An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.
Draft ontology to support Semantic Annotation of SASAP and salmon-related datasets housed in the SASAP Data Portal (https://knb.ecoinformatics.org/portals/SASAP/About). April 7, 2022 UPDATE (Mark Schildhauer; schild@nceas.ucsb.edu) This version of the salmon ontology preserves all terms and their original URI identifiers ("GUIDS") used to semantically annotate datasets in the SASAP data archives as of April 7, 2022, while also containing a number of additional terms that are not yet used. There are a number of "provisional" terms that have been added throughout the Ontology, i.e. as Classes, Individuals, Object, Datatype and Annotation Properties-- some are stubs for further axiomatization, other patterns are experimental and need to be cleaned up or revised as work progresses. In addition, a number of relationships have been created-- using Object Properties, Existential and Universal Quantifier Axioms, and "Annotation Properties as Flags"-- are in this Ontology due to experimentation with various approaches to inferencing. These are especially apparent in the treatment of Taxonomic and Vernacular names of Pacific Salmon. These should also be considered provisional and experimental. None of these issues should impact proper interpretation of annotated items in our SASAP archive Developed with Protege 5.5.0 Inferences using Pellet ============== creator: Samantha Csik, scsik@nceas.ucsb.edu created: 2021-04-12 updated: 2021-06-14 2021-07-20 mps (schild@nceas.ucsb.edu) 2021-08-05 mps (schild@nceas.ucsb.edu) 2021-08-09 mps (schild@nceas.ucsb.edu) 2021-08-11 mps (schild@nceas.ucsb.edu) 2021-08-13 mps (schild@nceas.ucsb.edu) merged in missing Classes from Sam's earlier version 2021-09-08 mps (schild@nceas.ucsb.edu) corrected all ID's to be 8 chars long 2021-10-04 mps with import of ENVO "ecology" subset 2021-10-13 mps added fisheries types; test modeling of different representation of taxonomies-- scoped domains/ranges? 2021-11-15 mps fixed "Age class Y" recruits to "Age class Y.x recruits" etc removed some test Classes 2021-12-21 mps 2022-01-13 mps: reorganized the "Names" and "Code" Classes and added comments 2022-01-13 mps: added comments where flagged by Sam as missing 2022-01-28 mps: imported Geosparql 1.0 2022-02-03 mps:added some classes; refined descriptions that Sam had flagged as needing attention 2022-02-17 mps: the ENVO Subset import is now deprecated due to change in the build workflow of ENVO, making its original import materialization inaccessible. 2022-03-24 mps: added more salmon common names, searching for most concise way to infer equivalences of vernacular and scientifically named types/individuals...NOT YET FULLY RESOLVED 2022-03-31 mps: removed SKOS-DL import from Object Properties but a number of "Usages" of SKOS-DL structures still need to be cleansed 2022-04-06 mps: discussed Import process with ENVO folks, and was able to successfully re-import the "astronomical-body-part-hiearchy.owl" subset that contains a number of useful entities that are nicely organized and axiomatized. 2022-04-07 mps: sent current revision to Bryce for upload to Ontology dereference PURLs that are provided as semantic annotations to data components in our SASAP data archive EOF
hasNativeWaterbody
hasMigratoryPattern
hasReproductiveStrategy
reproductiveStrategyOf
migratoryPatternOf
Object property to enable linking an information-bearing object such as a dataset, to its assertion of some organismal occurrence (sensu Darwin Core)
contains occurrence data about
has vernacular name
has scientific name
As of 30April2021, Darwin Core (DWC) does not specify domains and ranges. Currently, I am considering 'Salmon specimen and occurrence' to be the domain and 'Author citation' to be the range.
The reference to the source in which the specific taxon concept circumscription is defined or implied - traditionally signified by the Latin "sensu" or "sec." (from secundum, meaning "according to"). For taxa that result from identifications, a reference to the keys, monographs, experts and other sources should be given.
As of 30April2021, Darwin Core (DWC) does not specify domains and ranges. Currently, I am considering 'Vernacular name' to be the domain and 'Salmon specimen and occurrence' to be the range.
The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term.
Alaska Department of Fish and Game (ADF&G) uses a list of numeric codes to describe (a) commercially-harvested aquatic species, (b) gear used for harvest, (c) method of catch processing, and (d) delivery form and product type.
hasADF&GCode
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.
Interval of time representing duration of observation
Adapted from http://en.wikipedia.org/wiki/Time
estuary name
data quality assessment measurement type
data quality flag
time of measurement
date and time of measurement
measurement start time
measurement end time
month of year
hour of measurement time
year of measurement
date
part of season measurement made
seconds elapsed
day of year
fractional day of year
hour and minute of measurement time
hours elapsed
elapsed time
minute of measurement time
second of measurement time
year and day of measurement
geographic position measurement type
day of month
days elapsed
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 coordinate
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 coordinate
latitude minute component
longitude minute component
year and season
minutes elapsed
longitude degree component
latitude second component
latitude degree component
longitude second component
latitude and longitude coordinates
season
station name
Identifier associated, in some context, with a "station", i.e. a location having some established facilities for doing scientific research
station identifier
creek name
cruise name
observer confidence
valley name
signal quality
lake name
years elapsed
study location name
river or stream name
milliseconds elapsed
Identifier associated, in some context" with a "Site"-- i.e. a location where some research data have been or are being collected
site identifier
Union of Place and Location to enable searching over both less and more precise named designations of Regions
Place or location or region
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.
Water body
An accumulation of water of varying size.
https://en.wikipedia.org/wiki/Body_of_water, accessed 2021-03-30
https://en.wikipedia.org/wiki/Body_of_water, accessed 2021-03-30 https://www.wikidata.org/wiki/Q15324, accessed 2021-03-30
Pacific trout and char
Fish length measurement type
A numerical value which represents the length of a fish, typically in units of millimeters, centimeters, or inches.
Fork length
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).
https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31
Post-orbit to fork of tail length
A fish length measurement taken from the hind margin of the orbit to the tip of the median caudal fin rays.
"POFK" is an acronym used by Alaska Department of Fish & Game (ADF&G)
https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-03-31 https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31
Post orbit to hypural plate length
A fish length measurement taken from the hind margin of the orbit to the hypural plate.
"POHL" is an acronym used by Alaska Department of Fish & Game (ADF&G)
https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-03-31
Mid-orbit to hypural plate length
Mid-eye to hypural plate MEHL MEPS Mid-eye to posterior scale
A fish length measurement taken from the middle of the orbit (i.e. eye) to the hypural plate.
"MEHL" is an acronym used by Alaska Department of Fish & Game (ADF&G)
https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-03-31
The insertion of a fin is the posterior-most point where the fin connects with the body.
Mid-orbit to posterior insertion of anal fin length
Mid-eye to posterior insertion of anal fin
A fish length measurement taken from the mid-orbit (i.e. eye) to the posterior insertion of the anal fin.
https://www.seagrant.wisc.edu/our-work/focus-areas/fish-and-fisheries/fish-glossary/, accessed 2021-03-31
Mid-orbit to fork of tail length
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).
"MEFK" is an acronym used by Alaska Department of Fish & Game (ADF&G)
https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-03-31 https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31
Total length
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.
https://www.monitoringresources.org/Document/Method/Details/1551, accessed 2021-03-31
Standard length
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).
https://www.fishbase.in/glossary/Glossary.php?q=standard+length, accessed 2021-03-31
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."
Fishery type
https://en.wikipedia.org/wiki/Fishery, accessed 2021-04-01 https://www.wikidata.org/wiki/Q180538, accessed 2021-04-01 http://www.fao.org/faoterm/en/?defaultCollId=21, accessed 2021-04-01 Fletcher, W.J., Chesson, J. Fisher, M., Sainsbury K.J., Hundloe, T. Smith A.D.M., and B. Whitworth (2002): National ESD reporting framework for Australian fisheries: The "How To" guide for wild capture fisheries. FRDC Project 2000/145. Canberra, Australia
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.
Fishing gear type
Angling
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.
https://en.wikipedia.org/wiki/Angling, accessed 2021-04-01
Fish wheel
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.
https://en.wikipedia.org/wiki/Fish_wheel, accessed 2021-04-01 https://www.wikidata.org/wiki/Q5454688, accessed 2021-04-01
Spear
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.
https://en.wikipedia.org/wiki/Spearfishing, accessed 2021-04-01 https://www.wikidata.org/wiki/Q765706, accessed 2021-04-01
Set gillnet
A gillnet which is attached to poles fixed in the substrate or an anchor system to prevent movement of the net.
Weir
An obstruction placed in tidal waters, or wholly or partially across a river, to direct the passage of, or trap fish.
https://en.wikipedia.org/wiki/Fishing_weir, accessed 2021-04-01 https://www.wikidata.org/wiki/Q1417573, accessed 2021-04-01
Pot
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.
https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-traps-and-pots, accessed 2021-04-01
Beach seine
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
http://www.fao.org/fishery/geartype/202/en, accessed 01April2021
Dip 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.
https://en.wikipedia.org/wiki/Hand_net, accessed 2021-04-01 https://www.wikidata.org/wiki/Q640082, accessed 2021-04-01
Handpicked or carcass collection
The gathering live or deceased fishes by hand.
Troll
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.
https://en.wikipedia.org/wiki/Trolling_(fishing), accessed 2021-04-01
Gig
A multi-pronged spear, typically ranging in length from 8 to 14 feet, which is used to spear (or "gig") fishes for harvest.
https://en.wikipedia.org/wiki/Gigging, accessed 2021-04-01 https://www.wikidata.org/wiki/Q4412590, accessed 2021-04-01
Drift gillnet
A gillnet which is kept afloat at the proper depth using a system of weights and buoys attached to the headrope, footrope, or floatline.
Purse seine
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.
https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-purse-seines, accessed 01April2021
http://vocab.nerc.ac.uk/collection/M13/current/015/, accessed 01April2021
Electrofishing
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.
https://en.wikipedia.org/wiki/Electrofishing, accessed 2021-04-01 https://www.wikidata.org/wiki/Q1249133, accessed 2021-04-01
Gillnet
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.
https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-gillnets, accessed 01April2021
Seine
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.
https://en.wikipedia.org/wiki/Seine_fishing, accessed 01April2021 https://www.wikidata.org/wiki/Q600580, accessed 01April2021
Netting
Hand collection
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).
Fish measurement type
A measurement type taken of some physical, biological, or ecological aspect of a fish or fishes.
Commercial fishery
A fishery in which fishes and other seafood are harvested for commercial profit, mostly from wild fisheries.
https://en.wikipedia.org/wiki/Commercial_fishing, accessed 2021-04-02 https://www.wikidata.org/wiki/Q11202642, accessed 2021-04-02
Recreational (sport) fishery
A fishery in which fishes and other seafood are harvested for pleasure or competition.
https://en.wikipedia.org/wiki/Recreational_fishing, accessed 2021-04-02 https://www.wikidata.org/wiki/Q283534, accessed 2021-04-02
In Alaska, subsistence fisheries may not operate in "nonsubsistence areas" as designated by the state (AS 16.05.258(c)).
Subsistence fishery
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.
http://www.touchngo.com/lglcntr/akstats/statutes/title16/chapter05/section258.htm, accessed 2021-04-27
https://www.adfg.alaska.gov/index.cfm?adfg=fishingsubsistence.main, accessed 2021-04-02
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).
Hatchery
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.
https://www.adfg.alaska.gov/static/fishing/PDFs/hatcheries/2013_ak_hatcheries.pdf, accessed 2021-04-02
https://www.adfg.alaska.gov/index.cfm?adfg=fishingHatcheries.main, accessed 2021-04-02
https://www.adfg.alaska.gov/index.cfm?adfg=wildlifenews.view_article&articles_id=693, accessed 2021-06-15
https://en.wikipedia.org/wiki/Fish_hatchery, accessed 2021-04-02 https://www.wikidata.org/wiki/Q15615109, accessed 2021-04-02
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.
Personal use fishery
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)).
http://www.adfg.alaska.gov/index.cfm?adfg=fishingPersonalUse.main, accessed 2021-04-02
https://alaskasalmonandpeople.org/working-group/governance-and-subsistence/, accessed 2021-04-02
In Alaska, the aquaculture industry primarily produces Pacific oysters, littleneck clams, and mussels for commercial food production.
Aquaculture
The culturing of fish, shellfish, aquatic plants, and/or other organisms in captivity or under controlled conditions in the near shore environment.
https://www.adfg.alaska.gov/index.cfm?adfg=fishingaquaticfarming.programinfo, accessed 2021-04-02
https://en.wikipedia.org/wiki/Aquaculture, accessed 2021-04-02 https://www.wikidata.org/wiki/Q188989, accessed 2021-04-02
http://vocab.nerc.ac.uk/collection/M13/current/018/, accessed 2021-04-02
Fish measurement method
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 measurement type
The duration of time for which a fish has been alive.
This URI does not appear to dereference to the term. Including this URL, https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25150, to ensure findability.
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.
Fish age determination method
The way in which age is determined for a given individual.
https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-06
Fish sex determination method
The way in which sex is determined for a given individual.
Total age
The sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching.
http://courses.washington.edu/fish450/Lecture%20PDFs/Salmon_age_and_size_at_maturity.pdf, accessed 2021-04-06
Freshwater age
The number of years or winters a salmon spends in a freshwater environment as a free-swimming fish.
https://www.researchgate.net/profile/Darlene-Gillespie/publication/281285926_Chinook_Salmon_Oncorhynchus_tshawytscha_Scale_Age_Determination_Procedures/links/55df66d708aede0b572b8de7/Chinook-Salmon-Oncorhynchus-tshawytscha-Scale-Age-Determination-Procedures.pdf, accessed 2021-04-06
Saltwater age
The number of years or winters a salmon spends in a saltwater environment.
River
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.
https://en.wikipedia.org/wiki/River, accessed 2021-04-07 https://www.wikidata.org/wiki/Q4022, accessed 2021-04-07
Lake
A body of water or other liquid of considerable size contained in a depression on a landmass.
Ocean
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
Stream
A watercourse which is linear and flows across the solid portion of a planetary surface.
https://en.wikipedia.org/wiki/Stream, accessed 2021-04-07 https://www.wikidata.org/wiki/Q47521, accessed 2021-04-07
Tributary
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.
https://en.wikipedia.org/wiki/Tributary, accessed 2021-04-07 https://www.wikidata.org/wiki/Q159675, accessed 2021-04-07
Lotic water body
A water body in which the accumulated water, in its totality, is flowing.
Lentic water body
A water body in which the accumulated water, in its totality, has very little to no directed flow.
Pond
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
Fish age (European notation)
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).
https://www.researchgate.net/profile/Darlene-Gillespie/publication/281285926_Chinook_Salmon_Oncorhynchus_tshawytscha_Scale_Age_Determination_Procedures/links/55df66d708aede0b572b8de7/Chinook-Salmon-Oncorhynchus-tshawytscha-Scale-Age-Determination-Procedures.pdf, accessed 20212-04-09
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'.
Fish age (Gilbert-Rich notation)
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.
https://www.researchgate.net/profile/Darlene-Gillespie/publication/281285926_Chinook_Salmon_Oncorhynchus_tshawytscha_Scale_Age_Determination_Procedures/links/55df66d708aede0b572b8de7/Chinook-Salmon-Oncorhynchus-tshawytscha-Scale-Age-Determination-Procedures.pdf, accessed 20212-04-09 https://www.pac.dfo-mpo.gc.ca/fm-gp/fraser/docs/abor-autoc/2010FrasRvrChkInformDoc.htm, accessed 20212-04-09
https://www.researchgate.net/profile/Darlene-Gillespie/publication/281285926_Chinook_Salmon_Oncorhynchus_tshawytscha_Scale_Age_Determination_Procedures/links/55df66d708aede0b572b8de7/Chinook-Salmon-Oncorhynchus-tshawytscha-Scale-Age-Determination-Procedures.pdf, accessed 20212-04-09 https://pdxscholar.library.pdx.edu/cgi/viewcontent.cgi?article=3220&context=open_access_etds, accessed 20212-04-09
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)
Environmental feature
A material entity which determines an environmental system.
Note that this ENVO term, 'environmental feature' is deprecated
http://purl.obolibrary.org/obo/ENVO_00002297 [DEPRECATED]
On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/l, 35 ppt, 599 mM).
Marine water body
A significant accumulation of saline water which is part of a marine biome.
https://en.wikipedia.org/wiki/Seawater https://www.wikidata.org/wiki/Q184395
I altered the definition slightly from ENVO to include "...accumulation of SALINE water..." but have left this as owl:equivalentClass since ENVO axiomatizes 'marine water body' (http://purl.obolibrary.org/obo/ENVO_00001999) as 'composed primarily of some sea water'. MPS changed from owl:equivalentClass being used as an Annot Prop to skos:exactMatch
Sea
A large expanse of saline water usually connected with an ocean.
Measurement method
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.
Environmental measurement type
A measurement type taken of some non-living chemical or physical component of the environment.
https://en.wikipedia.org/wiki/Abiotic_component, accessed 2021-04-14 https://www.wikidata.org/wiki/Q461335, accessed 2021-06-14
Salmonid species name or identifier
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
Fish sex measurement type
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.
This URI does not appear to dereference to the term. Including this URL, https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C28421, to ensure findability.
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.
Temperature measurement type
The degree of hotness or coldness of a body or environment (corresponding to its molecular activity).
An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust.
Air temperature
Objective comparative measure of hot or cold of air.
Stream water temperature
Objective comparative measure of hot or cold of water in a stream.
Precipitation measurement type
Measurement types which pertain to any product of the condensation of atmospheric water vapor that falls under gravity.
Inlet
An opening of the sea into the land, or of a lake into its shore.
Coastal inlet
Bay
An area of water bordered by land on three sides.
Cove
A circular or round inlet with a narrow entrance.
Sound
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.
Fjord
A long and narrow sea inlet with high steeply sloped walled sides. A fjord is a landform created during a period of glaciation.
Lake inlet
Term not currently in ENVO, will be submitted for consideration to ENVO curation team. 03AUG2021
Creek
A stream that is usually smaller than a river.
https://en.wikipedia.org/wiki/Creek, accessed 2021-04-15 https://www.wikidata.org/wiki/Q63565252, accessed 2021-04-15
Watercourse
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
Measuring the distance between scale circuli
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).
https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-15
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
Counting otolith annuli
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).
https://www.adfg.alaska.gov/fedaidpdfs/FRED.132.pdf, accessed 2021-04-15
Fish ages are often estimated using proxy measurements, such as the space or distance between scale circuli.
Fish age proxy measurement type
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.
Distance between scale circuli
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.
Aquatic temperature
Objective comparative measure of hot or cold of water temperature in an aquatic environment.
Male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
Female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
Chinook salmon
"Sikayujak" @ipk "Ggaal" [Denaakk'e, Koyukon Athabaskan] "Gath" [Benhti Kenaga, Lower Tanana] "Luk Choo" @gwi "Kiagtaq" @ypk "Taryaqvak" @ypk "Aciirturtet" @ypk "sumgax̂" @ale [Unangam tunuu variant] "chaguchax̂" @ale [Unangam tunuu variant] "chavichax̂" @ale [Unangam tunuu variant] "Aamasuuk" [Alutiiq/Sugpiaq] "Liliksak" [Alutiiq/Sugpiaq] "Luk'ece'e" [Ahtna] "Kentsinai'i" [Ahtna] "luq'aka'a" [Kenai Dena'ina] "nudlaghi" [Kenai Dena'ina] "te'ya'lee" @eya "Yee" @tsi @tli "t'á" @tsi @tli
Oncorhynchus tshawytscha O. tshawytscha "king salmon" @en "Quinnat salmon" @en "spring salmon" @en "chrome hog" @en "Blackmouth" @en "Tyee salmon" @en
https://alaskasalmonandpeople.org/regions/, accessed 2021-04-16
Indigenous names for salmon can be found by exploring each SASAP region's page on the State of Alaska's Salmon and People website (for example, see the Arctic Region here: https://alaskasalmonandpeople.org/region/arctic/)
https://en.wikipedia.org/wiki/Chinook_salmon, accessed 2021-04-16
https://www.wikidata.org/wiki/Q833503, accessed 2021-04-16
Chum salmon
"Iqalugruaq" @ipk "Aqalugruaq" @ipk "Noolaaghe" [Denaakk'e, Koyukon Athabaskan] "Nahdlii" @gwi "Shii" @gwi "Aluyak" @ypk "Iqalluk" @ypk "Kangitneq" @ypk "Mac'utaq" @ypk "Teggmaarrluk" @ypk [Unangam tunuu variant] "x̂aykix̂" @ale "Alimaq" [Alutiiq/Sugpiaq] "alima" [Kenai Dena'ina] "tiitl'" @eya "Gaynii"@tsi @tli "téel'" @tsi @tli
Oncorhynchus keta O. keta "dog salmon" @en "keta salmon" @en "silverbrite salmon" @en
Pink salmon
"Amaqtuq" @ipk "Amaqaayak" @ypk "Amaqsuq" @ypk "Cuqpeq" @ypk "Terteq" @ypk "Qungaayux" @ale [Unangam tunuu variant] "Amartuq" [Alutiiq/Sugpiaq] "Amaqaayak" [Alutiiq/Sugpiaq] "Dak'aay" [Ahtna] "Dak'aagi" [Ahtna] "qughuna" [Kenai Dena'ina] "giyah sdilahL" @eyk "kaashk'" @eyk "Sti'moon" @tsi @tli "Cháas'" @tsi @tli
Oncorhynchus gorbuscha O. gorbuscha "humpback salmon" @en "humpbacked salmon" @en
Sockeye salmon
"Cayak" @ypk "Sayak" @ypk "Niklliq" [Alutiiq/Sugpiaq] "Nulaeggi" [Ahtna] "Sesluugge"' [Ahtna] "Natael luugge'" [Ahtna] "k'q'uya" [Kenai Dena'ina] "tahi'id" @eyk "cha'ch" @eyk "Misoo" @tsi @tli "g̲aat" @tsi @tli
Oncorhynchus nerka O. nerka "red salmon" @en "kokanee" @en "kokanee salmon" @en "blueback salmon" @en "blue-back" @en "Fraser River salmon" @en "redfish" @en "sock-eye salmon" @en "sox" @en
Coho salmon
"Saanlaaghe" [Denaakk'e, Koyukon Athabaskan] "Khwyhts'en'" [Benhti Kenaga, Lower Tanana] "Shii" @gwi "Caayuryaq" @ypk "Qakiiyaq" @ypk "Qavlunaq" @ypk "Uqurliq" @ypk "Qakiidax̂: @ale [Unangam tunuu variant] "Qakiiyaq" [Alutiiq/Sugpiaq] "ta'ay" @eyk "ÜÜx" @tsi @tli "L'ook" @tsi @tli
Oncorhynchus kisutch O. kisutch "silver salmon" @en "silvers" @en
Unknown sex
Immature
Life history stage of salmonid fish
The age class or life stage of the biological individual(s) at the time the occurrence was recorded.
Egg
In fish, the term egg usually refers to female haploid gametes.
http://www.fishbase.us/glossary/Glossary.php?q=egg&language=english&sc=is, accessed 2021-06-15
Alevin
Larval salmon that have hatched but have not yet completely absorbed their yolk sacs and usually have not yet emerged from the gravel.
http://www.fishbase.us/glossary/Glossary.php?q=alevin&language=english&sc=is, accessed 2021-04-21
Smolt
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.
https://www.fishbase.in/Glossary/Glossary.php?q=smolt&language=english&sc=is, accessed 2021-04-21
Fry
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.
http://www.fishbase.us/glossary/Glossary.php?q=fry&language=english&sc=is, accessed 2021-04-21
Adult
Fish that have fully developed morphological and meristic characters and that have attained sexual maturity.
http://www.fishbase.us/glossary/Glossary.php?q=adult&language=english&sc=is, accessed 2021-04-21
Numeric age of fish
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).
Fish age notation type
A standardized notation format for describing the age of a salmon.
Freshwater temperature
The objective measure of hot or cold in freshwater (i.e. non-saline water).
https://en.wikipedia.org/wiki/Temperature, accessed 2021-04-22 https://www.wikidata.org/wiki/Q11466, accessed 2021-04-22
Seawater temperature
An objective measure of hot or cold of water in a marine (i.e. ocean or sea) environment.
River water temperature
The objective measure of hot or cold of water in a river.
Lake water temperature
Objective comparative measure of hot or cold of water in a lake.
Sea surface temperature
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.
Water salinity measurement type
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.
Sea surface salinity
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.
Subsurface sea temperature
Alkalinity measurement type
A measure of the quantitative capacity of an aqueous solution to neutralize an acid.
https://en.wikipedia.org/wiki/Alkalinity, accessed 2021-04-22 https://www.wikidata.org/wiki/Q432016, accessed 2021-04-22
Freshwater alkalinity
Alkalinity which is measured in freshwater.
Seawater alkalinity
Alkalinity which is measured in seawater.
Dissolved oxygen measurement type
The amount of gaseous oxygen (O2) dissolved in water.
https://arcos.disl.org/main/whatisDO#:~:text=Dissolved%20Oxygen%20is%20the%20amount,can%20affect%20dissolved%20oxygen%20levels, accessed 2021-04-22
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 (%).
Dissolved oxygen saturation
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.
https://en.wikipedia.org/wiki/Oxygen_saturation, accessed 22April2021 https://www.wikidata.org/wiki/Q6294669, accessed 22April2021
Dissolved oxygen concentration
A concentration of the amount of oxygen present in water.
Salmonid Type
Scientific name Binomial name Binomen Latin name
In biological taxonomy, Type generically refers to the official name applied to a taxon. This Class constrains Type members as belonging to family Salmonidae
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.
NCBI:txid8017 ITIS: 161975 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161975#null) GBIF: 5204037 (https://www.gbif.org/species/5204037) EOL: 46563135 (https://eol.org/pages/46563135) COL: 74N5S (https://www.catalogueoflife.org/data/taxon/74N5S) Wikidata: Q673380 (https://www.wikidata.org/wiki/Q673380)
Oncorhynchus gorbuscha
The class which contains all instances of Oncorhynchus gorbuscha.
https://en.wikipedia.org/wiki/Pink_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q673380, accessed 2021-06-15
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.
NCBI:txid8018 ITIS: 161976 (https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161976#null) GBIF: 5204014 (https://www.gbif.org/species/5204014) EOL: 46563136 (https://eol.org/pages/46563136) COL: 49JF6 (https://www.catalogueoflife.org/data/taxon/49JF6) Wikidata: Q475211 (https://www.wikidata.org/wiki/Q475211)
Oncorhynchus keta
The class which contains all instances of Oncorhynchus keta.
https://en.wikipedia.org/wiki/Chum_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q475211, accessed 2021-06-15
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.
NCBI:txid8019 ITIS: 161977 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161977#null) GBIF: 5204034 (https://www.gbif.org/species/5204034) EOL: 46563137 (https://eol.org/pages/46563137) COL: 49JF8 (https://www.catalogueoflife.org/data/taxon/49JF8) Wikidata: Q934874 (https://www.wikidata.org/wiki/Q934874)
Oncorhynchus kisutch
The class which contains all instances of Oncorhynchus kisutch.
https://en.wikipedia.org/wiki/Coho_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q934874, accessed 2021-06-15
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.
NCBI:txid8023 ITIS: 161979 (https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161979#null) GBIF: 5204039 (https://www.gbif.org/species/5204039) EOL: 46563140 (https://eol.org/pages/46563140, currently produces an error 505) COL: 49JFH (https://www.catalogueoflife.org/data/taxon/49JFH) Wikidata: Q44064 (https://www.wikidata.org/wiki/Q44064)
Oncorhynchus nerka
The class which contains all instances of Oncorhynchus nerka.
https://en.wikipedia.org/wiki/Sockeye_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q44064, accessed 2021-06-15
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.
NCBI:txid74940 ITIS: 161980 (https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161980#null) GBIF: 5204024 (https://www.gbif.org/species/5204024) EOL: 46563139 (https://eol.org/pages/46563139, currently produces and error 505) COL: 49JFR (https://www.catalogueoflife.org/data/taxon/49JFR) Wikidata: Q833503 (https://www.wikidata.org/wiki/Q833503)
Oncorhynchus tshawytscha
The class which contains all instances of Oncorhynchus tshawytscha.
https://en.wikipedia.org/wiki/Chinook_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q833503, accessed 2021-06-15
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
Quality of a population measurement type
A quality that inheres in a population of organisms.
[NEEDS ALIGNMENT] http://semanticscience.org/resource/SIO_001385
Notation type
A series or system of written symbols used to represent numbers, amounts, or elements.
https://en.wikipedia.org/wiki/Notation, accessed 2021-06-14 https://www.wikidata.org/wiki/Q2001982, accessed 2021-06-14
Salmon escapement count
The number of salmon which do not get caught by commercial or recreational fisheries and return to their freshwater spawning habitat.
https://en.wikipedia.org/wiki/Salmon_escapement, accessed 2021-04-26 https://www.wikidata.org/wiki/Q23582242, accessed 2021-04-26
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?
Annual escapement count
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?
Daily escapement count
The number of salmon from a given population that escape the fishery in a day.
Bycatch abundance
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.
Number of otolith annuli
The number of annuli on a given otolith.
https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-27
[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
Proxy measurement type
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.
Sex determined on basis of organism's external morphology
External sex determination method
Determination of fish gender based on internal examination, e.g. examination of gonads
Internal sex determination method
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
Genetic sexing
Used to designate that some individual or individuals in a group of organisms possessed functional qualities of more than one gender, simultaneously or sequentially.
Hermaphrodite
A method that uses the presence or other features of a trait ("characteristic") of an organism to differentiate or assign gender
Sexual dimorphic characteristic
Salmon harvest count
The number of recruits which survive to a legal age and/or size and are captured by a fishery.
Estimates of number of fish caught based on some commerical harvest
Commercial harvest count
A measurement of the weight of a fish, or of a sample of fish/fishes
Fish biomass
Taxon concept
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.
https://github.com/darwin-sw/dsw/wiki/ClassTaxon#equivalence-of-taxon-and-taxoncon-%20cept-in-the-tdwg-ontology-and-the-darwin-core-standard, accessed 2021-04-28
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".
Author citation
The name of the scientist or scientists who first validly published the scientific name of a particular organism.
https://code.iczn.org/authorship/article-51-citation-of-names-of-authors/?frame=1, accessed 2021-04-28
https://en.wikipedia.org/wiki/Taxonomy_(biology), accessed 2021-04-28
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.
Fish abundance
Abundance of salmon estimated from modeling techniques, rather than direct counts, weights, etc.
Modeled salmon abundance
[ADDRESS COMMENT, THEN DELETE] needs defintion
Pre-fishery abundance
Quality of an ecological community
A measurement or estimate of the number of salmon, based on counts, densities, weights, or other methods.
Salmon abundance
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.'
Spawner abundance
adult spawning stock abundance adult spawning stock
The total number of recruits which successfully return to spawn in freshwater habitats for a given brood year.
Juvenile standing stock abundance
Juvenile
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.
http://www.fishbase.us/glossary/Glossary.php?q=juvenile&language=english&sc=is, accessed 2021-06-15
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.
Year of fish harvest
Year of commercial fish harvest
Brood year
The parental year for a group of returning salmon, i.e. the calendar year when the majority of parents of these fish spawned.
https://www.pac.dfo-mpo.gc.ca/fm-gp/salmon-saumon/gloss-eng.html, accessed 2021-05-04
Left pectoral fin clip
The left pectoral fin of the fish is removed.
[NEEDS ALIGNMENT] http://purl.dataone.org/odo/ECSO_00002490
Species code
A numeric or alphanumeric code, which represents a particular species and may be recorded in place of a formal scientific or vernacular name.
Fish tag code or color
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
ADF&G species code
Alaska Department of Fish and Wildlife species code
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.
https://www.adfg.alaska.gov/static/license/fishing/pdfs/coar_fish_codes.pdf, accessed 04May2021
Fishing gear code
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)
ADF&G gear code
Alaska Department of Fish and Game gear code
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.
Sample code
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
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
Fish tag or identification type
A marking which is used to differentiate individual fish or groups of fish(es).
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.
Coded wire tag
A small metal pin which is inserted into the fish, usually into the cartilage of the snout.
https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05
https://en.wikipedia.org/wiki/Coded_wire_tag, accessed 2021-05-05 https://www.wikidata.org/wiki/Q23581650, accessed 2021-05-05
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.
Genetic identification
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.
Internal acoustic tag
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.
Adipose fin clip
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
Bismarck brown dye tag
Bismarck brown Machester brown Phenylene brown Bismarck brown Y C.I. 21000 C.I. Basic Brown 1 Basic Brown 1 Vesuvine BA
Tag based on application of a dilution of diazo dye in which fish are immersed and which stains the fins a brown/tan color.
https://fishbio.com/field-notes/inside-fishbio/spray-on-tan, accessed 05May2021
https://en.wikipedia.org/wiki/Bismarck_brown_Y, accessed 05May2021
https://fishbio.com/field-notes/inside-fishbio/spray-on-tan, accessed 2021-05-05 https://en.wikipedia.org/wiki/Bismarck_brown_Y, accessed 2021-05-05
Though not well studied, this type of identification may last up to 3 years post-immersion, and is used for group marking.
Calcein dye tag
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.
https://www.fws.gov/guidance/sites/default/files/documents/Calcein_%28SE%20Mark%29_Study_Protocol.pdf, accessed 2021-05-05
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.
Freeze brand
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
Dye tag
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.
Fin or maxilla clip
The removal of a portion or entirety of a fin or the maxilla of a fish, for identification purposes.
Lower caudal fin clip
A portion of the lower caudal fin lobe is removed.
https://www.solitudelakemanagement.com/blog/know-your-pond-life-fin-clipping-for-fisheries-management-success/, accessed 2021-05-05
Upper caudal fin clip
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.
Maxilla clip
The flap in the corner of the mouth is clipped away (the maxilla - sometimes also the supermaxilla).
Pelvic fin clip
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.
Electronic tag
A tag which transmits information about a fish via an electronic receiver.
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.
External acoustic tag
A small, electronic, sound-emitting device which is attached externally to a fish and collects information on fish movement patterns and the physical environment.
https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 https://en.wikipedia.org/wiki/Acoustic_tag, accessed 2021-05-05
External visual tag
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).
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.
Carlin tag
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.
Dart tag
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.
RFID
A system which uses electromagnetic fields to automatically identify and track tags attached to objects.
https://en.wikipedia.org/wiki/Radio-frequency_identification, accessed 2021-05-05 https://www.wikidata.org/wiki/Q104954, accessed 2021-05-05
PIT tag
Passive Integrated Transponder tag Microchip
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.
https://fishbio.com/field-notes/fish-monitoring/pit-tag-the-full-story, accessed 05May2021 https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 05May2021
https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 05May2021
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.
Natural pattern or unique marking
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.
Otolith marking
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.
Visible implant elastomer
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.
Tattoo
An ink solution, which is injected into the skin.
Subcutaneous color mark
A colored marking, which is placed beneath the skin of a fish for identification.
Fish body modification
The alteration of a physical bodily feature of a fish, either internally or externally, for identification purposes.
Acoustic tag
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.
A mark or tag which is placed beneath the skin of a fish.
Subcutaneous tag
Pectoral fin clip
A pectoral fin is removed, typically as close to the body as possible, using scissors or a razor blade.
https://risaa.org/newsletter/0516/0516_09.pdf, accessed 2021-05-06
Right pectoral fin clip
The right pectoral fin of the fish is removed.
Sex ratio
The ratio of males to females in a population.
https://en.wikipedia.org/wiki/Sex_ratio, accessed 10May2021 https://www.wikidata.org/wiki/Q1068155, accessed 10May2021
Sex ratio of adult spawning stock
The proportion of males and females in an adult spawning stock.
Sex ratio of juvenile standing stock
The ratio of males and females in a juvenile standing stock.
Sex ratio of smolts
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"
Dolly Varden trout
Salvelinus malma S. malma "Dolly Varden" @en
https://en.wikipedia.org/wiki/Dolly_Varden_trout, accessed 2021-06-15 https://www.wikidata.org/wiki/Q327067, accessed 2021-06-15
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.
Pacific salmon
Schiewe, MH (2013) Salmon. Encyclopedia of Biodiversity (Second Edition). pg. 522-531. https://doi.org/10.1016/B978-0-12-384719-5.00293-8
https://www.fisheries.noaa.gov/species/pacific-salmon-and-steelhead#overview, accessed 2021-06-01
Region or location code
An identifier which represents a region or location in and is used in place of the full name.
Cutthroat trout
https://en.wikipedia.org/wiki/Cutthroat_trout, accessed 2021-06-15 https://www.wikidata.org/wiki/Q2717060, accessed 2021-06-15
Atlantic salmon are the only anadromous salmonid native to the Atlantic coast of North America.
Atlantic salmon
https://en.wikipedia.org/wiki/Atlantic_salmon, accessed 2021-06-01 https://www.wikidata.org/wiki/Q188879, accessed 2021-06-01
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 spp.
https://en.wikipedia.org/wiki/Oncorhynchus, accessed 2021-06-15 https://www.wikidata.org/wiki/Q133325, accessed 2021-06-15
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 spp.
https://en.wikipedia.org/wiki/Salmo, accessed 2021-06-15 https://www.wikidata.org/wiki/Q310436, accessed 2021-06-15
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.
NCBI:txid8030 ITIS: 161996 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161996#null) GBIF: 7595433 (https://www.gbif.org/species/7595433) EOL: 46563143 (https://eol.org/pages/46563143) COL: 6XCXT (https://www.catalogueoflife.org/data/taxon/6XCXT) Wikidata: Q188879 (https://www.wikidata.org/wiki/Q188879)
Salmo salar
The class which contains all instances of Salmo salar.
https://en.wikipedia.org/wiki/Atlantic_salmon, accessed 2021-06-15 https://www.wikidata.org/wiki/Q188879, accessed 2021-06-15
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.
ITIS: 161989 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161989#null) GBIF: 5204019 (https://www.gbif.org/species/5204019) EOL: 46563138 (https://eol.org/pages/46563138, NOTE: refers to 'rainbow trout') COL: 49JFF (https://www.catalogueoflife.org/data/taxon/49JFF) Wikidata: Q64437771 (https://www.wikidata.org/wiki/Q64437771)
NCBI:txid8022 ITIS: 161989 (https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161989#null) GBIF: 5204019 (https://www.gbif.org/species/5204019) EOL: 46563138 (https://eol.org/pages/46563138) COL: 49JFF (https://www.catalogueoflife.org/data/taxon/49JFF) Wikidata: Q187986 (https://www.wikidata.org/wiki/Q187986)
Oncorhynchus mykiss
The class which contains all instances of Oncorhynchus mykiss.
https://en.wikipedia.org/wiki/Rainbow_trout, accessed 2021-06-15 https://www.wikidata.org/wiki/Q187986, accessed 2021-06-15
Chose not to assert owl:equivalentClass here, because all Steelhead trout are Oncorhynchus mykiss, but not all Oncorhynchus mykiss are considered Steelhead trout.
Chose not to assert owl:equivalentClass here, because all Rainbow trout are Oncorhynchus mykiss, but not all Oncorhynchus mykiss are considered Rainbow trout.
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 spp.
https://en.wikipedia.org/wiki/Salvelinus, accessed 2021-06-15 https://www.wikidata.org/wiki/Q548682, accessed 2021-06-15
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.
NCBI:txid8039 ITIS: 162000 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=162000#null) GBIF: 4284020 (https://www.gbif.org/species/4284020) EOL: 225241 (https://eol.org/pages/225241) COL: 79FQR (https://www.catalogueoflife.org/data/taxon/79FQR) Wikidata: Q327067 (https://www.wikidata.org/wiki/Q327067)
Salvelinus malma
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.
NCBI:txid30962 ITIS: 161983 (https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=161983#null) GBIF: 5711980 (https://www.gbif.org/species/5711980) EOL: 212910 (https://eol.org/pages/212910) COL: 6SN65 (https://www.catalogueoflife.org/data/taxon/6SN65) Wikidata: Q2717060 (https://www.wikidata.org/wiki/Q2717060)
Oncorhynchus clarkii
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.
Reproductive strategy
A broad category that may be useful for classifying fish based on patterns in migratory trajectories.
Migratory pattern
Smolt abundance
Egg abundance
Precipitation volume
Volume of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity.
Species diversity
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
A community species diversity that is the mean species diversity at a site or within a specific habitat.
Beta diversity
A community species diversity that is the ratio between regional and local species diversity.
Gamma 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.
Species evenness
A quality of an ecological community that reflects how close in abundance all species in a community are.
Species richness
The number of different species represented in an ecological community.
Fish length determination method
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.
Fork length measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14
Mid-orbit to fork of tail measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-06-14 https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14
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.
Mid-orbit to hypural plate measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-06-14
Mid-orbit to posterior insertion of anal fin measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-06-14 https://www.seagrant.wisc.edu/our-work/focus-areas/fish-and-fisheries/fish-glossary/, accessed 2021-06-14
Post-orbit to fork of tail measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-06-14 https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14
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.
Post-orbit to hypural plate measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-06-14
Standard length measurement method
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.
Total length measurement method
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.
https://www.monitoringresources.org/Document/Method/Details/1551, accessed 2021-06-14
Fish stock type
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.
https://www.fishbase.se/Glossary/Glossary.php?q=stock&language=english&sc=is, accessed 2021-06-15
Wild stock
A stock that is sustained by natural spawning and rearing in the natural habitat, regardless of parentage or origin.
https://www.fishbase.se/Glossary/Glossary.php?q=wild+stock&language=english&sc=is, accessed 2021-06-15
Fish total age
An integer, which represents the sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching.
Rainbow trout
Oncorhychus mykiss O. mykiss "lake trout" @en "rainbow" @en "silver trout" @en "steelhead" @en "brook trout" @en
Parr
A young salmonid (salmon or trout) with parr-marks before migration to the sea and after dispersal from the redd.
http://www.fishbase.us/glossary/Glossary.php?q=parr&language=english&sc=is, accessed 2021-06-15
Coastal cutthroat trout
Oncorhynchus clarkii clarkii Oncorhynchus c. clarkii O. c. clarkii
https://en.wikipedia.org/wiki/Coastal_cutthroat_trout, accessed 2021-06-15 https://www.wikidata.org/wiki/Q5138345, accessed 2021-06-15
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.
Oncorhynchus clarkii clarkii
O. c. clarkii Onchorhynchus c. clarkii sea-run cutthroat trout blueback trout harvest trout
The class which contains all instances of Oncorhynchus clarkii clarkii.
https://en.wikipedia.org/wiki/Coastal_cutthroat_trout, accessed 2021-06-18 https://www.wikidata.org/wiki/Q5138345, accessed 2021-06-18
Class intended to facilitate search by "dataset type"
Dataset type
Brood table
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.
https://nceas.github.io/sasap-training/materials/reproducible_research_in_r_fairbanks/example-brood-table-analysis.html, accessed 2021-06-16
Fish weight measurement type
fish weight weight of fish fish mass mass of fish
Wet weight
The weight of a fish, typically taken when the specimen is still alive or freshly deceased, but before being frozen or further processed.
Frozen weight
The weight of a fish, taken after the specimen has been frozen.
Standard weight
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.
https://en.wikipedia.org/wiki/Standard_weight_in_fish, accessed 2021-06-16 https://www.wikidata.org/wiki/Q7598325, accessed 2021-06-16
For example, salmon of age class 2 include all individuals in a population of interest that are two years old.
Age class
A group of individuals of the same species that have the same age.
Recruits do not include individuals lost to predation.
Total recruit abundance
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.
Age class 0.x recruits
Total number of recruits of age class zero.
Age class 1.x recruits
Total number of recruits of age class one.
Age class 2.x recruits
Total number of recruits of age class two.
Age class 3.x recruits
Total number of recruits of age class three.
Age class 4.x recruits
Total number of recruits of age class four.
Age class 5.x recruits
Total number of recruits of age class five.
Age class 6.x recruits
Total number of recruits of age class six.
Fish stock code
A numeric or alphanumeric code, which represents a particular salmon stock and may be recorded in place of a formal scientific or vernacular name.
Identifiers and Codes are differentiated here from their potentially more commonly identifying "labels" that would called "Names", which are typically expressed more in natural language. In some cases, the distinction between a Station "Identifier/Code" and the "Station Name" may be ambiguous, or the same label might apply to both.
Identifiers and Codes
A name that identifies (that is, labels the identity of) either a unique object or a unique class of objects, where the "object" of class may be an idea, physical countable object (of class thereof), or physical noncountable substance (or class thereof). The abbreviation ID often refers to identity, identification (the process of identifying), or an identifier (that is, an instance of identification). An identifier may be a word, number, letter, symbol, or any combination of those.
https://en.wikipedia.org/wiki/Identifier, accessed 2021-06-22 https://www.wikidata.org/wiki/Q853614, accessed 2021-06-22
Fish stock name
Geospatial information
In geography, location or place are used to denote a region (point, line, or area) on Earth’s surface or elsewhere. The term location generally implies a higher degree of certainty than place, the latter often indicating an entity with an ambiguous boundary, relying more on human or social attributes of place identity and sense of place than on geometry.
[NEEDS ALIGNMENT] http://purl.obolibrary.org/obo/GAZ_00000448
Location
A reference to a position on the Earth, by its name or by its geographical location.
http://purl.obolibrary.org/obo/GAZ_00000448 https://www.washoeschools.net/cms/lib/NV01912265/Centricity/Domain/1141/Five%20Themes%20of%20Geo%20packet%202017.pdf, accessed 2021-06-22
Place
In geography, regions are areas that are broadly divided by physical characteristics (physical geography), human impact characteristics (human geography), and the interaction of humanity and the environment (environmental geography). Geographic regions and sub-regions are mostly described by their imprecisely defined, and sometimes transitory boundaries, except in human geography, where jurisdiction areas such as national borders are defined in law.
Region
A spatial region whose boundaries are typically defined against some material frame of reference (like the earth).
A subregion is a part of a larger region or continent and is usually based on location. Cardinal directions, such as south or sou commonly used to define a subregion.
Subregion
Gum cards are used to mount and label the identity of sampled fish scales.
Gum card number
A numeric value assigned to a scale gum card.
Age error code
A numeric or alphanumeric code which represents potential sources of error in determining the age of a fish specimen.
The label, acronym, or other preferred way to refer to a Project
Project name
Whole fish weight
Stomach weight
Weight of full stomach
The weight of a specimen's stomach, taken after the stomach has been dissected from the fish but before being emptied of its contents.
Weight of empty stomach
The weight of a specimen's stomach, taken after the stomach has been dissected from the fish and emptied of its contents.
Fish parasite measurement type
A sea louse (plural sea lice, not to be confused with sea fleas), is a member of the Caligidae family of copepods (small crustaceans) within the order Siphonostomatoida. The roughly 559 species in 37 genera include around 162 Lepeophtheirus and 268 Caligus species. Sea lice are marine ectoparasites (external parasites) that feed on the mucus, epidermal tissue, and blood of host marine fish.
Sea lice count
The number of sea lice counted on an individual fish.
https://en.wikipedia.org/wiki/Sea_louse, accessed 2021-06-23 https://www.wikidata.org/wiki/Q3808922, accessed 2021-06-23
Age class 0.1 recruits
Total number of recruits of age class 0.1.
Age class 0.2 recruits
Total number of recruits of age class 0.2.
Age class 0.3 recruits
Total number of recruits of age class 0.3.
Age class 0.4 recruits
Total number of recruits of age class 0.4.
Age class 0.5 recruits
Total number of recruits of age class 0.5.
Age class 1.1 recruits
Total number of recruits of age class 1.1.
Age class 1.2 recruits
Total number of recruits of age class 1.2.
Age class 1.3 recruits
Total number of recruits of age class 1.3.
Age class 1.4 recruits
Total number of recruits of age class 1.4.
Age class 1.5 recruits
Total number of recruits of age class 1.5.
Age class 1.6 recruits
Total number of recruits of age class 1.6.
Age class 1.7 recruits
Total number of recruits of age class 1.7.
Age class 1.8 recruits
Total number of recruits of age class 1.8.
Age class 1.9 recruits
Total number of recruits of age class 1.9.
Age class 0.6 recruits
Total number of recruits of age class 0.6.
Age class 0.7 recruits
Total number of recruits of age class 0.7.
Age class 0.8 recruits
Total number of recruits of age class 0.8.
Age class 0.9 recruits
Total number of recruits of age class 0.9.
Age class 2.1 recruits
Total number of recruits of age class 2.1.
Age class 2.2 recruits
Total number of recruits of age class 2.2.
Age class 2.3 recruits
Total number of recruits of age class 2.3.
Age class 2.4 recruits
Total number of recruits of age class 2.4.
Age class 2.5 recruits
Total number of recruits of age class 2.5.
Age class 2.6 recruits
Total number of recruits of age class 2.6.
Age class 2.7 recruits
Total number of recruits of age class 2.7.
Age class 2.8 recruits
Total number of recruits of age class 2.8.
Age class 2.9 recruits
Total number of recruits of age class 2.9.
Age class 3.1 recruits
Total number of recruits of age class 3.1.
Age class 3.2 recruits
Total number of recruits of age class 3.2.
Age class 3.3 recruits
Total number of recruits of age class 3.3.
Age class 3.4 recruits
Total number of recruits of age class 3.4.
Age class 3.5 recruits
Total number of recruits of age class 3.5.
Age class 3.6 recruits
Total number of recruits of age class 3.6.
Age class 3.7 recruits
Total number of recruits of age class 3.7.
Age class 3.8 recruits
Total number of recruits of age class 3.8.
Age class 3.9 recruits
Total number of recruits of age class 3.9.
Age class 4.1 recruits
Total number of recruits of age class 4.1.
Age class 4.2 recruits
Total number of recruits of age class 4.2.
Age class 4.3 recruits
Total number of recruits of age class 4.3.
Age class 4.4 recruits
Total number of recruits of age class 4.4.
Age class 4.5 recruits
Total number of recruits of age class 4.5.
Age class 4.6 recruits
Total number of recruits of age class 4.6.
Age class 4.7 recruits
Total number of recruits of age class 4.7.
Age class 4.8 recruits
Total number of recruits of age class 4.8.
Age class 4.9 recruits
Total number of recruits of age class 4.9.
Age class 5.1 recruits
Total number of recruits of age class 5.1.
Age class 5.2 recruits
Total number of recruits of age class 5.2.
Age class 5.3 recruits
Total number of recruits of age class 5.3.
Age class 5.4 recruits
Total number of recruits of age class 5.4.
Age class 5.6 recruits
Total number of recruits of age class 5.6.
Age class 5.7 recruits
Total number of recruits of age class 5.7.
Age class 5.8 recruits
Total number of recruits of age class 5.8.
Age class 5.9 recruits
Total number of recruits of age class 5.9.
Age class 5.5 recruits
Total number of recruits of age class 5.5.
Age class 6.1 recruits
Total number of recruits of age class 6.1.
Age class 6.2 recruits
Total number of recruits of age class 6.2.
Age class 6.3 recruits
Total number of recruits of age class 6.3.
Age class 6.4 recruits
Total number of recruits of age class 6.4.
Age class 6.5 recruits
Total number of recruits of age class 6.5.
Age class 6.6 recruits
Total number of recruits of age class 6.6.
Age class 6.7 recruits
Total number of recruits of age class 6.7.
Age class 6.8 recruits
Total number of recruits of age class 6.8.
Age class 6.9 recruits
Total number of recruits of age class 6.9.
Age class 7.1 recruits
Total number of recruits of age class 7.1.
Age class 7.2 recruits
Total number of recruits of age class 7.2.
Age class 7.3 recruits
Total number of recruits of age class 7.3.
Age class 7.4 recruits
Total number of recruits of age class 7.4.
Age class 7.5 recruits
Total number of recruits of age class 7.5.
Age class 7.6 recruits
Total number of recruits of age class 7.6.
Age class 7.7 recruits
Total number of recruits of age class 7.7.
Age class 7.8 recruits
Total number of recruits of age class 7.8.
Age class 7.9 recruits
Total number of recruits of age class 7.9.
Age class 8.1 recruits
Total number of recruits of age class 8.1.
Age class 8.2 recruits
Total number of recruits of age class 8.2.
Age class 8.3 recruits
Total number of recruits of age class 8.3.
Age class 8.4 recruits
Total number of recruits of age class 8.4.
Age class 8.5 recruits
Total number of recruits of age class 8.5.
Age class 8.6 recruits
Total number of recruits of age class 8.6.
Age class 8.7 recruits
Total number of recruits of age class 8.7.
Age class 8.8 recruits
Total number of recruits of age class 8.8.
Age class 8.9 recruits
Total number of recruits of age class 8.9.
Fish weight proxy measurement type
Girth of fish
A measurement taken around the thickest portion of the midsection of a fish.
Fish weight determination method
Measuring the girth of a fish
A method which is used to approximate the total weight of a fish and which involves wrapping a cloth tape measure perpendicular to the longitudinal axis of the fish to measure its circumference at the thickest point.
https://www.adfg.alaska.gov/FedAidPDFs/fds06-70.pdf, accessed 2021-07-16
AWC water body code
Anadromous Waters Catalog water body code State of Alaska's Anadromous Waters Stream Catalog
Recruit abundance
A count or other estimate of the number of fish returning to a breeding site from a spawning individual.
Recruits per spawner
Estimates of number of fish caught based on some subsistence harvest
Subsistence fishery harvest count
Estimates of number of fish caught based on some sport harvest
Sport fishery harvest count
Jacks are precocial male salmon that have spent one winter less in the ocean than the youngest females of a given species. Because they are younger, jack salmon are smaller than other age classes of conspecifics. Coho jacks return to spawn the same year they smolted and so are particularly small. Jack coloration can differ from that of older adults. Jacks are able to successfully sneak-spawn in spite of efforts by the female and occasionally the other males.
Jack
a young Atlantic salmon returning to its native river to spawn for the first time after one winter at sea
Grilse
Labour-intensive fisheries using relatively small crafts (if any) and little capital and equipment per person-on-board. Most often family-owned. May be commercial or for subsistence (see below). Usually low fuel consumption. Often equated with artisanal fisheries.
Small-scale fishery
Capital-intensive fisheries using relatively large vessels with a high degree of mechanization and that normally have advanced fish finding and navigational equipment. Such fisheries have a high production capacity and the catch per unit effort is normally relatively high. In some areas of the world, the term "industrial fisheries" is synonymous with fisheries for species that are used for reduction to fishmeal and fish oil (e.g. the trawl fishery for sandeel in the North Sea or the Peruvian ourse-seine fishery for anchoveta).
Industrial Fishery
Fisheries established long ago, usually by specific communities that have developed customary patterns of rules and operations. Traditional fisheries reflect cultural traits and attitudes and may be strongly influenced by religious practices or social customs. Knowledge is transmitted between generations by word of mouth. They are usually small-scale and/or artisanal.
Traditional fishery
Typically traditional fisheries involving fishing households (as opposed to commercial companies), using relatively small amount of capital, relatively small fishing vessels, making short fishing trips, close to shore, mainly for local consumption. In practice, definition varies between countries, e.g. from hand-collection on the beach or a one-person canoe in poor developing countries, to more than 20 m. trawlers, seiners, or long-liners over 20m in developed countries. Artisanal fisheries can be subsistence or commercial fisheries, providing for local consumption or export. Sometimes referred to as small-scale fisheries In general, though by no means always, using relatively low level technology. Artisanal and industrial fisheries frequently target the same resources that may give rise to conflict.
Artisanal fishery
Instances of this Class contain one or more occurrence records, and may contain other information associated with those occurrences. "Occurrence" is used here in the sense of its Darwin Core definition: "An existence of an Organism (sensu http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a particular time."
Occurrence record(s)
"hasDbXref' is used here to indicate the equivalence of this Class with its usage in a Darwin Core context
Organism name or identifier
Geocoordinates
Dog salmon
King salmon
Silver salmon
Humpback salmon
European system Age designation recruits
European System Age Designation
Places and Locations
Used to designate that some individual or individuals in a group of organisms possessed functional qualities of more than one gender "sequentially", i.e. not at the "same time" or within a single spawning event or season, but more typically across spawning events or seasons.
Sequential hermaphrodite
Used to designate that some individual or individuals in a group of organisms possessed functional qualities of more than one gender "simultaneously", i.e. "at one time" or within a single spawning event or season.
Simultaneous hermaphrodite
Taxon (name)
Keta salmon
A body of structured information describing some topic(s) of interest. (schema.org)
Johann Julius Walbaum (30 June 1724, Wolfenbüttel, Brunswick-Wolfenbüttel – 21 August 1799, Lübeck) was a German physician, naturalist and fauna taxonomist.
Walbaum, 1792
https://en.wikipedia.org/wiki/Johann_Julius_Walbaum, accessed 2021-04-26 https://www.wikidata.org/wiki/Q68096, accessed 2021-04-26
Sea-running, i.e. anadromous individuals of Rainbow Trout, are called Steelhead.
Pacific Ocean
An ocean that extends from the Arctic in the north to the Antarctic in the south, bounded by Asia and Australia on the west and the Americas on the east.
https://en.wikipedia.org/wiki/Pacific_Ocean, accessed 2021-06-15 https://www.wikidata.org/wiki/Q98, accessed 2021-06-15
Atlantic Ocean
An ocean bounded on the west by North and South America. In the north and northeast, it is separated from the Arctic Ocean by the Canadian Arctic Archipelago, Greenland, Iceland, Svalbard, and mainland Europe. It connects to the Arctic Ocean through the Denmark Strait, Greenland Sea, Norwegian Sea, and Barents Sea. To the east, the boundaries of the ocean proper are Europe, the Strait of Gibraltar (where it connects with the Mediterranean Sea, one of its marginal seas), and Africa. In the southeast, the Atlantic merges into the Indian Ocean, the border being defined by the 20 East meridian, running south from Cape Agulhas to Antarctica.
https://en.wikipedia.org/wiki/Atlantic_Ocean, accessed 2021-06-15 https://www.wikidata.org/wiki/Q97, accessed 2021-06-15
The 10th edition of Systema Naturae is a book written by Swedish naturalist Carl Linnaeus and published in two volumes in 1758 and 1759, which marks the starting point of zoological nomenclature. In it, Linnaeus introduced binomial nomenclature for animals, something he had already done for plants in his 1753 publication of Species Plantarum.
Linnaeus, 1758
https://en.wikipedia.org/wiki/10th_edition_of_Systema_Naturae, accessed 2021-06-15 https://www.wikidata.org/wiki/Q4547210, accessed 2021-06-15
Sir John Richardson (5 ovember 1787 - 5 June 1865) was a Scottish naval surgeon, naturalist and arctic explorer.
Richardson, 1836
https://en.wikipedia.org/wiki/John_Richardson_(naturalist), accessed 2021-06-15 https://www.wikidata.org/wiki/Q545944, accessed 2021-06-15
Some populations of the coastal cutthroat trout (O. c. clarkii) are semi-anadromous. (source: https://en.wikipedia.org/wiki/Cutthroat_trout)
Some Dolly Varden individuals are anadromous
Iteroparity
A reproductive strategy which is characterized by multiple reproductive cycles over the course of an organism's lifetime.
https://en.wikipedia.org/wiki/Semelparity_and_iteroparity#Semelparity, accessed 01June2021 https://www.wikidata.org/wiki/Q522960, accessed 01June2021
Semelparity
A reproductive strategy which is characterized by a single reproductive episode, typically before death.
Anadromous
﻿A classification of fishes which spawn in freshwater, migrate to the ocean to forage and mature, and return to freshwater to spawn and begin the cycle again.
Catadromous
A classification of fishes which spawn in marine habitats, migrate to freshwater areas to forage and mature, then return to marine habitats to spawn.
https://en.wikipedia.org/wiki/Fish_migration, accessed 01June2021 https://www.wikidata.org/wiki/Q852569, accessed 01June2021
In 1855, William P. Gibbons, the curator of Geology and Mineralogy at the California Academy of Sciences, found a population and named it Salmo iridia (Latin: rainbow), later corrected to Salmo irideus. These names faded once it was determined that Walbaum's description of type specimens was conspecific and therefore had precedence. In 1989, morphological and genetic studies indicated that trout of the Pacific Basin were genetically closer to Pacific salmon (Oncorhynchus species) than to the Salmos – brown trout (Salmo trutta) or Atlantic salmon (Salmo salar) of the Atlantic Basin. Thus, in 1989, taxonomic authorities moved the rainbow, cutthroat, and other Pacific Basin trout into the genus Oncorhynchus. Walbaum's name had precedence, so the species name Oncorhynchus mykiss became the scientific name of the rainbow trout. The previous species names irideus and gairdneri were adopted as subspecies names for the coastal rainbow and Columbia River redband trout, respectively.
Gibbons, 1855
https://en.wikipedia.org/wiki/Rainbow_trout, accessed 2021-06-16 https://www.wikidata.org/wiki/Q187986, accessed 20212-06-16
Sea-running, i.e. anadromous individuals of Rainbow Trout are called Steelhead.
Oncorhynchus mykiss irideus
Coastal rainbow trout
Term to designate that some, but not all, individuals of the taxon migrate from freshwater into the ocean for part of their life history. Used as Existential Quantifier on the appropriate taxonomic Class to indicate anadromous behavior of some Instances of that Class.
Semi-anadromous
Red salmon
Kokanee salmon
Fish belonging to a taxon that is typically anadromous, that do not migrate seaward at some time in their life-cycle.
non-anadromous
Bristol Bay
Oncorhynchus mykiss irideus Oncorhynchus m. irideus O. m. irideus "steelhead" @en
Steelhead trout
https://en.wikipedia.org/wiki/Steelhead_trout, accessed 2021-06-15 https://www.wikidata.org/wiki/Q64437771, accessed 2021-06-15
search for '[ADDRESS COMMENT, THEN DELETE]' to find terms that need further review
Salmonid species identification and classification still needs work. Instances of 'Pink salmon', for example, will not be inferred as instances of 'Oncorhynchus gorbuscha' (and vice versa) at the moment. Asserting owl:equivalentClass between these classes causes weird protege behavior after saving/closing/reopening Protege. Went with skos:exactMatch for now to avoid this problem.
search for '[NEEDS ALIGNMENT]' to find terms that should have owl:equivalentClass assertions (but were removed for now b/c Protege was having issues)