Salmon Ontology

A MeasurementType describes the type of a Measurement in which the Measurement would follow the associated Protocol to record the value of the associated Characteristic of the associated Entity using the associated Standard. Any of these associated properties may be omitted, in which case the MeasurementType is only constrained by the provided associations. A MeasurementType is a hypothetical construct, in that it is not associated with a particular instance of a Measurement.

• temporal_MeasurementType ^c
• data quality assessment measurement type ^c
• geographic position measurement type ^c
• Fish measurement type ^c
• Environmental measurement type ^c
• Quality of a population measurement type ^c
• Quality of an ecological community ^c

• Time Step ^c
• date and time of measurement ^c
• part of season measurement made ^c
• year and season ^c

• data quality flag ^c
• observer confidence ^c
• signal quality ^c

• measurement start time ^c
• measurement end time ^c
• hour of measurement time ^c
• hour and minute of measurement time ^c
• minute of measurement time ^c
• second of measurement time ^c

• time of measurement ^c
• month of year ^c
• year of measurement ^c
• date ^c
• day of year ^c
• year and day of measurement ^c
• day of month ^c

• Year of fish harvest ^c
• Brood year ^c

• seconds elapsed ^c
• hours elapsed ^c
• days elapsed ^c
• minutes elapsed ^c
• years elapsed ^c

In geography, latitude is a geographic coordinate that specifies the north–south position of a point on the Earth's surface. Latitude is an angle (defined below) which ranges from 0° at the Equator to 90° (North or South) at the poles. Lines of constant latitude, or parallels, run east–west as circles parallel to the equator. Latitude is used together with longitude to specify the precise location of features on the surface of the Earth. On its own, the term latitude should be taken to be the geodetic latitude as defined below. Briefly, geodetic latitude at a point is the angle formed by the vector perpendicular (or normal) to the ellipsoidal surface from that point, and the equatorial plane. Also defined are six auxiliary latitudes that are used in special applications.

• latitude minute component ^c
• latitude second component ^c
• latitude degree component ^c

Longitude (/ˈlɒndʒɪtjuːd/, AU and UK also /ˈlɒŋɡɪ-/)[1][2] is a geographic coordinate that specifies the east–west position of a point on the Earth's surface, or the surface of a celestial body. It is an angular measurement, usually expressed in degrees and denoted by the Greek letter lambda (λ). Meridians (lines running from pole to pole) connect points with the same longitude. The prime meridian, which passes near the Royal Observatory, Greenwich, England, is defined as 0° longitude by convention. Positive longitudes are east of the prime meridian, and negative ones are west.

• longitude minute component ^c
• longitude degree component ^c
• longitude second component ^c

• latitude coordinate ^c
• longitude coordinate ^c

Identifier associated, in some context, with a "station", i.e. a location having some established facilities for doing scientific research

• estuary name ^c
• creek name ^c
• cruise name ^c
• valley name ^c
• lake name ^c
• river or stream name ^c

Identifier associated, in some context" with a "Site"-- i.e. a location where some research data have been or are being collected

Union of Place and Location to enable searching over both less and more precise named designations of Regions

• The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.

• An accumulation of water of varying size.

• Lotic water body ^c
• Lentic water body ^c
• Inlet ^c

• Dolly Varden trout ^c
• Steelhead trout ^c
• Cutthroat trout ^c
• Rainbow trout ^c

A numerical value which represents the length of a fish, typically in units of millimeters, centimeters, or inches.

• Fork length ^c
• Post-orbit to fork of tail length ^c
• Post orbit to hypural plate length ^c
• Mid-orbit to hypural plate length ^c
• Mid-orbit to posterior insertion of anal fin length ^c
• Mid-orbit to fork of tail length ^c
• Total length ^c
• Standard length ^c

A fish length measurement taken from the most anterior part of a fish to the tip of the median caudal fin rays (i.e. fork).

A fish length measurement taken from the hind margin of the orbit to the tip of the median caudal fin rays.

A fish length measurement taken from the hind margin of the orbit to the hypural plate.

A fish length measurement taken from the middle of the orbit (i.e. eye) to the hypural plate.

• The insertion of a fin is the posterior-most point where the fin connects with the body.

• A fish length measurement taken from the mid-orbit (i.e. eye) to the posterior insertion of the anal fin.

A fish length measurement taken from the middle of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork).

A fish length measurement of the entire length of a fish's body, taken from the most anterior part of the fish to the tip of the longest caudal fin rays.

The measurement from the most anterior tip of the body to the midlateral posterior edge of the hypural plate (in fish with a hypural plate) or to the posterior end of the vertebral column (in fish lacking hypural plates).

The Food and Agriculture Organization of the United Nations (FAO) defines a fishery as "...an activity leading to harvesting of fish. It may involve capture of wild fish or raising of fish through aquaculture."

• Commercial fishery ^c
• Recreational (sport) fishery ^c
• Subsistence fishery ^c
• Small-scale fishery ^c
• Industrial Fishery ^c
• Traditional fishery ^c
• Artisanal fishery ^c

• Equipment which is used to harvest aquatic resources, and in particular fish(es).

• [ADDRESS THIS COMMENT, THEN DELETE]

  Could use some input on subclass hierarchy. E.g. 'Hand collection' includes methods which are largely done with tools that can be operated by hand. 'Netting' includes things like gillnets and seines, which, while largely set from fishing vessels (particularly in commercial fisheries), can also be set by hand at smaller scales.

• Fish wheel ^c
• Weir ^c
• Pot ^c
• Troll ^c
• Netting ^c
• Hand collection ^c

Fishing by means of an "angle" (fish hook). The hook is usually attached to a fishing line and baited with natural bait or artificial lures to attract fish. The line is often attached to a fishing rod.

A device which (a) is situated in rivers for catching fish, and (b) looks and operates like a watermill that is outfitted with wire baskets designed to catch and carry fish from the water and into a nearby holding tank.

A barbed pole, which is used to strike and collect a fish. Spearheads come in a variety of different shapes (e.g. arrow, trident), and can be thrown by hand or deployed using elastic-powered spearguns and slings or compressed gas pneumatic powered spearguns.

A gillnet which is attached to poles fixed in the substrate or an anchor system to prevent movement of the net.

An obstruction placed in tidal waters, or wholly or partially across a river, to direct the passage of, or trap fish.

A three-dimensional wire or wood device which is submerged and commonly baited. A pot (or "trap") permits organisms to enter the enclosure, but makes escape extremely difficult or impossible.

A seine net operated from the shore. The gear is composed of a bunt (bag or lose netting) and long wings often lengthened with long ropes for towing the seine to the beach. The headrope with floats is on the surface, the footrope is in permanent contact with the bottom and the seine is therefore a barrier which prevent the fish from escaping from the area enclosed by the net

A net or mesh basket held open by a hoop which may or may not be on the end of a handle and is used for scopping fish near the surface of the water.

The gathering live or deceased fishes by hand.

One or more fishing lines, which are baited with lures or bait fish and drawn through the water (often behind a moving vessel) to catch pelagic fishes.

A multi-pronged spear, typically ranging in length from 8 to 14 feet, which is used to spear (or "gig") fishes for harvest.

A gillnet which is kept afloat at the proper depth using a system of weights and buoys attached to the headrope, footrope, or floatline.

A large wall of netting deployed around an entire area or school of fish. The seine has floats along the top line with a lead line threaded through rings along the bottom. Once a school of fish is located, a skiff encircles the school with the net. The lead line is then pulled in, "pursing" the net closed on the bottom, preventing fish from escaping by swimming downward. The catch is harvested by either hauling the net aboard or bringing it alongside the vessel.

A type of fishing gear which uses direct current electricity flowing between a submerged cathod and anode to cause galvanotaxis, or an uncontrolled muscular convulsion, which affects the movement of the fish such that it swims towards the anode, where it is then collected.

A wall of netting which hangs in the water column, typically made of monofilament or multifilament nylon. Mesh sizes are designed to allow fish to get only their head through the netting but not their body. The fish's gills then get caught in the mesh as the fish tries to back out of the net. As the fish struggles to free itself, it becomes more and more entangled.

• Set gillnet ^c
• Drift gillnet ^c

A type of net which hangs vertically in the water with its bottom edge held down by weights and its top edge buoyed by floats. Seine nets can be deployed from the shore as a beach seine, or from a boat.

• Beach seine ^c
• Purse seine ^c

• Gillnet ^c
• Seine ^c

Fishing gear which is used to collect fish and can be operated by hand by one or few people. Hand collection methods may also include the collection of fish without the aid of any gear (i.e. gathering live fish or carcasses using only one's hands).

• Angling ^c
• Spear ^c
• Dip net ^c
• Handpicked or carcass collection ^c
• Electrofishing ^c

A measurement type taken of some physical, biological, or ecological aspect of a fish or fishes.

• Fish length measurement type ^c
• Fish age measurement type ^c
• Fish sex measurement type ^c
• Life history stage of salmonid fish ^c
• Proxy measurement type ^c
• Fish weight measurement type ^c
• Fish parasite measurement type ^c

A fishery in which fishes and other seafood are harvested for commercial profit, mostly from wild fisheries.

A fishery in which fishes and other seafood are harvested for pleasure or competition.

• In Alaska, subsistence fisheries may not operate in "nonsubsistence areas" as designated by the state (AS 16.05.258(c)).

• A fishery in which fishes or other seafood are harvested for noncommercial, customary and traditional uses. These uses include direct personal or family consumption as food, shelter, fuel, clothing, tools, or transportation, for the making and selling of handicraft articles out of nonedible by-products of fish and wildlife resources taken for personal or family consumption, and for the customary trade, barter, or sharing for personal or family consumption.

• The Alaska hatchery program was designed to increase salmon abundance and enhace fisheries, while protecting wild stocks. The program was built in response to depressed commercial fisheries, to meet the needs of the people of the state.

• Oftentimes, hatchery-reared salmon will have their adipose fins removed (i.e. clipped) to mark that they come from a hatchery (versus a wild stock).

• The artificial breeding, hatching, and rearing through the early life stages of animals -- finfish and shellfish in particular. Hatcheries produce larval and juvenile fish, shellfish, and crustaceans, primarily to support the aquaculture industry where they are transferred to on-growing systems, such as fish farms, to reach harvest size.

• Personal use fishing is open to Alaskan residents only, and you must have a valid resident Sport Fishing License to participate in personal use fisheries.

  The bag, possession, and gear limits in personal use fisheries MAY NOT be added to the bag, possession, and gear limits under sport or subsistence regulations.

  It is unlawful to buy, sell, trade or barter personal use finfish, shellfish, aquatic plants, or their parts.

  Many, but not all, personal use fisheries require a permit issued by the Department of Fish and Game. Personal use fisheries have many different regulations for bag limits, allowable gear, and time and area restrictions. Some personal use fisheries are managed in-season by emergency order, so regulations can change at any time.

• A regulatory category of Alaskan fishery which is legally defined as, "the taking, fishing for, or possession of finfish, shellfish, or other fishery resources, by Alaska residents for personal use and not for sale or barter, with gill or dip net, seine, fish wheel, long line, or other means defined by the Board of Fisheries." Personal use fisheries may exist only in "nonsubsistence areas" as determined by the state of Alaska (AS 16.05.258(c)).

• In Alaska, the aquaculture industry primarily produces Pacific oysters, littleneck clams, and mussels for commercial food production.

• The culturing of fish, shellfish, aquatic plants, and/or other organisms in captivity or under controlled conditions in the near shore environment.

The manner, procedure or technique by which a morphological or physiological state or property in a single fish or sample or a group of fish(es) or samples is assessed and a quantitative or qualitative value assigned.

• Fish age determination method ^c
• Fish sex determination method ^c
• Fish length determination method ^c
• Fish weight determination method ^c

The duration of time for which a fish has been alive.

• There are three basic methods for age and growth determination of fishes: (1) observation of the growth of fishes of known age, (2) study of fish size-frequencies, and (3) study of seasonal ring formation in hard body parts such as scales and bones.

• The way in which age is determined for a given individual.

• Measuring the distance between scale circuli ^c
• Counting otolith annuli ^c

The way in which sex is determined for a given individual.

• External sex determination method ^c
• Internal sex determination method ^c
• Genetic sexing ^c

The sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching.

The number of years or winters a salmon spends in a freshwater environment as a free-swimming fish.

The number of years or winters a salmon spends in a saltwater environment.

A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.

A body of water or other liquid of considerable size contained in a depression on a landmass.

A marine water body which is constitutes the majority of an astronomical body's hydrosphere.

A watercourse which is linear and flows across the solid portion of a planetary surface.

• River ^c
• Tributary ^c
• Creek ^c

A stream or river which flows into another river (a parent river) or body of water but which may not flow directly into the sea.

A water body in which the accumulated water, in its totality, is flowing.

A water body in which the accumulated water, in its totality, has very little to no directed flow.

• Lake ^c
• Pond ^c
• Marine water body ^c

A body of water, usually of smaller size than a lake.

• e.g. An age written in European notation as '1.3' is interpreted as 1 year over-wintered in freshwater and 3 years in the ocean. The total age is 4 years (1 + 3 years). The Gilbert-Rich equivalent age is written as '5sub2'.

• The European Age System Designation is based on a count of Freshwater (FW) and Saltwater (SW) Annuli in recruit otoliths, represented as "number of FW annuli" "." "number of SW annuli", e.g "1.4" indicating 1 FW annulus and 4 SW annuli.

  Some interpret the "Total Age" of a recruit with an "Age designation= 0.0" as a 1-year old salmon, while others interpret "Total Age" as a 0-year old salmon.

  That is, in some cases "Total Age" might be reported FW+SW+1, while in other cases it would simply be FW+SW:

  1.3=total age of 4, or 5 years 2.3=total age of 5, or 6 years

• An age designation notation that includes two number separated by a period. The first number represents the number of years or winters a salmon has spent in freshwater after emergence from the gravel, and the second number represents the number of years spent in the ocean. Added together, these numbers can provide the total age or age class of a salmon. (although see Comment for further detail).

• e.g. An age written in Gilbert-Rich notation as '5sub2' (spoken as "five sub two") is interpreted as a fish that is in its fifth year of life (i.e. a fish that will be 5 on its next "birthday" or the number of winters from its deposition in the gravel as an egg to the time of sampling) and which migrated to the ocean during its second year of life. The European notation equivalent age is written as '1.3'.

• An age designation notation that includes two numbers, of which the second is a subscript. The first numeral indicates the total age of the fish and the subscript indicates the time spent in freshwater prior to saltwater immigration.

• This Class and all its Subclasses are taken from the Environment Ontology, ENVO-- where the Class "Environmental feature" is now deprecated.

  To address this issue, we have imported the "astronomical-body-parts--hierarchy.owl" file from the ENVO ontology framework into this Salmon ontology. That subset of ENVO includes all the relevant subclass terms included here, except for "Creek". We will put in a request to ENVO curators to add the term "Creek", probably as a subclass of "Stream".

  Aside from Creek, we would recommend using the Classes included under the ENVO "water body" Class hierarchy for annotation of Salmon data as to "features" of their habitat, because these are more comprehensive than the terms in this native "salmon ontology" subClass hierarchy.

  (Mark Schildhauer, 2021Jul20)

• A material entity which determines an environmental system.

• On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/l, 35 ppt, 599 mM).

• A significant accumulation of saline water which is part of a marine biome.

• Ocean ^c
• Sea ^c

A large expanse of saline water usually connected with an ocean.

The manner, procedure or technique by which a morphological or physiological state or property in a single individual or sample or a group of individuals or samples is assessed and a quantitative or qualitative value assigned.

A measurement type taken of some non-living chemical or physical component of the environment.

• Temperature measurement type ^c
• Precipitation measurement type ^c
• Water salinity measurement type ^c
• Alkalinity measurement type ^c
• Dissolved oxygen measurement type ^c

• May be better to map to PATO, that has some potentially better definitions-- e.g. biological sex: http://purl.obolibrary.org/obo/PATO_0000047 phenotypic sex: http://purl.obolibrary.org/obo/PATO_0001894

• A categorical measurement type which describes the sex of a fish or group of fish(es), where sex is defined as the assemblage of physical properties or qualities of a fish by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.

• Male ^c
• Female ^c
• Unknown sex ^c
• Immature ^c
• Hermaphrodite ^c

• Temperature is measured with thermometers that may be calibrated to a variety of temperature scales. Most scientists measure temperature using the Celsius scale and thermodynamic temperature using the Kelvin scale, which is the Celsius scale offset so that its null point is 0K = −273.15°C, or absolute zero. The basic unit of temperature in the International System of Units (SI) is the kelvin. It has the symbol K.

• The degree of hotness or coldness of a body or environment (corresponding to its molecular activity).

• Air temperature ^c
• Aquatic temperature ^c

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• Objective comparative measure of hot or cold of air.

Objective comparative measure of hot or cold of water in a stream.

Measurement types which pertain to any product of the condensation of atmospheric water vapor that falls under gravity.

An opening of the sea into the land, or of a lake into its shore.

• Coastal inlet ^c
• Lake inlet ^c

An opening of the sea into the land.

• Bay ^c
• Cove ^c
• Sound ^c
• Fjord ^c

An area of water bordered by land on three sides.

A circular or round inlet with a narrow entrance.

A large sea or ocean inlet larger than a bay, deeper than a bight, wider than a fjord, or it may identify a narrow sea or ocean channel between two bodies of land.

A long and narrow sea inlet with high steeply sloped walled sides. A fjord is a landform created during a period of glaciation.

An opening of a lake into its shore.

• Term not currently in ENVO, will be submitted for consideration to ENVO curation team. 03AUG2021

• A stream that is usually smaller than a river.

A flowing body of water.

• A Basic Guide to Aging & Identification of Pacific Salmon Scales by Alaska Department of Fish & Game is available at: https://www.adfg.alaska.gov/static/education/educators/curricula/pdfs/salmon_scales_guide_aging_identification.pdf

• A method which is used to approximate the age of a fish, and which generally involves removing and preserving a scale from a fish, then counting the number of annuli (i.e. year marks).

• Alaska Department of Fish & Game, Division of Fisheries Rehabilitation, Enchancement and Development's report on Juvenile Salmonid Otolith Extraction and Preparation Techniques for Microscopic Examination can be accessed at: https://www.adfg.alaska.gov/fedaidpdfs/FRED.132.pdf

• A method which is used to approximate the age of a fish and which generally involves extracting the otoliths from a fish, then counting the number of annuli (i.e. year marks).

Fish ages are often estimated using proxy measurements, such as the space or distance between scale circuli.

• Distance between scale circuli ^c
• Number of otolith annuli ^c

• Circuli are more widely spaced in warmer months when food is abundant and growth is rapid, and more narrowly spaced in colder months when food availability is low and growth slows.

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• The measured distance between the fine ridges of a scale (i.e. circuli) which are laid down annually in a circular pattern around the focus, or center, of a scale as the growth of the fish proceeds.

Objective comparative measure of hot or cold of water temperature in an aquatic environment.

• Freshwater temperature ^c
• Seawater temperature ^c

A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.

A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.

The age class or life stage of the biological individual(s) at the time the occurrence was recorded.

• Egg ^c
• Alevin ^c
• Smolt ^c
• Fry ^c
• Adult ^c
• Juvenile ^c
• Parr ^c
• Jack ^c
• Grilse ^c

In fish, the term egg usually refers to female haploid gametes.

Larval salmon that have hatched but have not yet completely absorbed their yolk sacs and usually have not yet emerged from the gravel.

1) A young salmonid which has developed silvery coloring on its sides, obscuring the parr marks, and which is about to migrate or has just migrated into the sea, 2) to undergo the transformation from parr to smolt.

A young fish at the post-larval stage. May include all fish stages from hatching to fingerling. An advanced fry is any young fish from the start of exogenous feeding after the yolk is absorbed while a sac fry is from hatching to yolk sac absorption. In Salmonidae the stage from end of dependence on the yolk sac as the primary source of nutrition to dispersal from the redd.

Fish that have fully developed morphological and meristic characters and that have attained sexual maturity.

Elapsed time, typically expressed in years, (a) since birth or (b) which describes the how long a salmon has spent in a particular environment (e.g. saltwater vs. freshwater).

• Total age ^c
• Freshwater age ^c
• Saltwater age ^c

A standardized notation format for describing the age of a salmon.

• Fish age (European notation) ^c
• Fish age (Gilbert-Rich notation) ^c
• Fish total age ^c

The objective measure of hot or cold in freshwater (i.e. non-saline water).

• Stream water temperature ^c
• Lake water temperature ^c

An objective measure of hot or cold of water in a marine (i.e. ocean or sea) environment.

• Sea surface temperature ^c
• Subsurface sea temperature ^c

The objective measure of hot or cold of water in a river.

Objective comparative measure of hot or cold of water in a lake.

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• An aquatic temperature which inheres in water close to the surface of an ocean or sea. The exact meaning of surface varies according to the measurement method used, but it is between 1 millimetre (0.04 in) and 20 metres (70 ft) below the sea surface.

• Salinity is an important factor in determining many aspects of the chemistry of natural waters and of biological processes within it, and is a thermodynamic state variable that, along with temperature and pressure, governs physical characteristics like the density and heat capacity of the water.

• A measure of the saltiness or dissolved salt content of a body of water.

• Is also an Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• Salinity measured at the surface of the sea. The exact meaning of surface varies according to the measurement method used, but it is between 1 millimetre (0.04 in) and 20 metres (70 ft) below the sea surface.

An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

A measure of the quantitative capacity of an aqueous solution to neutralize an acid.

• Freshwater alkalinity ^c
• Seawater alkalinity ^c

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• Alkalinity which is measured in freshwater.

Alkalinity which is measured in seawater.

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• The amount of gaseous oxygen (O2) dissolved in water.

• Dissolved oxygen saturation ^c
• Dissolved oxygen concentration ^c

• Dissolved oxygen saturation can be measured with a dissolved oxygen probe such as an oxygen sensor or an optode in liquid media, usually water. The standard unit of oxygen saturation is percent (%).

• odo:ECSO_00002386

• A relative measure of the concentration of oxygen that is dissolved or carried in a given medium as a proportion of the maximal concentration that can be dissolved in that medium.

• odo:ECSO_00001669

• A concentration of the amount of oxygen present in water.

In biological taxonomy, Type generically refers to the official name applied to a taxon. This Class constrains Type members as belonging to family Salmonidae

• Pacific trout and char ^c
• Pacific salmon ^c
• Atlantic salmon ^c
• Salvelinus spp. ^c

• Oncorhynchus gorbuscha (i.e. pink salmon) is the smallest and most abundant of the five species of Pacific salmon.

  Physical Description: In the ocean, pink salmon are bright silver fish. After returning to their spawning streams, their coloring changes to pale grey on the back with yellowish-white belly (although some turn an overall dull green color). As with all salmon, in addition to the dorsal fin, they also have an adipose fin. The fish is characterized by a white mouth with black gums, no teeth on the tongue, large oval-shaped black spots on the back, a v-shaped tail, and an anal fin with 13-17 soft rays. During their spawning migration, males develop a pronounced humped back, hence their nickname "humpies". Pink salmon average 4.8 pounds (2.2 kg) in weight. The maximum recorded size was 30 inches (76 cm) and 15 pounds (6.8 kg).

  Range: The native range of the species is in the Pacific and Arctic coastal waters and rivers, from the Sacramento River in northern California to the Mackenzie River in Canada; and in the west from the Lena River in Siberia to Korea and Honshu in Japan. In North America pink salmon spawn from the Mackenzie River in the Arctic to as far south as tributaries of Puget Sound, Washington, although they were also reported in the San Lorenzo River near Santa Cruz, California in 1915 and the Sacramento River in northern California in the 1950s. In 2013 a new record for the southernmost extent of spawning pink salmon was published for the Salinas River. In the fall of 2017 a dozen pink salmon were counted in Lagunitas Creek about 25 miles (40 km) north of San Francisco, California.

• The class which contains all instances of Oncorhynchus gorbuscha.

• Oncorhynchus keta (i.e. chum salmon) is one of the five species of Pacific salmon.

  Physical Description: The body of the chum salmon is deeper than most salmonid species. In common with other species found in the Pacific, the anal fin has 12 to 20 rays, compared with a maximum of 12 in European species. Chum have an ocean coloration of silvery blue green with some indistinct spotting in a darker shade, and a rather paler belly. When they move into fresh water the color changes to dark olive green and the belly color deepens. When adults are near spawning, they have purple blotchy streaks near the caudal peduncle, darker towards the tail. Spawning males typically grow an elongated snout or kype, their lower fins become tipped with white and they have enlarged teeth. Some researchers speculate these characteristics are used to compete for mates.

  Range: Chum salmon have the largest natural range of any Pacific salmon, and undergo the longest migrations within the genus Oncorhynchus, far up the Yukon River and deep into the Amur River basin in Asia. In lesser numbers they migrate thousands of kilometres up the Mackenzie River. Chum are found around the north Pacific, in the waters of Korea, Japan, and the Okhotsk and Bering seas (Kamchatka, Chukotka, Kuril Islands, Sakhalin, Khabarovsk Krai, Primorsky Krai), British Columbia in Canada, and from Alaska to California in the United States. In the Arctic Ocean they are found in limited numbers from the Laptev Sea to the Beaufort Sea. In North America chum salmon spawn from the Mackenzie River in the Arctic to as far south as Tillamook Bay, Oregon, although they were also reported in the San Lorenzo River near Santa Cruz, California in 1915 and the Sacramento River in northern California in the 1950s. In fall 2017 a half dozen chum salmon were counted in Lagunitas Creek about 25 miles (40 km) north of San Francisco, California.

• The class which contains all instances of Oncorhynchus keta.

• Oncorhynchus spp. ^c
• dwcterms:scientificName ^op some Taxon (name) ^c
  and dwcterms:nameAccordingTo ^op some Author citation ^c
  

• Oncorhynchus kisutch (i.e. coho salmon) is one of the five species of Pacific salmon.

  Physical Description: During their ocean phase, coho salmon have silver sides and dark-blue backs. During their spawning phase, their jaws and teeth become hooked. After entering fresh water, they develop bright-red sides, bluish-green heads and backs, dark bellies and dark spots on their backs. Sexually maturing fish develop a light-pink or rose shading along the belly, and the males may show a slight arching of the back. Mature adults have a pronounced red skin color with darker backs and average 28 inches (71 cm) and 7 to 11 pounds (3.2 to 5.0 kg), occasionally reaching up to 36 pounds (16 kg). They also develop a large kype (hooked beak) during spawning. Mature females may be darker than males, with both showing a pronounced hook on the nose.

  Range: The traditional range of the coho salmon runs along both sides of the North Pacific Ocean, from Hokkaidō, Japan and eastern Russia, around the Bering Sea to mainland Alaska, and south to Monterey Bay, California. Coho salmon have also been introduced in all the Great Lakes, as well as many landlocked reservoirs throughout the United States. A number of specimens, (more than 20), were caught in waters surrounding Denmark and Norway in 2017. Their source is currently unknown, but the salmon species is farmed at several locations in Europe, making it probable that the animal has slipped the net at such a farm.

• The class which contains all instances of Oncorhynchus kisutch.

• Oncorhynchus nerka (i.e. sockeye salmon) is one of the five species of Pacific salmon.

  Physical Description: The sockeye salmon is sometimes called red or blueback salmon, due to its color. Sockeye are blue tinged with silver in color while living in the ocean. When they return to spawning grounds, their bodies become red and their heads turn green. Sockeye can be anywhere from 60 to 84 cm (2 ft 0 in–2 ft 9 in) in length and weigh from 2.3 to 7 kg (5–15 lb). Two distinguishing features are their long, serrated gill rakers that range from 30 to 40 in number, and their lack of a spot on their tail or back.

  Range: Sockeye salmon range as far south as the Columbia River in the eastern Pacific (although individuals have been spotted as far south as the 10 Mile River on the Mendocino Coast of California) and in northern Hokkaidō Island in Japan in the western Pacific. They range as far north as the Bathurst Inlet in the Canadian Arctic in the east and the Anadyr River in Siberia in the west. The farthest inland sockeye salmon travel is to Redfish Lake, Idaho, over 1,400 km (900 mi) from the ocean and 2,000 m (6,500 ft) in elevation. In the United States, populations of sockeye salmon have been extirpated from Idaho and Oregon.

• The class which contains all instances of Oncorhynchus nerka.

• Oncorhynchus tshawytscha (i.e. Chinook salmon) is the largest of the five species of Pacific salmon.

  Physical Description: The Chinook is blue-green, red, or purple on the back and top of the head, with silvery sides and white ventral surfaces. It has black spots on its tail and the upper half of its body. Although spots are seen on the tail in pink salmon, and silver on the tail in coho and chum salmon, Chinook are unique among the Pacific salmon in combining black spots and silver on the tail. Another distinctive feature is a black gum line that is present in both salt and freshwater. Adult fish range in size from 24 to 36 in (61 to 91 cm), but may be up to 58 in (150 cm) in length; they average 10 to 50 lb (4.5 to 22.7 kg), but may reach 130 lb (59 kg). The meat can be either pink or white in color, depending on what the salmon have been feeding on.

  Range: Chinook are anadromous fish native to the North Pacific Ocean and the river systems of western North America, ranging from California to Alaska, as well as Asian rivers ranging from northern Japan to the Palyavaam River in the Arctic northeast Siberia. They have been introduced to other parts of the world, including New Zealand, thriving in Lake Michigan Great Lakes of North America and Michigan's western rivers, and Patagonia.

• The class which contains all instances of Oncorhynchus tshawytscha.

• Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism.

• [NEEDS ALIGNMENT]

  http://purl.obolibrary.org/obo/PCO_0000003

• A quality that inheres in a population of organisms.

• Fish biomass ^c
• Fish abundance ^c
• Sex ratio ^c

• [NEEDS ALIGNMENT]

  http://semanticscience.org/resource/SIO_001385

• A series or system of written symbols used to represent numbers, amounts, or elements.

The number of salmon which do not get caught by commercial or recreational fisheries and return to their freshwater spawning habitat.

• Annual escapement count ^c
• Daily escapement count ^c

• Need to think more about how to model time over which measurement is taken. E.g. do we want to have separate terms for annual escapement counts vs. daily escapement counts, OR have a predicate which encapsulates the time period over which a measurement occurs, OR something else?

• The number of salmon from a given population that escape the fishery in a year.

• Compare with "Annual escapement count"

  Need to think more about how to model time over which measurement is taken. E.g. do we want to have separate terms for annual escapement counts vs. daily escapement counts, OR have a predicate which encapsulates the time period over which a measurement occurs, OR something else?

• The number of salmon from a given population that escape the fishery in a day.

Amount of Bycatch

• Otoliths, or "earstones" (structures formed of calcium in the heads of bony fishes, and which function as organs of balance), grow concentrically from the center origin. Factors, such as watertemperature, that affect fish growth cause seasonal changes in the density of layers laid down in otoliths and in some cases it is possible to determine fish age from the banding that results. When otoliths are viewed under a low-power microscope, the layers making up spring and summer growth appear as a white, opaque band. Layers laid down in the fall, and also in the winter in some fishes, appear as a dark translucent band. A light and a dark band together make up the annual growth, and age in years is determined by counting the number of dark bands.

• The number of annuli on a given otolith.

• [ADDRESS COMMENT, THEN DELETE]

  This probably isn't the best place for this, since there may be proxy measures for non-fish measurement types; leaving for now but need input on the best way to model these in general

• A variable that is not in itself directly measured but inferred, and that serves in place of an unobservable or immeasurable variable. In order for a variable to be a good proxy, it must have a close correlation, not necessarily linear, with the variable of interest. This correlation might be either positive or negative.

• Fish age proxy measurement type ^c
• Fish weight proxy measurement type ^c

Sex determined on basis of organism's external morphology

Determination of fish gender based on internal examination, e.g. examination of gonads

Determination of fish gender based on genetic evidence rather than morphological evidence alone

This may be a good resource: https://www.fws.gov/r7/fisheries/genetics/pdf/09_rf_2004_OlsenMillerHarperNaglerVanHattenWhittonWenburg_OS.pdf

Used to designate that some individual or individuals in a group of organisms possessed functional qualities of more than one gender, simultaneously or sequentially.

• Sequential hermaphrodite ^c
• Simultaneous hermaphrodite ^c

A method that uses the presence or other features of a trait ("characteristic") of an organism to differentiate or assign gender

The number of recruits which survive to a legal age and/or size and are captured by a fishery.

• Commercial harvest count ^c
• Subsistence fishery harvest count ^c
• Sport fishery harvest count ^c

Estimates of number of fish caught based on some commerical harvest

A measurement of the weight of a fish, or of a sample of fish/fishes

A reference which is made to a taxon name along with a publication which explains how the author intends for the name to be applied.

• The International Code of Zoological Nomenclature (ICZN), a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals, establishes guidelines for author citation. See Chapter 11 of the Fourth Edition.

• For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758".

• The name of the scientist or scientists who first validly published the scientific name of a particular organism.

General Class for organizing various measurements and estimates of the Abundance of Fish, that can involve methods focusing on assessments during different life-stages, using different harvest methods, etc.

• Bycatch abundance ^c
• Salmon abundance ^c

Abundance of salmon estimated from modeling techniques, rather than direct counts, weights, etc.

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

• [ADDRESS COMMENT, THEN DELETE]

  needs defintion

A quality that inheres in a community.

• Species diversity ^c
• Species evenness ^c
• Species richness ^c

A measurement or estimate of the number of salmon, based on counts, densities, weights, or other methods.

• Salmon escapement count ^c
• Salmon harvest count ^c
• Modeled salmon abundance ^c
• Spawner abundance ^c
• Juvenile standing stock abundance ^c
• run size ^c
• Smolt abundance ^c
• Egg abundance ^c
• Recruit abundance ^c

• An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. The ESV list uses the label 'Adult spawning stock abundance' rather than 'Spawner abundance.'

• The total number of recruits which successfully return to spawn in freshwater habitats for a given brood year.

An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

Young fish, mostly similar in form to adult but not yet sexually mature (Hubbs, 1943). In some cases refers to a stage unlike the adult in appearance.

The Year in which some commercial fish harvest was taken. Given a Class structure here to enable filtering by Year(s) of interest, although this temporal descriptor could and should also be assigned to any observations of "Commercial Fish Harvest", e.g. potentially by using the SOSA:PhenomenonTime attribute.

The Year in which some commercial fish harvest was taken. Given a Class structure here to enable filtering by Year(s) of interest, although this temporal descriptor could and should also be assigned to any observations of "Commercial Fish Harvest", e.g. potentially by using the SOSA:PhenomenonTime attribute.

The parental year for a group of returning salmon, i.e. the calendar year when the majority of parents of these fish spawned.

The left pectoral fin of the fish is removed.

• [NEEDS ALIGNMENT]

  http://purl.dataone.org/odo/ECSO_00002490

• A numeric or alphanumeric code, which represents a particular species and may be recorded in place of a formal scientific or vernacular name.

The unique alphanumeric code or marking color(s) of a tagged fish.

• ADF&G salmon species codes:

  410 salmon, chinook 420 salmon, sockeye 430 salmon, coho 440 salmon, pink 450 salmon, chum

• The Alaska Department of Fish and Game defines unique three-digit "Codes for the Commercial Operator's Annual Report" which represent each of the commercially harvested aquatic species.

A numeric or alphanumeric code, which represents a particular type of fishing gear or equipment.

• ADF&G gear codes:

  01 purse seine 02 beach seine 03 drift gillnet 04 set gillnet 05 hand line/jig/troll 07 non-pelagic/bottom trawl 08 fish wheel 10 ring net 11 diving 12 handpicked 13 dip net 14 weir 15 power gurdy troll 17 beam trawl 18 shovel 21 pound 22 dredge 23 hydro/mechanical dredge 25 dinglebar 26 mechanical jigs 27 double otter trawl 34 herring gillnet 37 pair trawl 41 sunken gillnet 47 pelagic/mid-water trawl 61 longline (hook and line) 77 fish ladder/raceway 90 trap 91 pot gear 99 other (please specify)

• The Alaska Department of Fish and Game defines unique two-digit "Codes for the Commercial Operator's Annual Report" which represent each of the gear types and harvest methods used Alaskan fisheries.

A numeric or alphanumeric code which represents a particular sample. A sample is defined as a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.

• Fish sample code ^c
• Gum card number ^c

An identifier, which may be assigned to a physical sample taken from a fish (e.g. tissue, fin, otolith) or an entire fish specimen.

• An overview of many popular tag types and methods: https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05

• A marking which is used to differentiate individual fish or groups of fish(es).

• Genetic identification ^c
• Dye tag ^c
• Electronic tag ^c
• External visual tag ^c
• Natural pattern or unique marking ^c
• Fish body modification ^c
• Subcutaneous tag ^c

• This identification type will often last the entire life of the fish, is primarily used for group marking, and is most suitable for fish at least 2.5cm in length. The fish must be euthanized for reading. The tags are delivered on a spool, and the tagging machine magnetises, cuts and inserts the tag into the fish. While a detector can be used to determine if a fish is marked or not, a fish must be euthanized in order to remove the tag and read the engraved code.

• A small metal pin which is inserted into the fish, usually into the cartilage of the snout.

• There are four main methods for collecting tissue samples for DNA sequencing: (1) collecting a fin sample, (2) swabbing the mucus layer of the fish, (3) collecting a scale sample, and (4) blood sampling. Genetic identification can provide better answers to some questions that are also answered through typical fish marking and tagging, such as effective population size, whether populations differ and the degree of inbreeding. However, genetic identification cannot answer questions about, for example migration patterns, movement in the water and growth.

• The use of a DNA sample to identify fish which have known biomarkers.

• This type of identification can remain in a fish for several years, is used for individual tagging, and is most suitable for fish that weigh at least 100g (given current technology). Tags may be inserted several different ways: (a) placed in a fish's stomach using a finger or guide, (b) implanted in the abdominal cavity, or (c) anchored inside the abdomen, usually to the abdominal wall with stiches. Data is transmitted wirelessly, usually through the use of radio waves (in fresh water and air), acoustic signals (in water; the receiver must also be in the water) or via satellite communication (in air; the tag sends data after it releases from the fish and floats up to the surface). Many types of telemetry devices also act as bio-loggers and store information locally on the device. Reading is done using the tag’s associated equipment, often through a computer connection.

• A small, electronic, sound-emitting device which is placed inside a fish and collects information on that fish's physiology and/or movement patterns.

• When done correctly, this identification type will last the entire life of the fish, and is used for group marking.

• The adipose fin is removed using scissors or a razor blade.

• This type of identification can remain on a fish from a couple days up to several weeks, and is used for group marking. and is most suitable for fish

• Tag based on application of a dilution of diazo dye in which fish are immersed and which stains the fins a brown/tan color.

• Though not well studied, this type of identification may last up to 3 years post-immersion, and is used for group marking.

• Tag based on application of a dilution of fluorochrome dye in which fish are immersed and which binds to bony structures (such as fin rays, jaw bones, and scales), manifesting as a green fluorescence.

• This identification type may be clearly visible for several months and can be felt for up to a year, is primarily used for group marking, and is most suitable for salmonids that are at least 7.5cm in length. Freeze branding is done by cooling a metal rod and/or brand in liquid nitrogen, then pressing the rod lightly against the fish for ~3sec. A dark spot is temporarily created and the fish's scales are deformed. The dark spot disappears after about a month, while the deformation of the scales can be seen at certain light angles and felt with fingers for up to a year.

• A scar made on the dermal tissue using liquid nitrogen.

• The URI http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C461 does not resolve to the term. Including the URL to BioPortal to ensure findability: https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C461

• [NEEDS ALIGHMENT]

  http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C461

• Tag based on application of chemical agents used to enhance the color or contrast of target materials or samples. Dyes have some affinity for their substrates and are usually applied in a solution.

• Bismarck brown dye tag ^c
• Calcein dye tag ^c

The removal of a portion or entirety of a fin or the maxilla of a fish, for identification purposes.

• Adipose fin clip ^c
• Lower caudal fin clip ^c
• Upper caudal fin clip ^c
• Maxilla clip ^c
• Pelvic fin clip ^c
• Pectoral fin clip ^c

A portion of the lower caudal fin lobe is removed.

A portion of the upper caudal fin lobe is removed.

• This identification type will last the entire lifetime of the fish, is used for group marking, and is most suitable for salmonids that are at least 10cm in length.

• The flap in the corner of the mouth is clipped away (the maxilla - sometimes also the supermaxilla).

• One of the pelvic fins is removed using scissors.

• This identification type will last the lifetime of the fish, is used for group marking, and is most suitable for salmonids that are at least 7cm in length.

A tag which transmits information about a fish via an electronic receiver.

• RFID ^c
• Acoustic tag ^c

• This type of identification can remain on a fish for several years, is used for individual tagging, and is most suitable for fish that weigh at least 100g (given current technology). One or more sutures are typically used to attach the tag to the fish's skin using a needle. Data is transmitted wirelessly, usually through the use of radio waves (in fresh water and air), acoustic signals (in water; the receiver must also be in the water) or via satellite communication (in air; the tag sends data after it releases from the fish and floats up to the surface). Many types of telemetry devices also act as bio-loggers and store information locally on the device. Reading is done using the tag’s associated equipment, often through a computer connection.

• A small, electronic, sound-emitting device which is attached externally to a fish and collects information on fish movement patterns and the physical environment.

A static tag, which is attached externally to the body of the fish and visually read or interpreted (as opposed to read with an electronic device e.g. an acoustic tag reader).

• Carlin tag ^c
• Dart tag ^c

• A metal plate with a unique identifying code, which is attached to a fish below the dorsal fin via two stainless steel wires.

• If performed correctly, this identification type may remain attached for the entire life of the fish, is used for individual tagging, and is most suitable for fish at least 15cm in length and which live in open environments. To attach a Carlin tag, double cannulas are first inserted through the fish at the height of the center of the pterygiophores (the bones that support the dorsal fin). Two stainless steel wires are then pulled through the cannulas and then the cannulas are pulled out of the fish. A small metal plate with an alphanumeric code is atached to the steel wires, which are then twisted tightly against the fish's body to hold the plate in place.

• If performed correctly, this type of identification can remain in place for at least a year, is used for individual tagging, and is suitable for fish at lest 20cm in length and which live in open environments. With the cannula attached to a special tag applicator, a scale is removed just below the base of the dorsal fin and the tag is attached. The barb on the tag must hook securely into the pterygiophores (the bones that supports the dorsal fin), otherwise the tag will come loose. Most of the tag then hangs outside the fish’s body like a stiff, narrow tube. The tag is colour-coded, pre-printed with relevant text and numbered by the manufacturer according to the requests of the end user.

• A barbed plastic tag which is inserted under the dorsal fin of the fish using a cannula.

• An RFID system consists of a tiny transponder, a radio receiver, and an transmitter. When triggered by an electromagnetic interrogation pulse from a nearby FRID reader device, the tag transmits digital data, usually an identifying inventory number, back to the reader.

• A system which uses electromagnetic fields to automatically identify and track tags attached to objects.

• A small, passive (i.e. does not actively send out a signal and does not require a battery) radio transponder tag which, when in range, is activated by a signal emitted from a tag reader. The tag then emits a unique identification code back to the reader.

• This identification type may last for several years or up to the lifetime of a fish, and is used for individual tagging. The tag is placed in the abdominal cavity or in the muscular tissue. Reading PIT tags can be done (a) automatically by detecting fish as they swim past (this is usually done by building an obstacle so that fish must pass close to the reader), or (b) manually by taking the fish up in the air to be scanned with a reader.

• Natural patterns or unique markings are primarily used for identification of individuals. This type of identification does not involve marking a fish in any way, but rather relies on stable and individual differences in appareance, such as color, patterns, and scars. This method is based on the use of still images or videos taken of individual fish, which are then analyzed manually or using digital image processing.

• An appearance that varies between individuals.

• This identification type will last the entire life of the fish and is primarily used for group marking, though the fish must be euthanized for reading. Altering the appearance of otoliths may be achieved in a variety of ways, including (a) exposing a fish to variations in water temperature of at least 3 degrees Celsius a number of times to create darker and lighter bands in the otoliths, (b) bathing the fish or eggs in an aqueous solution with fluorescent dye, which is absorbed into the otoliths, or (c) bathing the fish in strontium chloride solution or feeding the fish food that contains the metallic substance strontium.

• The appearance of the otoliths (located in the inner ear of the fish) are changed.

• When done correctly, this identification type will remain visible for the entire lifetime of the fish and can be used for group or individual marking. Neon or fluorescent colors are often used, and best placement is in light areas and fin rays, though even semi-transparent and transparent tissue may be suitable for easy visual reading.

• A colored two-component plastic which is injected into the fish's epidermis or fins.

• This type of identification is usually visible for one year on salmon, is primarily used for group marking, and is suitable for fish that weigh at least 20g. An ink solution (often Alcian blue dissolved in distilled water) is typically injected under the skin using a syringe with a cannula. Marking a fish using the "square dot system" with up to 3x3 dots is common. Unlike VIE, tattoos do not require transparent skin to be visible. However, in salmon, the tattoo should be placed in areas in front of the pelvic fins, under the pectoral fins and/or behind the anal fins to enable reading during spawning, when the fish's natural pigmentation may cover up the tattoo.

• An ink solution, which is injected into the skin.

A colored marking, which is placed beneath the skin of a fish for identification.

• Visible implant elastomer ^c
• Tattoo ^c

The alteration of a physical bodily feature of a fish, either internally or externally, for identification purposes.

• Freeze brand ^c
• Fin or maxilla clip ^c
• Otolith marking ^c

A small, electronic, sound-emitting device which may be placed inside or attached to a fish and collects information on that fish's physiology, environmentm and/or movement patterns.

• Internal acoustic tag ^c
• External acoustic tag ^c

A mark or tag which is placed beneath the skin of a fish.

• Coded wire tag ^c
• Subcutaneous color mark ^c

A pectoral fin is removed, typically as close to the body as possible, using scissors or a razor blade.

• Left pectoral fin clip ^c
• Right pectoral fin clip ^c

The right pectoral fin of the fish is removed.

The ratio of males to females in a population.

• Sex ratio of adult spawning stock ^c
• Sex ratio of juvenile standing stock ^c
• Sex ratio of smolts ^c

The proportion of males and females in an adult spawning stock.

The ratio of males and females in a juvenile standing stock.

The proportion of males and females in a smolt population.

ADF&G says that dolly varden are actually char (http://www.adfg.alaska.gov/index.cfm%3Fadfg=dollyvarden.main), though Wikipedia suggests that they are trout (https://en.wikipedia.org/wiki/Dolly_Varden_trout). Formally, members of Genus Salvelinus are considered "char", but Dolly Varden are often interchangeably called "trout"

There are five species of Pacific salmon, which occur in the North Pacific waters of the United States and Canada -- Chinook, Chum, Coho, Pink, and Sockeye. All five species are anadromous, meaning that they spawn in freshwater, migrate to the ocean to forage and mature, and return to freshwater to spawn and begin the cycle again.

• Chinook salmon ^c
• Chum salmon ^c
• Pink salmon ^c
• Sockeye salmon ^c
• Coho salmon ^c
• Oncorhynchus spp. ^c
• Dog salmon ^c
• King salmon ^c
• Silver salmon ^c
• Humpback salmon ^c
• Keta salmon ^c

An identifier which represents a region or location in and is used in place of the full name.

• Sample code ^c
• AWC water body code ^c

Atlantic salmon are the only anadromous salmonid native to the Atlantic coast of North America.

Oncorhynchus is a genus of fish in the family Salmonidae; it contains the Pacific salmon and Pacific trout. The name of the genus is derived from the Greek ὄγκος (ónkos, “lump, bend”) + ῥύγχος (rhúnkhos, “snout”), in reference to the hooked jaws of males in the mating season (the "kype").

• Oncorhynchus gorbuscha ^c
• Oncorhynchus keta ^c
• Oncorhynchus kisutch ^c
• Oncorhynchus nerka ^c
• Oncorhynchus tshawytscha ^c
• Oncorhynchus mykiss ^c
• Oncorhynchus clarkii ^c

Salmo is a genus of fish in the salmon family Salmonidae that includes the European species of salmon and trout, among them the familiar Atlantic salmon Salmo salar and the brown trout Salmo trutta.

• Salmo salar is the only species of Atlantic salmon.

  Physical Description: Atlantic salmon are the largest species in their genus, Salmo. After two years at sea, the fish average 71 to 76 cm (28 to 30 in) in length and 3.6 to 5.4 kg (7.9 to 11.9 lb) in weight. The colouration of young Atlantic salmon does not resemble the adult stage. While they live in fresh water, they have blue and red spots. At maturity, they take on a silver-blue sheen. The easiest way of identifying them as an adult is by the black spots predominantly above the lateral line, though the caudal fin is usually unspotted. When they reproduce, males take on a slight green or red colouration. The salmon has a fusiform body, and well-developed teeth. All fins, except the adipose fin, are bordered with black.

• The class which contains all instances of Salmo salar.

• Oncorhynchus mykiss (i.e. rainbow trout) is a species of Pacific trout.

  Physical Description: Resident freshwater rainbow trout adults average between 1 and 5 lb (0.5 and 2.3 kg) in riverine environments, while lake-dwelling and anadromous forms may reach 20 lb (9 kg). Coloration varies widely between regions and subspecies. Adult freshwater forms are generally blue-green or olive green with heavy black spotting over the length of the body. Adult fish have a broad reddish stripe along the lateral line, from gills to the tail, which is most pronounced in breeding males. The caudal fin is squarish and only mildly forked. Lake-dwelling and anadromous forms are usually more silvery in color with the reddish stripe almost completely gone. Juvenile rainbow trout display parr marks (dark vertical bars) typical of most salmonid juveniles. In some redband and golden trout forms parr marks are typically retained into adulthood. Some coastal rainbow trout (O. m. irideus) and Columbia River redband trout (O. m. gairdneri) populations and cutbow hybrids may also display reddish or pink throat markings similar to cutthroat trout. In many regions, hatchery-bred trout can be distinguished from native trout via fin clips. Fin clipping the adipose fin is a management tool used to identify hatchery-reared fish.

  Range: The native range of Oncorhynchus mykiss is in the coastal waters and tributary streams of the Pacific basin, from the Kamchatka Peninsula in Russia, east along the Aleutian Islands, throughout southwest Alaska, the Pacific coast of British Columbia and southeast Alaska, and south along the west coast of the U.S. to northern Mexico. It is claimed that the Mexican forms of Oncorhynchus mykiss represent the southernmost native range of any trout or salmon (Salmonidae), though the Formosan landlocked salmon (O. masou formosanus) in Asia inhabits a similar latitude. The range of coastal rainbow trout (O. m. irideus) extends north from the Pacific basin into tributaries of the Bering Sea in northwest Alaska, while forms of the Columbia River redband trout (O. m. gairdneri) extend east into the upper Mackenzie River and Peace River watersheds in British Columbia and Alberta, Canada, which eventually drain into the Beaufort Sea, part of the Arctic Ocean. Since 1875, the rainbow trout has been widely introduced into suitable lacustrine and riverine environments throughout the United States and around the world. Many of these introductions have established wild, self-sustaining populations.

• The class which contains all instances of Oncorhynchus mykiss.

Salvelinus is a genus of salmonid fish often called char or charr; some species are called "trout". Salvelinus is a member of the subfamily Salmoninae within the family Salmonidae.

• Salvelinus malma (i.e. the dolly varden trout) is a species of Pacific trout, belonging to the genus Salvelinus of true chars.

  Physical Description: The back and sides are olive green or muddy gray, shading to white on the belly. The body has scattered pale yellow or pinkish-yellow spots. There are no black spots or wavy lines on the body or fins. Small red spots are present on the lower sides. These are frequently indistinct. The fins are plain and unmarked except for a few light spots on the base of the caudal fin rays. S. malma is extremely similar in appearance to the bull trout (S. confluentus) and Arctic char (S. alpinus), so much so that they are sometimes referred to as "native char" without a distinction.

  Range: The Dolly Varden trout is found in coastal waters of the North Pacific from Puget Sound north along the British Columbia Coast to the Alaska Peninsula and into the eastern Aleutian Islands, along the Bering Sea and the Arctic Sea to the Mackenzie River. The range in Asia extends south through the Kamchatka Peninsula into northern Japan.

• The class which contains all instances of Salvelinus malma.

• Oncorhynchus clarkii (i.e. cutthroat trout) is a species of Pacific trout.

  Physical Description: Throughout their native and introduced ranges, cutthroat trout vary widely in size, coloration and habitat selection. Their coloration can range from golden to gray to green on the back. Cutthroat trout can generally be distinguished from rainbow trout by the presence of basibranchial teeth at the base of tongue and a maxillary that extends beyond the posterior edge of the eye. Depending on subspecies, strain and habitat, most have distinctive red, pink, or orange linear marks along the underside of their mandibles in the lower folds of the gill plates.

  At maturity, different populations and subspecies of cutthroat trout can range from 6 to 40 inches (15 to 102 cm) in length, depending on habitat and food availability. Sea-run forms of coastal cutthroat trout average 2 to 5 pounds (0.9 to 2.3 kg). The length and weights of mature inland forms vary widely depending on their particular environment and availability of food. Stream-resident fish are much smaller, 0.4 to 3.2 ounces (11 to 91 g), while lacustrine populations have attained weights ranging from 12 to 17 lb (5.4 to 7.7 kg) in ideal conditions. The largest cutthroat trout subspecies is the Lahontan cutthroat trout (O. c. henshawi). These fish average 8 to 9 in (20 to 23 cm) in small streams and 8 to 22 in (20 to 56 cm) in larger rivers and lakes. In ideal environments, the Lahontan cutthroat trout attains typical weights of 0.25 to 8 lb (0.11 to 3.63 kg). The world record cutthroat trout is a Lahontan at 39 in (99 cm) and 41 lb (19 kg).

  Range: Cutthroat trout are native to western North America and have evolved through geographic isolation into 14 subspecies, each native to a different major drainage basin. Native cutthroat trout species are found along the Pacific Northwest coast from Alaska through British Columbia into northern California, in the Cascade Range, the Great Basin and throughout the Rocky Mountains including southern Alberta. Some coastal populations of the coastal cutthroat trout (O. c. clarkii) are semianadromous, spending a few months in marine environments to feed as adults and returning to fresh water from fall through early spring to feed on insects and spawn. Cutthroat trout have the second-largest historic native range of North American trout; the lake trout (Salvelinus namaycush) having the largest. Ranges of some subspecies, particularly the westslope cutthroat trout (O. c. lewisi), have been reduced to less than 10 percent of their historic range due to habitat loss and introduction of non-native species.

  Although members of Oncorhynchus, the Pacific trout/salmon species, three subspecies—the westslope (O. c. lewisi), the greenback (O. c. stomias) and Yellowstone cutthroat trout (O. c. bouvierii)—evolved populations east of the Continental Divide in the upper Missouri River basin, upper Arkansas and Platte River basins and upper Yellowstone River basin, each which drain into the Atlantic basin via the Mississippi River. Scientists believe that the climatic and geologic conditions 3-5 million years ago allowed cutthroat trout from the Snake River to migrate over the divide into the Yellowstone plateau via Two Ocean Pass. There is also evidence that Yellowstone Lake once drained south into the Snake River drainage. Evidence suggests that the westslope cutthroat trout was able to establish populations east of the divide via Summit Lake at Marias Pass which at one time connected the Flathead River drainage with the upper Missouri River drainage. Scientists speculate that there are several mountain passes associated with the headwaters of the Colorado River drainage and Arkansas/Platte River drainages that would have allowed migration of cutthroat trout east of the divide.

  Cutthroat trout have been introduced into non-native waters outside their historic native range, but not to the extent of the rainbow trout (O. mykiss). Within the native range of the Yellowstone cutthroat trout, U.S. Fisheries Bureau and National Park Service authorities introduced Yellowstone cutthroat trout into many fishless lakes in Yellowstone National Park. Cutthroat trout were introduced into Lake Michigan tributaries in the 1890s and sporadically in the early 20th century, but never established wild populations. A population of Yellowstone cutthroat trout purportedly has been established in Lake Huron. Although cutthroat trout are not native to Arizona, they are routinely introduced by the Arizona Game and Fish Department into high mountain lakes in the White Mountains in the northeastern region of that state.

• The class which contains all instances of Oncorhynchus clarkii.

A general category for gathering traits (morphological, behavioral, and otherwise) that have some evolutionary basis for achieving reproductive success.

A broad category that may be useful for classifying fish based on patterns in migratory trajectories.

An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.

Volume of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity.

The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.

• Alpha diversity ^c
• Beta diversity ^c
• Gamma diversity ^c

A community species diversity that is the mean species diversity at a site or within a specific habitat.

A community species diversity that is the ratio between regional and local species diversity.

A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity.

A quality of an ecological community that reflects how close in abundance all species in a community are.

The number of different species represented in an ecological community.

• Fork length measurement method ^c
• Mid-orbit to fork of tail measurement method ^c
• Mid-orbit to hypural plate measurement method ^c
• Mid-orbit to posterior insertion of anal fin measurement method ^c
• Post-orbit to fork of tail measurement method ^c
• Post-orbit to hypural plate measurement method ^c
• Standard length measurement method ^c
• Total length measurement method ^c

• The fork length measurement method is commonly used in fish species that have forked caudal fins -- where the dorsal and ventral rays are longer than median rays. Longer rays are often damaged or eroded by contact with rocks, debris, or hatchery walls.

• A fish measurement method in which the length from the most anterior part of a fish to the tip of the median caudal fin rays (i.e. fork) is recorded. Two common procedures are:

  (a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the most anterior part to the tip of the median caudal fin rays (i.e. fork).

  (b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the most anterior part to the tip of the median caudal fin rays (i.e. fork). It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

A fish measurement method in which the length from the middle of the orbit to the tip of the median caudal fin rays is recorded. Two common procedures are:

(a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the middle of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork).

(b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the middle of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork). It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

• Measurements of specific parts of a fish are sometimes necessary when intact fish are not available. For instance, spawning or dead salmon often have eroded tails (from redd excavation) or enlarged or damaged jaws. When researchers want to compare fish lengths of male spawners versus female spawners or hatchery spawned females versus carcasses, it is a good idea to use this type of length measurement to remove the bias of the eroded tails on female spawners. So length measurements are made from specific parts of the body that are intact, such as the orbit and the hypural plate. The hypural plate is comprised of modified vertebrae that support the rays of the caudal fin and originate from the posterior end of the vertebral column. This measurement is also commonly referred to as MEPS, or mid-eye to posterior scale, noting that researchers typically take the measurement to an external feature when the hypural plate is not visible.

• A fish measurement method in which the length from the middle of the orbit (i.e. eye) to the hypural plate is recorded. Two common procedures are:

  (a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the middle of the orbit (i.e. eye) to the hypural plate.

  (b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the middle of the orbit (i.e. eye) to the hypural plate. It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

  In the case that hypural plate is not visible, the measurement may be made to some external feature (e.g. the position of the last lateral line scale; end of the fleshy caudal peduncle; midline of a crease that forms when the tail is bent sharply). It is important to note this adjustment in measurement protocol.

A fish measurement method in which the length from the middle of the orbit (i.e. eye) to the the posterior-most point where the fin connects with the body is recorded. Two common procedures are:

(a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the middle of the orbit (i.e. eye) to the posterior-most point where the fin connects with the body.

(b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the middle of the orbit (i.e. eye) to the posterior-most point where the fin connects with the body. It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

A fish measurement method in which the length from the hind margin of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork) is recorded. Two common procedures are:

(a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from hind margin of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork).

(b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the hind margin of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork). It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

• Measurements of specific parts of a fish are sometimes necessary when intact fish are not available. For instance, spawning or dead salmon often have eroded tails (from redd excavation) or enlarged or damaged jaws. When researchers want to compare fish lengths of male spawners versus female spawners or hatchery spawned females versus carcasses, it is a good idea to use this type of length measurement to remove the bias of the eroded tails on female spawners. So length measurements are made from specific parts of the body that are intact, such as the orbit and the hypural plate. The hypural plate is comprised of modified vertebrae that support the rays of the caudal fin and originate from the posterior end of the vertebral column.

• A fish measurement method in which the length from the hind margin of the orbit (i.e. eye) to the hypural plate is recorded. Two common procedures are:

  (a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from hind margin of the orbit (i.e. eye) to the hypural plate.

  (b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the hind margin of the orbit (i.e. eye) to the hypural plate. It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

  In the case that hypural plate is not visible, the measurement may be made to some external feature (e.g. the position of the last lateral line scale; end of the fleshy caudal peduncle; midline of a crease that forms when the tail is bent sharply). It is important to note this adjustment in measurement protocol.

A fish measurement method in which the length from the most anterior tip of the body to the midlateral posterior edge of the hypural plate (in fish with a hypural plate) or to the posterior end of the vertebral column (in fish lacking hypural plates) is recorded. Two common procedures are:

(a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the most anterior tip of the body to the midlateral posterior edge of the hypural plate (in fish with a hypural plate) or to the posterior end of the vertebral column (in fish lacking hypural plates).

(b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the most anterior tip of the body to the midlateral posterior edge of the hypural plate (in fish with a hypural plate) or to the posterior end of the vertebral column (in fish lacking hypural plates). It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

A fish measurement method in which the length from the most anterior tip of the body to the tip of the longest caudal fin rays is recorded. Total length can be measured by two conventions -- by leaving the caudal fin spread in a natural position or by compressing the lobes of the caudal fin dorsoventrally. Two common procedures are:

(a) Using a measuring board: A fish is placed on its side on a measuring board with its snout against the rigid headpiece. A measurement is taken from the most anterior tip of the body to the tip of the longest caudal fin rays.

(b) Using a tape measure: A fish is placed on its side, either on top of a tape measure or the tape measure is placed just above the dorsal side of the fish to record the measurement from the most anterior tip of the body to the tip of the longest caudal fin rays. It is important to not allow the tape to curve along the contoured side of the fish that is facing up, which can introduce bias into the measurement due to girth.

Group of individuals of a species which can be regarded as an entity for management or assessment purposes; a separate breeding population of a species; term used to identify a management unit of fishery species. A distinct genetic population, a population defined by movement pattern, part of a population potentially harvestable, or a quantity of fish from a given area. May be a total or a spawning stock.

• Hatchery ^c
• Aquaculture ^c
• Wild stock ^c

A stock that is sustained by natural spawning and rearing in the natural habitat, regardless of parentage or origin.

An integer, which represents the sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching.

A young salmonid (salmon or trout) with parr-marks before migration to the sea and after dispersal from the redd.

• Oncorhynchus clarkii clarkii (i.e. coastal cutthroat trout) is a subspecies of Oncorhynchus mykiss and one fo the Pacific trout species. The coastal cutthroat trout occurs in four distinct forms. A semi-anadromous or sea-run form is the most well known. Freshwater forms occur in both large and small rivers and streams and lake environments. The native range of the coastal cutthroat trout extends south from the southern coastline of the Kenai Peninsula in Alaska to the Eel River in Northern California. Coastal cutthroat trout are resident in tributary streams and rivers of the Pacific basin and are rarely found more than 100 miles (160 km) from the ocean.

  Physical Description: Freshwater forms of the coastal cutthroat trout are generally dark green to greenish-blue on back, olive-green on upper flank, silvery on lower flank and belly. They display more numerous flank spots below lateral line, irregular spots on dorsal, adipose and caudal fins and the anal, pectoral and pelvic fin bases. The gill covers are pinkish. Sea-run forms while in salt water and shortly after returning to fresh water are silvery with a bluish back, yellowish lower flanks and fins, and display sparse spots. Cutthroats usually display distinctive red, pink, or orange linear marks along the undersides of their mandibles in the lower folds of the gill plates. These markings are responsible for the common name "cutthroat" given to the trout by outdoor writer Charles Hallock in an 1884 article in The American Angler., although the red slashes are not unique to the cutthroat trout and some coastal rainbow trout and redband trout also display throat slashes. The sea-run forms of coastal cutthroat average 2 to 5 lb (0.9 to 2.3 kg), while stream-resident forms attain much smaller sizes 0.4 to 3.2 oz (11 to 91 g).

  Range: The native range of the coastal cutthroat trout extends south from the southern coastline of the Kenai Peninsula in Alaska to the Eel River in Northern California. Coastal cutthroat trout are resident in tributary streams and rivers of the Pacific basin and are rarely found more than 100 miles (160 km) from the ocean. Semi-anadromous, stream resident, fluvial and lake resident forms exist. The great majority of coastal cutthroat trout habitat coincides with the belt of Pacific coast coniferous rainforest that extends from Alaska southward into Northern California.

• The class which contains all instances of Oncorhynchus clarkii clarkii.

Class intended to facilitate search by "dataset type"

Brood tables, also called run reconstructions, utilize annual estimates of the total run (commercial catch plus escapement), and samples of ages, to estimate the number of recruits per age class. These data are useful for salmon biologists to understand salmon productivity and salmon life histories.

• Whole fish weight ^c
• Stomach weight ^c

The weight of a fish, typically taken when the specimen is still alive or freshly deceased, but before being frozen or further processed.

The weight of a fish, taken after the specimen has been frozen.

The typical or expected weight at a given total length for a specific species of fish. Most standard weight equations are for freshwater fish species.

• For example, salmon of age class 2 include all individuals in a population of interest that are two years old.

• A group of individuals of the same species that have the same age.

• Recruits do not include individuals lost to predation.

• The number of salmon which survive to reach legal age and/or size for harvest. Recruits include both individuals that are captured by a fishery and individuals that escape the fishery -- total recruitment is calculated as catch plus escapement.

Total number of recruits of age class zero.

• Age class 0.1 recruits ^c
• Age class 0.2 recruits ^c
• Age class 0.3 recruits ^c
• Age class 0.4 recruits ^c
• Age class 0.5 recruits ^c
• Age class 0.6 recruits ^c
• Age class 0.7 recruits ^c
• Age class 0.8 recruits ^c
• Age class 0.9 recruits ^c