
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
compression injury
Food content condition in which the amount of probiotics in the diet is manipulated
probiotic content
Experimental condition in which gravity forces are smaller than in control conditions. An example of a microgravity condition would be trips to outerspace.
microgravity
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.
increased gravity