Ontology of Zebrafish Experimental Conditions Zebrafish Experimental Conditions Ontology zebrafish_experimental_conditions_ontology 2022-02-14 definition term replaced by term replaced by ZECO_AGR_slim abstract upper-level terms not directly useful for analysis subset_property consider database_cross_reference has_exact_synonym has_obo_format_version has_obo_namespace in_subset shorthand 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 http://www.obofoundry.org/ro/#OBO_REL: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. 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 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 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 Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates The state in which an organism exists. 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. innocuous condition 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. high density 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 pH 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 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 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. UV UV light ultraviolet 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. https://en.wikipedia.org/wiki/Ultraviolet x-ray gamma 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. low density undercrowding Food availability condition in which food is provided in increased supply. overfeeding 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 crush injury 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 https://en.wikipedia.org/wiki/Ultraviolet https://en.wikipedia.org/wiki/Ultraviolet