From 28cbf917bd4149a6372ef4c328a7279807727afb Mon Sep 17 00:00:00 2001 From: Bryce Mecum Date: Thu, 11 Aug 2022 23:25:00 -0800 Subject: [PATCH] Add ontologies, update query expansion rules Port of https://github.com/DataONEorg/d1_cn_index_processor/pull/33, ref https://github.com/DataONEorg/d1_cn_index_processor/issues/29 --- ...ication-context-ontology-model-service.xml | 69 +- src/main/resources/ontologies/ADCAD.owl | 481 + src/main/resources/ontologies/ARCRC.owl | 1116 + src/main/resources/ontologies/MOSAiC.owl | 151097 +++++++++++++++ src/main/resources/ontologies/SALMON.owl | 7168 + .../resources/ontologies/SALMON_alignment.owl | 639 + src/main/resources/ontologies/SASAP.owl | 3592 + src/main/resources/ontologies/SENSO.owl | 126 + .../annotation/OntologyModelServiceTest.java | 264 + 9 files changed, 164524 insertions(+), 28 deletions(-) create mode 100644 src/main/resources/ontologies/ADCAD.owl create mode 100644 src/main/resources/ontologies/ARCRC.owl create mode 100644 src/main/resources/ontologies/MOSAiC.owl create mode 100644 src/main/resources/ontologies/SALMON.owl create mode 100644 src/main/resources/ontologies/SALMON_alignment.owl create mode 100644 src/main/resources/ontologies/SASAP.owl create mode 100644 src/main/resources/ontologies/SENSO.owl diff --git a/src/main/resources/application-context-ontology-model-service.xml b/src/main/resources/application-context-ontology-model-service.xml index ade6f45c..033dfdc5 100644 --- a/src/main/resources/application-context-ontology-model-service.xml +++ b/src/main/resources/application-context-ontology-model-service.xml @@ -1,7 +1,4 @@ - + @@ -11,7 +8,7 @@ - + http://purl.dataone.org/ontologies/observation/d1-ECSO.owl http://purl.dataone.org/ontologies/provenance/ProvONE/v1/owl/provone.owl @@ -29,6 +26,13 @@ http://ecoinformatics.org/oboe/oboe.1.2/oboe-chemistry.owl http://ecoinformatics.org/oboe/oboe.1.2/oboe-anatomy.owl http://ecoinformatics.org/oboe-ext/sbclter.1.0/oboe-sbclter.owl + https://purl.dataone.org/odo/MOSAIC_ + http://purl.dataone.org/odo/ARCRC + https://purl.dataone.org/odo/ADCAD_ + http://purl.dataone.org/odo/SENSO_ + http://purl.dataone.org/odo/SALMON_ + http://purl.dataone.org/odo/SALMON_alignment_ + http://purl.dataone.org/odo/SASAP_ @@ -37,24 +41,31 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -69,7 +80,7 @@ SELECT ?annotation_property_uri WHERE { - <$CONCEPT_URI> rdfs:subPropertyOf* ?annotation_property_uri . + <$CONCEPT_URI> (owl:equivalentProperty|^owl:equivalentProperty)*/rdfs:subPropertyOf* ?annotation_property_uri . } ]]> @@ -84,12 +95,14 @@ PREFIX rdf: PREFIX rdfs: PREFIX owl: + PREFIX skos: SELECT ?annotation_value_uri - WHERE { - <$CONCEPT_URI> rdfs:subClassOf* ?annotation_value_uri . - } - ]]> + WHERE + { + <$CONCEPT_URI> (rdf:type|(owl:equivalentClass|^owl:equivalentClass)*|(owl:sameAs|^owl:sameAs)*|(skos:exactMatch|^skos:exactMatch)*)/rdfs:subClassOf* ?annotation_value_uri . + } + ]]> diff --git a/src/main/resources/ontologies/ADCAD.owl b/src/main/resources/ontologies/ADCAD.owl new file mode 100644 index 00000000..bf11f6aa --- /dev/null +++ b/src/main/resources/ontologies/ADCAD.owl @@ -0,0 +1,481 @@ + + + + + Ethnology + + + + + + + Soil Science + + + + + + Logic + + + + + + Data science + + + + + + Formal Science + + + + + + + Electrical Engineering + + + + + + + Geochemistry + + + + + Academic Discipline + + + + + + + Linguistics + + + + Version 1.0.0 + + + Arctic Data Center Academic Disciplines Ontology (ADCAD) + + Ontology to support disciplinary annotation of datasets housed at the Arctic Data Center (https://arcticdata.io) + + 2021-12-09 + + + + + + Forestry + + + + + + + Neuroscience + + + + + + Structural Biology + + + + + + + Social Science + + + + + + + Astronomy + + + + + + + Political Science + + + + + + + Biodiversity + + + + + + + Theoretical Biology + + + + + + + Geophysics + + + + + + + Agricultural Research + + + + + + + Mechanical Engineering + + + + + + Cyberinfrastructure + + + + + + + Engineering + + + + + + + Physics + + + + + + + Glaciology + + + + + + + Ecology + + + + + + Natural Science + + + + + + + Systems Engineering + + + + + + + Geodesy + + + + + + + Atmospheric Science + + + + + + + Epidemiology + + + + + + + Cell Biology + + + + + + + Archaeology + + + + + + + Bioinformatics + + + + + + + International Relations + + + + + + + Materials Science + + + + + + + Geology + + + + + + + Civil Engineering + + + + + + + Human Geography + + + + + + + Chemistry + + + + + + + Zoology + + + + + + + Evolutionary Biology + + + + + + + Life Science + + + + + + + Psychology + + + + + + + Geoscience + + + + + + + Biophysics + + + + + + + Software Engineering + + + + + + + Developmental Biology + + + + + + Cryology + + + + + + + Statistics + + + + + + + Anatomy + + + + + + Materials Engineering + + + + + + + Oceanography + + + + + + + Chemical Engineering + + + + + + + Computer Science + + + + + + + Biochemistry + + + + + + + Physical Geography + + + + + + + Sociology + + + + + + + Physical Science + + + + + + + Anthropology + + + + + + + Plant Science + + + + + + + Genetics + + + + + + + Hydrology + + + + + + + Education + + + + + + + Mathematics + + + + + + + Palaeontology + + + + + + + Microbiology + + + + + + + Economics + + + diff --git a/src/main/resources/ontologies/ARCRC.owl b/src/main/resources/ontologies/ARCRC.owl new file mode 100644 index 00000000..034fc34a --- /dev/null +++ b/src/main/resources/ontologies/ARCRC.owl @@ -0,0 +1,1116 @@ + + + + + + + + + + + + + + + + + + + + 2020-11-04T19:46:54Z + definition + + + + + + + + + 2020-11-04T19:47:37Z + definition source + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-11-04T22:51:54Z + might want to delete before we import ECSO so that there are no conflict issues (usesProtocol already exists in ECSO) + usesProtocol + + + + + + + + + 2020-11-04T22:53:03Z + adding this object property, but can delete later if not appropriate + +e.g. of usage for NSIDC sea ice index (a target variable) that is calculated using both ice extent and ice concentration data: + +axiom = calculatedUsing only (Sea Ice Extent and Sea Ice Concentration) + calculatedUsing + + + + + + + + + + + + + + + + + + + + Vital Signs are indicators of the state of the Arctic environmental system. They are assessed using measurements of and/or proxies for target variables. + inferred from https://arctic.noaa.gov/Report-Card + + 2020-11-04T19:24:38Z + Issued annually since 2006, the Arctic Report Card (ARC) is a timely and peer-reviewed source for clear, reliable and concise environmental information on the current state of different components of the Arctic environmental system relative to historical records. The Report Card is intended for a wide audience, including scientists, teachers, students, decision-makers and the general public interested in the Arctic environment and science. + Arctic Essays 2020 + + + + + + + + + Snow covering the Arctic land surface, which is characterized by three variables: snow cover extent (how much area is covered by snow), snow cover duration (how long snow continuously remains on the land surface), and snow water equivalent (how much water is stored in solid form by the snowpack; a function of snow depth and density). + + 2020-11-04T19:42:36Z + Terrestrial Snow Cover Indicator + + + + + + Snow covering the Arctic land surface, which is characterized by three variables: snow cover extent (how much area is covered by snow), snow cover duration (how long snow continuously remains on the land surface), and snow water equivalent (how much water is stored in solid form by the snowpack; a function of snow depth and density). + adapted from https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/843/Terrestrial-Snow-Cover + + + + + + + + + The quantity of aboveground vegetation in the Arctic tundra. + + 2020-11-04T19:42:42Z + Tundra Greenness Indicator + + + + + The quantity of aboveground vegetation in the Arctic tundra. + Normalized Difference Vegetation Index, NDVI (http://www.purl.dataone.org/odo/ECSO_00010076) is highly correlated with Tundra Greeness. + + + + + + + + + An air temperature measured two-meters above the land or ocean surface. + + 2020-11-04T19:42:51Z + Surface Air Temperature Indicator + + + + + + + + + A vast body of ice covering 1.71 million km2, roughly 80% of the surface of Greenland. + + Greenland Ice Sheet Indicator + https://nsidc.org/cryosphere/glossary/ + + + + + + + + + The process of carbon fixation in the Arctic Ocean, primarily by autotrophic single-celled algae living in sea ice (ice algae) and water column (phytoplankton). + + 2020-11-04T19:43:13Z + Arctic Ocean Primary Productivity Indicator + Arctic Ocean Primary Productivity Carbon Flux + + + + + + + + + A water 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. + + 2020-11-04T19:43:19Z + Sea Surface Temperature Indicator + http://purl.dataone.org/odo/ECSO_00001523 + SST +temperature of sea surface +ocean surface temperature +temperature of the ocean surface + + + + + + + + + Ice which has formed by the freezing of sea (saline) water. + + 2020-11-04T19:43:23Z + Sea Ice Indicator + http://purl.obolibrary.org/obo/ENVO_00002200 + + + + + + + + + + + + + + + + + + 2020-12-03T22:29:42Z + Arctic Report Card Supporting Dataset + + + + + + + + + Vital Signs are indicators of the state of the Arctic environmental system. They are assessed using measurements of and/or proxies for Key Variables. + inferred from https://arctic.noaa.gov/Report-Card + + 2020-11-05T00:43:25Z + Arctic Vital Signs + + + + + Vital Signs are indicators of the state of the Arctic environmental system. They are assessed using measurements of and/or proxies for Key Variables. + Issued annually since 2006, the Arctic Report Card is a timely and peer-reviewed source for clear, reliable and concise environmental information on the current state of different components of the Arctic environmental system relative to historical records. The Report Card is intended for a wide audience, including scientists, teachers, students, decision-makers and the general public interested in the Arctic environment and science. + +Find current and past assessments of the Arctic Report Card Vital Signs by visiting: https://arctic.noaa.gov/Report-Card + + + + + + + + + + 2020-12-03T22:30:07Z + Arctic Report Card Supporting Dataset for the 2020 Report + + + + + + + + + + 2020-11-05T23:04:20Z + Measurements and/or proxies used in the assessments of Arctic Report Card Essays. + Arctic Key Variable + Arctic Target Variables + + + + + + + + + Measurements and/or proxies for assessing the 2020 Arctic Vital Signs. + + 2020-11-05T23:04:37Z + Arctic Key Variables 2020 + + + + + + + + + + + + + + + + + The height of a given point in the atmosphere in units proportional to the potential energy of unit mass (geopotential) at this height relative to sea level. + + 2020-11-05T23:06:48Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + geopotential height + geopotential altitude + + + + + + + + + The sum of mean monthly Land Surface Temperatures (LST) for months with mean temperatures above freezing (>0°C). + + 2020-11-05T23:07:00Z + This Key Variable is used to inform Vital Sign 'Tundra Greenness.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/838/Tundra-Greenness + Summer Warmth Index + SWI + + + + + + + + + Air temperature measured two-meters above the land or ocean surface. + + 2020-11-05T23:07:17Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + surface air temperature + + + + + + + + + An air temperature measured in the lower troposphere (i.e. at 925 hPa). + + 2020-11-05T23:08:13Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + near-surface air temperature + + + + + + + + + + + + + + + + + + + + + + + + + + How much area is covered in snow. + + 2020-11-05T23:10:34Z + This Key Variable is used to inform Vital Sign 'Terrestrial Snow Cover.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/843/Terrestrial-Snow-Cover + snow cover extent + + SCE + + + + + + + + + How long snow continuously remains on land surfaces. + + 2020-11-05T23:10:49Z + This Key Variable is used to inform Vital Sign 'Terrestrial Snow Cover.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/843/Terrestrial-Snow-Cover + snow cover duration + SCD + + + + + + + + + + + + + + + + + The fractional area coverage of sea ice over a given region. + + 2020-11-05T23:11:30Z + This Key Variable is used to inform Vital Sign 'Sea Ice.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/841/Sea-Ice + sea ice concentration + + + + + + + + + + + + + + + + + The total volume of sea ice (sea ice thickness multiplied by sea ice concentration) integrated over a given area. + + 2020-11-05T23:12:03Z + This Key Variable is used to inform Vital Sign 'Sea Ice.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/841/Sea-Ice + sea ice volume + + + + + + + + + The distance between the bottom of the ice to the top surface of the ice. + + 2020-11-05T23:12:13Z + This Key Variable is used to inform Vital Sign 'Sea Ice.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/841/Sea-Ice + sea ice thickness + + + + + + + + + + The duration of time a particular area of sea ice has persisted in its solid state. + + 2020-11-05T23:12:34Z + This Target Variable is used to inform Vital Sign 'Sea Ice.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/841/Sea-Ice + age of sea ice + + + + + The duration of time a particular area of sea ice has persisted in its solid state. + Age of sea ice is calculated using data from the National Snow & Ice Data Center (NSIDC). + + + + + + + + + The loss of solid ice from a glacier into the ocean via calving. + + 2020-11-05T23:13:10Z + This Key Variable is used to inform Vital Sign 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + solid ice discharge + + + + + The loss of solid ice from a glacier into the ocean via calving. + The rate of solid ice discharge depends on the speed of glacier ice flow, the thickness of the ice, and the advance or retreat of the terminus of the glacier. + + + + + + + + + The fraction of solar radiation reflected by a surface. + + 2020-11-05T23:13:19Z + This Key Variable is used to inform Vital Sign, 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + surface albedo + + + + + + + + + + Difference in Arctic land air temperature form the 1981-2010 mean (a positive anomaly is a higher temperature; a negative anomaly is a lower temperature). + + 2020-11-05T23:13:32Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + Arctic land air temperature anomaly + + + + + + + + + Difference in global temperature from the 1981-2010 mean (a positive anomaly is a higher temperature; a negative anomaly is a lower temperature). + + 2020-11-05T23:13:49Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + global land air temperature anomaly + + + + + + + + + Difference in seasonal or annual air temperatures from the 1981-2010 mean (a positive anomaly is a higher temperature; a negative anomaly is a lower temperature). + + 2020-11-05T23:14:06Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + seasonal/annual anomaly patterns for air temperatures + + + + + + + + + Quasi-liquid film that can occur on the surface of a solid even below melting point; the thickness of the film is temperature dependent. + + 2020-11-05T23:14:24Z + This Key Variable is used to inform Vital Sign 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + surface melt + + + + + + + + + + The net balance between mass gain vs. mass loss. + + 2020-11-05T23:14:38Z + This Key Variable is used to inform Vital Sign 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + total mass balance + + + + + + The net balance between mass gain vs. mass loss. + Total mass balance is commonly applied for measuring land ice (glaciers and ice sheets). It is typically measured over one year, which includes one accumulation season plus one ablation season (often September - August for the Arctic) + + + + + + + + + Net balance between ice gained (via accumulation) vs. ice loss (via ablation) at the surface. + + 2020-11-05T23:14:51Z + This Key Variable is used to inform Vital Sign 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + surface mass balance + + + + + + Net balance between ice gained (via accumulation) vs. ice loss (via ablation) at the surface. + Surface mass balance is commonly applied for measuring land ice (glaciers and ice sheets). + + + + + + + + + Loss in ice mass due to melting, sublimation, evaporation, ice calving, aeolian processes like blowing snow, avalanche, and any other ablation. + + 2020-11-05T23:15:01Z + This Key Variable was used to inform the Vital Sign, 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + ice ablation + ice ablation zone: http://purl.obolibrary.org/obo/ENVO_01000914 +glacial ice ablation process: http://purl.obolibrary.org/obo/ENVO_01000919 + + + + + + + + + The annual change in total ice area of a marine-terminating glacier as a result of the advance or retreat of the terminal end of a glacier. + + 2020-11-05T23:15:16Z + This Key Variable is used to inform Vital Sign, 'Greenland Ice Sheet.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/842/Greenland-Ice-Sheet + marine terminating glacier front annual area change + + + + + + + + + The large-scale movement of air, and together with ocean circulation, is the means by which thermal energy is redistributed on the surface of the earth. + + 2020-11-06T00:49:30Z + This Key Variable is used to inform Vital Sign 'Surface Air Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/835/Surface-Air-Temperature + atmospheric wind circulation + https://glossary.ametsoc.org/wiki/Wind + + + + + + + + + 2020-11-06T04:35:46Z + Issued annually since 2006, the Arctic Report Card is a timely and peer-reviewed source for clear, reliable and concise environmental information on the current state of different components of the Arctic environmental system relative to historical records. The Report Card is intended for a wide audience, including scientists, teachers, students, decision-makers and the general public interested in the Arctic environment and science. + +The main website for the Arctic Report Card as of Nov 1, 2020 is: https://arctic.noaa.gov/Report-Card + Arctic Report Card Component + + + + + + + + + + 2020-11-06T04:47:36Z + sea ice key variable + + + + + + + + + + 2020-11-06T04:48:36Z + snow key variable + + + + + + + + + + 2020-11-06T04:51:42Z + surface-based key variable + + + + + + + + + + 2020-11-06T04:59:24Z + Arctic Report Card 2020 Component + + + + + + + + + + + + + + + + + + 2020-11-06T16:07:02Z + Place + + + + + + + + + + 2020-11-19T00:56:31Z + Essays are indicators of the state of the Arctic environmental system. They are assessed using measurements of and/or proxies for Key Variables. Essays are classified under one of three categories: Vital Signs, Other Indicators, and Frostbites. + Arctic Report Card Essay + + + + + + + + + + 2020-12-01T01:21:33Z + Other Indicators + + + + + + + + + + 2020-12-01T01:21:50Z + Frostbites + + + + + + + + + + 2020-12-01T01:25:18Z + MaxNDVI is the peak NDVI value for the year and is related to the annual maximum biomass of aboveground vegetation that is reached in midsummer (typically late July or early August). + MaxNDVI + + + + + + + + + + 2020-12-01T01:28:06Z + TI (time-integrated) NDVI is the sum of the biweekly NDVI values for the growing season and is correlated with the total aboveground vegetation productivity. + TI-NDVI + TI (time-integrated) NDVI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-11-06T16:08:24Z + Greenland + + + + + + + + + + + + 2020-11-06T16:16:13Z + Greenland Ice Sheet + + + + + + + + + + + + 2020-11-07T01:31:38Z + Arctic Ocean + Arctic Sea + + + + + + + + + + + + + + + + + ECSO_00000324 + Particulate Organic Carbon + POC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-12-02T18:39:21Z + The depth of water contained within a snowpack if the snowpack were melted instantly. + https://nsidc.org/cryosphere/glossary/ + + snow water equivalent + This Key Variable is used to inform Vital Sign 'Terrestrial Snow Cover.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/843/Terrestrial-Snow-Cover + + + + NDVI + Normalized Difference Vegetation Index + 2020-11-05T23:06:29Z + A remotely sensed indicator of the quantity of aboveground vegetation in an area of land (pixel size). Calculated from distinct wavelengths of visible and near-infrared sunlight reflected by a vegetated land surface. NDVI is calculated using the equation: the near-infrared reflectance minus the red reflectance, divided by near-infrared reflectance plus red reflectance. + This Key Variable is used to inform Vital Sign 'Tundra Greenness.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/838/Tundra-Greenness + + + 2020-11-05T23:08:29Z + This Key Variable is used to inform Vital Sign 'Sea Surface Temperature.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/840/Sea-Surface-Temperature + sea surface temperature + + SST +temperature of sea surface +ocean surface temperature +temperature of the ocean surface + A water 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. + + + Chlorophyll-a is a specific form of chlorophyll used in oxygenic photosynthesis. + This Key Variable is used to inform Vital Sign 'Arctic Ocean Primary Productivity.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/839/Arctic-Ocean-Primary-Productivity-The-Response-of-Marine-Algae-to-Climate-Warming-and-Sea-Ice-Decline + chlorophyll-a concentration + + 2020-11-05T23:10:23Z + + + + Depth of snow, which is precipitation in the form of flakes of crystalline water ice that falls from clouds. + 2020-11-05T23:10:59Z + snow depth + This Key Variable is used to inform Vital Sign 'Terrestrial Snow Cover.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/843/Terrestrial-Snow-Cover + + + + + This Key Variable is used to inform Vital Sign 'Sea Ice.' See the 2019 Essay here: https://arctic.noaa.gov/Report-Card/Report-Card-2019/ArtMID/7916/ArticleID/841/Sea-Ice + Defines a region as "ice-covered' or "not ice-covered" based on a threshold percentage of sea ice concentration per data cell. + 2020-11-05T23:11:42Z + sea ice extent + + + + + Defines a region as "ice-covered' or "not ice-covered" based on a threshold percentage of sea ice concentration per data cell. + A threshold of 15% is used for the Arctic Report Card assessments and is the most commonly used threshold. + + + Geographic Named Place + 2020-11-06T16:06:54Z + + General class for containing places and locations referenced in the Arctic Report Card + + + + wasInfluencedBy + 2020-12-01T17:55:14Z + + + DOC + Dissolved Organic Carbon + + + List + + + + + + + diff --git a/src/main/resources/ontologies/MOSAiC.owl b/src/main/resources/ontologies/MOSAiC.owl new file mode 100644 index 00000000..f1b07d6a --- /dev/null +++ b/src/main/resources/ontologies/MOSAiC.owl @@ -0,0 +1,151097 @@ + + + + + + + + 2021-04-16 + + Ontology to support Semantic Annotation of MOSAiC datasets housed in the Arctic Data Center (https://arcticdata.io). + + MOSAiC Ontology + mosaic + https://purl.dataone.org/odo/MOSAIC_ + Developed with Protege 5.5.0 +Inferences using Pellet 2.2.0 + The MOSAiC ontology is created at NCEAS, UCSB by staff from the Arctic Data Center, and is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) + The MOSAiC ontology is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for anypurpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. + Updated 2021-09-02: New term isBasisFor (inverse hasBasis). Added missing hasChiefScientist and hasBasis triples. +Updated 2021-07-02: Added "_MOSAiC Specific Term" class that includes a description of overall ontology structure + Version 1.0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sello de tiempo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Beginning of a temporal entity + Comienzo de una entidad temporal. + has beginning + tiene principio + Beginning of a temporal entity. + Comienzo de una entidad temporal. + + + + + + + + + + + End of a temporal entity. + Final de una entidad temporal. + has end + tiene fin + End of a temporal entity. + Final de una entidad temporal. + + + + + + + + + + + + + + + + + + El sistema de referencia temporal utilizado por una posición temporal o descripción de extensión. + The temporal reference system used by a temporal position or extent description. + Temporal reference system used + sistema de referencia temporal utilizado + El sistema de referencia temporal utilizado por una posición temporal o descripción de extensión. + The temporal reference system used by a temporal position or extent description. + + + + + + + + + Proporciona soporte a la asociación de una entidad temporal (instante o intervalo) a cualquier cosa. + Supports the association of a temporal entity (instant or interval) to any thing + has time + tiene tiempo + Proporciona soporte a la asociación de una entidad temporal (instante o intervalo) a cualquier cosa. + Supports the association of a temporal entity (instant or interval) to any thing + Característica arriesgada -añadida en la revisión del 2017 que no ha sido todavía utilizada de forma amplia. + Feature at risk - added in 2017 revision, and not yet widely used. + + + + + + + + + Need to add: + +Domain: prov:Entity (http://www.w3.org/ns/prov#Entity) +Range: prov:Activity (http://www.w3.org/ns/prov#Activity) + Generation is the completion of production of a new entity by an activity. This entity did not exist before generation and becomes available for usage after this generation. + + + + + + + + Need to add: + +Domain: prov:Activity (http://www.w3.org/ns/prov#Activity) +Range: prov:Entity (http://www.w3.org/ns/prov#Entity) + Generation is the completion of production of a new entity by an activity. This entity did not exist before generation and becomes available for usage after this generatio + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2021-04-15T06:48:11Z + hasChiefScientist + + + + + + + + + + 2021-04-15T06:48:20Z + isChiefScientistOf + + + + + + + + + + + + + + + + + + + + + 2021-04-15T07:01:47Z + hasResearchLocation + + + + + + + + + 2021-04-15T07:34:06Z + isResearchLocationOf + + + + + + + + + + + + + + + + + + + 2021-04-16T01:30:42Z + hasProjectLabel + + + + + + + + + + + + + 2021-04-16T22:33:33Z + isPartOfCampaign + + + + + + + + + + 2021-04-16T22:34:41Z + hasDatasetPart + + + + + + + + + + + + 2021-04-16T22:39:01Z + hasBasis + + + + + + + + + + + + + 2021-05-19T06:19:25Z + hasEvent + + + + + + + + + + 2021-05-19T06:20:08Z + isEventFromCampaign + + + + + + + + + + + + 2021-05-19T06:22:51Z + has Device Long Name + + + + + + + + + + + 2021-05-19T07:07:50Z + madeBySystem + + + + + + + + + 2021-05-19T08:44:49Z + has Device Short Name + + + + + + + + + + 2021-09-01T23:17:48Z + isBasisFor + + + + + + + + + The subject matter of the content. + + about + + + + + + + + + + + + + + + + + + + + + + + + + The location depicted or described in the content. For example, the location in a photograph or painting. + + contentLocation + + + + + + + + + + + + + + + + + + + + A sub property of location. The original location of the object or the agent before the action. + + fromLocation + + + + + + + + + + + + + + + + + + + + + + + + + + Indicates an item or CreativeWork that is part of this item, or CreativeWork (in some sense). + + hasPart + + + + + + + + + + + + + + + + + + + + + + + + + Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. + + isPartOf + + + + + + + + + + + + + + + + + + + The location of, for example, where an event is happening, where an organization is located, or where an action takes place. + + location + + + + + + + + + + + + + + + + + Indicates the primary entity described in some page or other CreativeWork. + + mainEntity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sub property of location. The final location of the object or the agent after the action. + + toLocation + + + + + + + + + + + + + + + + + + + + + + + + + The variableMeasured property can indicate (repeated as necessary) the variables that are measured in some dataset, either described as text or as pairs of identifier and description using PropertyValue. + + variableMeasured + + + + + + + + + + + + + + + Extensión de una entidad temporal, expresada utilizando xsd:duration. + Extent of a temporal entity, expressed using xsd:duration + has XSD duration + tiene duración XSD + Extensión de una entidad temporal, expresada utilizando xsd:duration. + Extent of a temporal entity, expressed using xsd:duration + Característica arriesgada - añadida en la revisión de 2017, y todavía no ampliamente utilizada. + Feature at risk - added in 2017 revision, and not yet widely used. + + + + + + + + + + Posición de un instante, expresado utilizando xsd:dateTimeStamp. + Position of an instant, expressed using xsd:dateTimeStamp + en fecha-sello de tiempo XSD + in XSD Date-Time-Stamp + Posición de un instante, expresado utilizando xsd:dateTimeStamp. + Position of an instant, expressed using xsd:dateTimeStamp + + + + + + + + + + + 2021-05-19T06:15:51Z + has Sensor ID + + + + + + + + + + + + + + + + + + 2021-05-25T07:39:50Z + has AWI Sensor Information + + + + + + + + The end date and time of the item (in <a href="http://en.wikipedia.org/wiki/ISO_8601">ISO 8601 date format</a>). + + endDate + + + + + + + + The start date and time of the item (in <a href="http://en.wikipedia.org/wiki/ISO_8601">ISO 8601 date format</a>). + + startDate + + + + + + + + + + + + + + + NERC Research Vessel Concept + + + + + + + + + + + A type of current meter capable of simultaneous measurement of current velocity at a number of different depths based on determining Doppler shift of transmitted sound. + acoustic doppler current profiler (ADCP) + + + + + + + + + + + + + + + + A temporal entity with zero extent or duration + Una entidad temporal con una extensión o duración cero. + Time instant + instante de tiempo. + A temporal entity with zero extent or duration + Una entidad temporal con una extensión o duración cero. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A temporal interval or instant. + Un intervalo temporal o un instante. + Temporal entity + entidad temporal + A temporal interval or instant. + Un intervalo temporal o un instante. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2021-04-15T06:46:15Z + The CAMPAIGN (synonyms: cruise, expedition, leg) is related to a certain project. Campaign as the second level in the data model may be used as an option, but is recommended to more easily list separate sampling locations. + Campaign + Cruise + Expedition + Leg + + + + + The CAMPAIGN (synonyms: cruise, expedition, leg) is related to a certain project. Campaign as the second level in the data model may be used as an option, but is recommended to more easily list separate sampling locations. + https://wiki.pangaea.de/wiki/Campaign accessed 28APR2021 + Although the Pangaea Wiki reference above specifies that the terms Campaign, Cruise, Expedition, and Leg are "synonyms", they are clearly used to indicate different phenomena in the MOSAiC website and metadata descriptors. As an example, the term "MOSAiC" appears to refer to an Expedition (cf. the main website http://mosaic-expedition.org). + +On the Pangaea website for "Expeditions" (https://www.pangaea.de/expeditions/byproject/MOSAiC), however, +MOSAiC is described as a "Project" including nine "Campaigns". + +From that webpage one further sees that an "Expedition Program" is shared among Campaigns that have the same Basis (e.g. Polarstern, abbreviated "PS") with, for example, PS122/4 considered a separate Campaign from PS122/5. These Campaigns however appear to be "Legs" of a single "Cruise", though on the Maps provided showing each "Leg", these each have their own unique "Cruise No." + +In addition, the term "Leg" is used to describe a "Campaign", as seen here for PS122/5-- +https://doi.pangaea.de/10.1594/PANGAEA.928833 +or in the Comments section here for PS122/4-- +https://www.pangaea.de/expeditions/events/PS122%2F4 + +Thus, considering the terms Campaign, Cruise, Expedition, and Leg as "synonyms" may be misleading since these can flexibly indicate quite different features. + +MOSAiC is clearly not a "Leg" nor a "Cruise" nor a "Campaign". MOSAiC is most clearly an "Expedition", and a "Project", that consists of "Campaigns" that sometimes are "Legs" if they are components of an individual "Cruise" (e.g. on some common "Basis" such as the Polarstern's 122'nd "Expedition" that would be labeled "PS122". + + + + + + + + + + 2021-04-15T06:46:26Z + Person + + + + + + + + + + + + 2021-04-15T06:46:39Z + Chief Scientist + + + + + + + + + + 2021-04-15T07:00:36Z + Location + + + + + + + + + 2021-04-15T23:20:36Z + The PROJECT table is the uppermost level in the data model, used to define research projects. Projects defined in this table and linked to a dataset will appear in its metaheader. + +MOSAiC, the "Multidisciplinary drifting Observatory for the Study of Arctic Climate", is listed on the Pangaea site as one of numerous "International Projects", with 273 datasets as of 28APR2021 (M. Schildhauer, personal communication) + Project + + + + + The PROJECT table is the uppermost level in the data model, used to define research projects. Projects defined in this table and linked to a dataset will appear in its metaheader. + +MOSAiC, the "Multidisciplinary drifting Observatory for the Study of Arctic Climate", is listed on the Pangaea site as one of numerous "International Projects", with 273 datasets as of 28APR2021 (M. Schildhauer, personal communication) + https://www.pangaea.de/projects/ accessed 28APR2021 + + + + + + + + + + 2021-04-16T07:11:53Z + The Basis represents platforms (e.g. a ship) or institutions (e.g. research stations) from which campaigns were carried out or which were used to take samples (e.g. raft, helicopter, ice floe). The entry of the Basis appears in the metaheader of a data set after the campaign label. + +Information about BASIS +Name: Name of ship, station, platform etc. +URL link to basis +Institute: if a basis is operated by a certain institute + Basis + + + + + The Basis represents platforms (e.g. a ship) or institutions (e.g. research stations) from which campaigns were carried out or which were used to take samples (e.g. raft, helicopter, ice floe). The entry of the Basis appears in the metaheader of a data set after the campaign label. + +Information about BASIS +Name: Name of ship, station, platform etc. +URL link to basis +Institute: if a basis is operated by a certain institute + https://wiki.pangaea.de/wiki/Basis (accessed 28APR2021) + + + + + + + + + + 2021-04-16T07:15:14Z + Research Vessel + + + + + + + + + + + 2021-04-16T07:17:54Z + Large Research Vessel + + + + + + + + + + 2021-04-29T02:33:16Z + The Method/device provides information about instruments (tools/gears/equipment) used to take samples or measure something during an Event. It also defines analytical equipment, tools, or publications describing a specific method used for measuring or calculation individual parameters. + +Information about Method/device +Name: full official name of tool/instrument/device/gear +Abbreviation: may be used for import in an event list to avoid misspellings +URL: should contain a web address, where an official description of the device can be found + Method/Device + + + + + The Method/device provides information about instruments (tools/gears/equipment) used to take samples or measure something during an Event. It also defines analytical equipment, tools, or publications describing a specific method used for measuring or calculation individual parameters. + +Information about Method/device +Name: full official name of tool/instrument/device/gear +Abbreviation: may be used for import in an event list to avoid misspellings +URL: should contain a web address, where an official description of the device can be found + https://wiki.pangaea.de/wiki/Method accessed 28APR2021 + + + + + + + + + + 2021-04-30T00:52:11Z + Device Long Name + + + + + + + + + + 2021-04-30T00:52:37Z + Device Short Name + + + + + + + + + Broadband electromagnetic sensor + + + + + + + + + CTD, handheld + + + + + + + + + Sea ice buoy + + + + + + + + + Dynamic chamber surface flux system + + + + + + + + + Thermistor buoy + + + + + + + + + Snow buoy + + + + + + + + + Drift Towing Ocean Profiler + + + + + + + + + Ocean CTD buoy + + + + + + + + + Surface velocity profiler + + + + + + + + + Buoy, ice tracker + + + + + + + + + Buoy, universal tracker + + + + + + + + + Autonomous Ocean Flux Buoy + + + + + + + + + Ice corer + + + + + + + + + Helicopter + + + + + + + + + Magnaprobe Device + + + + + + + + + Ice thickness gauge Device + + + + + + + + + Snow sampler glove Method + + + + + + + + + Ice-Tethered Profiler + + + + + + + + + Buoy, radiation station + + + + + + + + + Seasonal Ice Mass Balance buoy + + + + + + + + + Atmospheric Surface Flux Station Device + + + + + + + + + Mobile radiation suite Device + + + + + + + + + Fixed-Layer Ocean Buoy + + + + + + + + + Ice-Tethered Profiler Buoy + + + + + + + + + Aircraft + + + + + + + + + Ship Weather Station + + + + + + + + + pCO2 sensor + + + + + + + + + Multibeam echosounder + + + + + + + + + Gravimetry + + + + + + + + + Magnetometer Device + + + + + + + + + Thermosalinograph + + + + + + + + + Sound velocity probe + + + + + + + + + + Acoustic Doppler Current Profiler Device + + + + + + + + + FerryBox Device + + + + + + + + + Camera + + + + + + + + + L-Band Microwave Radiometer + + + + + + + + + Radar dual Ka- and Ku-band altimeter Device + + + + + + + + + Buoy, stressmeter + + + + + + + + + Digital thermistor chain + + + + + + + + + Bottom temperature recorder Device + + + + + + + + + Aerodynamic Particle Sizer Device + + + + + + + + + Hygrometer + + + + + + + + + Trap, sediment + + + + + + + + + GNSS Receiver + + + + + + + + + Flux tower + + + + + + + + + Snow fall sensor + + + + + + + + + Scatterometer + + + + + + + + + Autonomous Underwater Recorder for Acoustic Listening + + + + + + + + + Buoy, GNSS + + + + + + + + + Stress sensor + + + + + + + + + Radiation Station + + + + + + + + + Infrared camera + + + + + + + + + Underwater membrane inlet mass spectrometer + + + + + + + + + Mooring + + + + + + + + + Accoustical backscatter sensor (ABS) + + + + + + + + + Stress logger + + + + + + + + + Multiple investigations + + + + + + + + + Microwave Radiometer + + + + + + + + + Datalogger + + + + + + + + + GNSS multiband antenna + + + + + + + + + Aerosol Mass Spectrometer Device + + + + + + + + + Ablation stakes hot wire thickness gauge Device + + + + + + + + + Ice observation Method + + + + + + + + + Weather station/meteorological observation + + + + + + + + + Aerosol Observing System + + + + + + + + + Radar + + + + + + + + + Remote sensing (Light detection and ranging, LiDAR) + + + + + + + + + Automatic weather station + + + + + + + + + Fish finder echolot, EK60 / EK80 + + + + + + + + + Spectrometer, trace gas + + + + + + + + + Aerosol sampler + + + + + + + + + Atmospheric Observatory Device + + + + + + + + + Floe navigation system + + + + + + + + + Radon counter + + + + + + + + + Gas chromatograph + + + + + + + + + Doppler Wind-LiDAR + + + + + + + + + Ice radar digitizing system + + + + + + + + + Spectral radiometer + + + + + + + + + 2D ultrasonic anemometer Device + + + + + + + + + 3D ultrasonic anemometer + + + + + + + + + Open path CO2 / H2O analyzer + + + + + + + + + Gas chromatograph - Mass spectrometer + + + + + + + + + Chemiluminescent nitrogen oxides analyzer Device + + + + + + + + + Gaseous mercury analyzer + + + + + + + + + Ozone analyzer + + + + + + + + + Particle counter, snow + + + + + + + + + Sonic anemometer + + + + + + + + + Mass spectrometer + + + + + + + + + GNSS microwave radiometer + + + + + + + + + Mesopelagic fish and jellyfish camera system FishCam + + + + + + + + + Cavity ring-down spectrometer + + + + + + + + + Chemiluminescent fast ozone analyzer Device + + + + + + + + + Cavity ring-down greenhouse gas flux analyzer + + + + + + + + + Hygrometer and RTD temperature sensor + + + + + + + + + Trace gas monitor + + + + + + + + + Ozone monitor Device + + + + + + + + + Condensation particle counter Device + + + + + + + + + Aethalometer Device + + + + + + + + + Cloud Condensation Nuclei Counter Device + + + + + + + + + Valve Device + + + + + + + + + Wideband integrated bioaerosol sensor Device + + + + + + + + + Neutral cluster and air ion spectrometer Device + + + + + + + + + Particle size magnifier Device + + + + + + + + + Dynamic Ocean Topography Buoy + + + + + + + + + this Method/Device spelled as "Laser Strain Obsering System" in source data from MOSAiC site + Laser Strain Obsering System + Laser Strain Obsering System + + + + + + + + + Snow sampler metal + + + + + + + + + Portable seismic station + + + + + + + + + Radiosonde + + + + + + + + + In situ pump + + + + + + + + + Underway water sampling Method + + + + + + + + + Snow pit Method + + + + + + + + + Laser Particle Sizer (LPS) + + + + + + + + + Surface water sample + + + + + + + + + Remotely operated sensor platform BEAST + + + + + + + + + Hydro-complex pressure sensor + + + + + + + + + Microstructure Profiler + + + + + + + + + CTD/Rosette + + + + + + + + + Terrestrial laser scanner Device + + + + + + + + + Hand pump Device + + + + + + + + + Longline deployment + + + + + + + + + Ring net + + + + + + + + + Air-sea ice CO2/CH4 flux chamber system Device + + + + + + + + + Multiple opening/closing net + + + + + + + + + Light frame on-sight keyspecies investigation + + + + + + + + + Tethered balloon + + + + + + + + + Unmanned aerial vehicle + + + + + + + + + Floe GNSS reflectometry + + + + + + + + + Ruler stick + + + + + + + + + Bucket water sampling Method + + + + + + + + + Ocean bottom seismometer Device + + + + + + + + + Air sampler + + + + + + + + + Gillnet + + + + + + + + + Snow/ice sample + + + + + + + + + Fishing rod Device + + + + + + + + + Salinometer + + + + + + + + + Borehole Jack Device + + + + + + + + + High volume air sampler Device + + + + + + + + + Buoy, acoustic doppler current profiler + + + + + + + + + RBR concerto CTD Device + + + + + + + + + Temperature sensor T-chain + + + + + + + + + Scatterometer Ku- and X-band Device + + + + + + + + + MicroRider Device + + + + + + + + + Differential global positioning system (DGPS) + + + + + + + + + Buoy + + + + + + + + + Gamma spectrometer + + + + + + + + + Buoy, drifting + + + + + + + + + NA + + + + + + + + + Ground-penetrating radar + + + + + + + + + Water pump Device + + + + + + + + + Remote operated vehicle Seebiber + + + + + + + + + Ice drill + + + + + + + + + Trap, shorttime + + + + + + + + + Mobile Eddy Covariance System + + + + + + + + + Bottle, Niskin 5-L + + + + + + + + + Apstein net + + + + + + + + + Conductivity meter + + + + + + + + + Water sample + + + + + + + + + MicroCAT + + + + + + + + + Vertical microstructure profiler + + + + + + + + + Tap + + + + + + + + + Bathythermograph + + + + + + + + + Radiation-meter + + + + + + + + + Aerosol pump Device + + + + + + + + + Broadband radiometer + + + + + + + + + Autoanalyzer + + + + + + + + + Hyperspectral camera + + + + + + + + + Cloud and aerosol spectrometer + + + + + + + + + Cloud imaging probe + + + + + + + + + Nansen closing net + + + + + + + + + Albedometer + + + + + + + + + Chamber for gas sampling + + + + + + + + + Optical particle counter + + + + + + + + + Helicopter towed system + + + + + + + + + DESY Myon Detector Device + + + + + + + + + Neutron monitor Device + + + + + + + + + Wave Radar System Device + + + + + + + + + AutoFim + + + + + + + + + Cloud camera Device + + + + + + + + + Water Vapour Isotopes Analyser Device + + + + + + + + + Strain Monitoring System + + + + + + + + + Radiometer + + + + + + + + + Sun photometer + + + + + + + + + GPS receiver + + + + + + + + + Light/Optics + + + + + + + + + Distributed temperature sensor + + + + + + + + + Cubic Aerosol Measurement Platform 2 Device + + + + + + + + + Salinity sensor + + + + + + + + + Spectroradiometer + + + + + + + + + Fish sampling Method + + + + + + + + + Buoy, CTD + + + + + + + + + Acoustical Zoological Fish Profiler + + + + + + + + + Buoy, optics + + + + + + + + + Aerosol chamber + + + + + + + + + Phytoplankton sampler + + + + + + + + + Temperature recorder + + + + + + + + + Expendable CTD + + + + + + + + + CTD, RINKO Profiler + + + + + + + + + Net radiometer + + + + + + + + + Documentation + + + + + + + + + Ice station + + + + + + + + + Thermometer probe + + + + + + + + + Vis/NIR Spectrometer + + + + + + + + + 2021-04-30T06:42:13Z + Time MOSAiC + + + + + + + + + 2021-05-20T01:30:36Z + NERC Terms + + + + + + + + + + + 2021-05-25T00:04:15Z + ResearchLocation + + + + + + + + + 2021-07-02T06:57:47Z + The "_MOSAiC Specific Term" class is a container to organize and isolate the terms that are most frequently used to describe the various components of the MOSAiC Expedition. + +Since other established ontologies are imported into this one, a number of extraneous, non-MOSAiC relevant, and unused terms may be present and clutter the presentation. Hopefully, simply presenting this one Class for reference will enable users to enjoy the main advantages of using and exploring this Ontology. + +Definitions or descriptions of these term as described on the Pangaea website are provided in the Annotation fields associated with each MOSAIC term. + +The main patterns semantically modeled here are as such: + +There are 9 Campaigns, which correspond most closely to a "Cruise", or "Leg" although campaigns can involve stationary or aerial platforms. + +Each Campaign has a Basis, which is typically a Research Vessel (e.g. the Polarstern) or Aircraft (Polar 5 & 6). + +Each Campaign has one or more Chief Scientists, and a Research Location. + +The Basis of a Campaign, and its hosted Events, are indicated by the first two initials in the labels of the Campaigns and Events-- e.g. PS122/1 is the first (indicated by the '/1') Campaign (or "Leg") of the 122'nd voyage of the Polarstern (Basis). PS122/2 would be the second Campaign of the 122'nd voyage of the Polarstern, etc. Again-- these "Campaigns" are irregularly referred to elsewhere as "Legs" or "Cruises"-- with their own unique Cruise numbers. + +Campaigns "host" numerous Events, meaning those Events occurred during that Campaign. Events bear cryptic labels that map to distinct Sensor or Sampling efforts that result in the collection of data. Events extend on the naming scheme for Campaigns, with a numbering system that appears to be temporally sequenced. For example, Event PS122/1_5-10 probably commenced before PS122/1_5-100. (Note that this temporal information is not captured in the Ontology as of version 1.001.) + +Each Event results in the collection of data by some Sensor or Sampling Device. These "Methods and Devices" are organized under the "Method/Device" hierarchy in the MOSAiC Ontology, that includes the names of each type of Sensor/Sampling device as SubClasses. Each Method/Device SubClass can further have one to several more specifically named devices that perform that type of Measurement. For example, the "Acoustic Doppler Current Profiler Device" SubClass contains 6 specific types of ADCP sensor instruments, modeled as Instances with their "Device Long Name". + +The MOSAiC team associated each Sensor/Sampling device with a "Short Name" as well. Most "Long Name" Sensor/Samplers have a only single "Short Name" associated with them (sometimes identical to the "Long Name"), but this is not always the case. For example, Device with "Long Name" = "particle size magnifer" has two Device "Short Names" associated with it-- "PSM_UHEL1" and "PSM_UHEL2". + +Method/Devices are associated with Events via their "Device Long Name", through the predicate "has deployment". Details about inverse and equivalent properties that are represented in the Ontology, providing other potential ways to discover connections, are too detailed to discuss here. Consult the Ontology. + +Associated with each "Short Name" in the Ontology is a URI on the Alfred Wegener Institue website, pointing to further detailed information about that Sensor, e.g. this one for one of the ADCP devices: + https://hdl.handle.net/10013/sensor.3bf53c89-fbed-4486-b5f3-2856fcd76def + +A Dataset is the outcome/output of an Event. Every dataset contains measurements that can be linked to some Event that used some Device (with most detailed description provided by the URI assocated with its "Short Name"); and is from some Campaign, that was performed on some Basis with some Chief Scientist(s), and some Research Location. + +(For demonstration purposes, this Ontology contains a single reference to a test dataset instance, findable by searching for "urn" -- where these assocations can be seen. We could link such datasets to specific Events, but since the Events are manifested at level of measurement values in the dataset, these associations are made evident through the Arctic Data Center search portal: http://arcticdata.io, where the PROVO "wasGeneratedBy" predicate is used.) + + +Comments or questions to Mark Schildhauer (schild@nceas.ucsb.edu). + _MOSAiC Specific Term + + + + + + + + + + + + + + + + + + + + + A data set is a collection of data (from one or several events that is organized in a matrix and is mostly put together in a scientific context. Data in PANGAEA are organized in predefined data sets which are quite similar to the original files uploaded by the author (e.g. one table in one Excel sheet). + +The granularity of a data set depends on the type of data and the number of data points, and is primarily in the decision of the data author. In principle, a PANGAEA data set can have an unlimited number of columns and lines (excel 2003: 65,536 x 256; excel 2008: >1 Mio x 16,384) - Examples: + +17 columns doi:10.1594/PANGAEA.821166 + +2,000,000+ lines doi:10.1594/PANGAEA.701279 + +22,600,000+ lines (in ascii: 551 MB; in ASE +index: 2.2 GB; export from IQ +DOI: 1.44 GB) (Fig. 2) doi:10.1594/PANGAEA.758918 + +A data set may contain one to many data series = parameters. Two or many data sets may be grouped into one parent set. Access restrictions can be defined for a complete data set only. Each data set consists of the data and the metadata according to ISO standard fields (ISO 19115). A data set appears on the Internet with a metaheader which contains the information as described below. + Schema.org describes "Dataset" thusly: A body of structured information describing some topic(s) of interest. + + Dataset + + + + + A data set is a collection of data (from one or several events that is organized in a matrix and is mostly put together in a scientific context. Data in PANGAEA are organized in predefined data sets which are quite similar to the original files uploaded by the author (e.g. one table in one Excel sheet). + +The granularity of a data set depends on the type of data and the number of data points, and is primarily in the decision of the data author. In principle, a PANGAEA data set can have an unlimited number of columns and lines (excel 2003: 65,536 x 256; excel 2008: >1 Mio x 16,384) - Examples: + +17 columns doi:10.1594/PANGAEA.821166 + +2,000,000+ lines doi:10.1594/PANGAEA.701279 + +22,600,000+ lines (in ascii: 551 MB; in ASE +index: 2.2 GB; export from IQ +DOI: 1.44 GB) (Fig. 2) doi:10.1594/PANGAEA.758918 + +A data set may contain one to many data series = parameters. Two or many data sets may be grouped into one parent set. Access restrictions can be defined for a complete data set only. Each data set consists of the data and the metadata according to ISO standard fields (ISO 19115). A data set appears on the Internet with a metaheader which contains the information as described below. + https://wiki.pangaea.de/wiki/Data_set accessed 28APR2021 + + + + + + + + + Data sets published in PANGAEA are usually associated with an EVENT (synonyms site, station). An EVENT typically refers to the sampling event at which the data was obtained. Data submitters must provide sufficient information about these events, the EVENT label and latitude/longitude being mandatory information. + +EVENT is a rather generic term, depending on the type of data it can refer to (for example): + +Stations (during a cruise, expedition, field campaign) +Deployments of sampling devices / sensors (device operation ID) +Sampling events/ measurements along a transect / profile +Sampling / observation time series +Geographical origin of organisms (also of culture organisms) +Time and space limited surveys +Mappings +Moorings +Multiple investigations at a single site +Field experiments +Sample labels + "Event" is ambiguous in the context of the MOSAiC Expedition, potentially indicating many different types of activities, places, or products, as described in the extract above taken verbatim from the Pangaea website. + +In this Ontology, "Event" is being presented in the way it was most typically used on the MOSAiC data archive accessed through the Pangaea website-- as a "label" for a Sampling Event, involving the collection of one type of data collected by a specific type of "Method/Device", that is described by the "Device Long Name" and an associated "Device Short Name". In the PROVO ontology, a Method/Device is characterized as a System, that includes either Samplers or Sensors. This Ontology does not classify Systems as being either Samplers or Sensors, and this would be a useful enhancement for future versions. + +The Event is also characterized by some additional metadata about the Latitude, Longitude, Datetime, etc. describing where and when the data were collected. + + + + + Data sets published in PANGAEA are usually associated with an EVENT (synonyms site, station). An EVENT typically refers to the sampling event at which the data was obtained. Data submitters must provide sufficient information about these events, the EVENT label and latitude/longitude being mandatory information. + +EVENT is a rather generic term, depending on the type of data it can refer to (for example): + +Stations (during a cruise, expedition, field campaign) +Deployments of sampling devices / sensors (device operation ID) +Sampling events/ measurements along a transect / profile +Sampling / observation time series +Geographical origin of organisms (also of culture organisms) +Time and space limited surveys +Mappings +Moorings +Multiple investigations at a single site +Field experiments +Sample labels + https://wiki.pangaea.de/wiki/Event (accessed 28APR2021) + + + + + "Event" is ambiguous in the context of the MOSAiC Expedition, potentially indicating many different types of activities, places, or products, as described in the extract above taken verbatim from the Pangaea website. + +In this Ontology, "Event" is being presented in the way it was most typically used on the MOSAiC data archive accessed through the Pangaea website-- as a "label" for a Sampling Event, involving the collection of one type of data collected by a specific type of "Method/Device", that is described by the "Device Long Name" and an associated "Device Short Name". In the PROVO ontology, a Method/Device is characterized as a System, that includes either Samplers or Sensors. This Ontology does not classify Systems as being either Samplers or Sensors, and this would be a useful enhancement for future versions. + +The Event is also characterized by some additional metadata about the Latitude, Longitude, Datetime, etc. describing where and when the data were collected. + Mark Schildhauer 2021, personal communication + + + + + + + + + + + + + + A person (alive, dead, undead, or fictional). + + Person + + + + + + + + Entities that have a somewhat fixed, physical extension. + + Place + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2021-04-15T06:47:12Z + Rex, Markus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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'2020-08-12' + + 2021-05-26T17:36:12Z + PS122/5-track + + + + + + + + + + + + + + + '2019-10-18' + '2019-09-21' + + 2021-05-26T17:38:35Z + AF-MOSAiC-1_track + + + + + + + + + + + + + + + + Oguz Demir and Joel Johnson. 2021. Arctic sea ice thermal emission measurements from the Ultra Wideband Microwave Radiometer (UWBRAD) at the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Expedition in January 2020. + + urn:uuid:af2ceda7-52b7-4009-bfef-bfe2f990eb6a + + + + + + + + + endTime + The endTime of something. For a reserved event or service (e.g. FoodEstablishmentReservation), the time that it is expected to end. For actions that span a period of time, when the action was performed. e.g. John wrote a book from January to <em>December</em>. For media, including audio and video, it's the time offset of the end of a clip within a larger file.<br/><br/> + +Note that Event uses startDate/endDate instead of startTime/endTime, even when describing dates with times. This situation may be clarified in future revisions. + + + + startTime + The startTime of something. For a reserved event or service (e.g. FoodEstablishmentReservation), the time that it is expected to start. For actions that span a period of time, when the action was performed. e.g. John wrote a book from <em>January</em> to December. For media, including audio and video, it's the time offset of the start of a clip within a larger file.<br/><br/> + +Note that Event uses startDate/endDate instead of startTime/endTime, even when describing dates with times. This situation may be clarified in future revisions. + + + + + + diff --git a/src/main/resources/ontologies/SALMON.owl b/src/main/resources/ontologies/SALMON.owl new file mode 100644 index 00000000..817d7905 --- /dev/null +++ b/src/main/resources/ontologies/SALMON.owl @@ -0,0 +1,7168 @@ + + + https://en.wikipedia.org/wiki/Latitude + 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. + + + + + + https://en.wikipedia.org/wiki/Pacific_Ocean, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q98, accessed 2021-06-15 + 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. + + + + + + A small, electronic, sound-emitting device which is attached externally to a fish and collects information on fish movement patterns and the physical environment. + External acoustic tag + 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. + 2021-05-05T16:38:49Z + + + + + + Total number of recruits of age class 7.9. + Age class 7.9 recruits + 2021-07-15T19:35:42Z + + + + + + Objective comparative measure of hot or cold of water in a stream. + + Stream water temperature + 2021-04-14T22:18:53Z + + + + + + 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. + + Fork length measurement 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. + 2021-06-14T20:44:42Z + + + + + + Total number of recruits of age class 5.6. + Age class 5.6 recruits + 2021-07-15T18:56:07Z + + + + + + + The weight of a specimen's stomach, taken after the stomach has been dissected from the fish but before being emptied of its contents. + + + + + + https://www.adfg.alaska.gov/FedAidPDFs/fds06-70.pdf, accessed 2021-07-16 + 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. + + + + + + Subregion + 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. + 2021-06-22T22:51:09Z + + + + + + The left pectoral fin of the fish is removed. + Left pectoral fin clip + 2021-05-04T19:41:04Z + + + + + + http://purl.dataone.org/odo/ECSO_00001528 + The objective measure of hot or cold of water in a river. + River water temperature + 2021-04-22T16:35:07Z + + + + + + + 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. + + + + + + + + + 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 + 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. + + + + + + + Salvelinus malma +S. malma +"Dolly Varden" @en + Dolly Varden trout + 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" + 2021-05-11T17:26:36Z + + + + + + + 2021-06-16T17:31:20Z + + + + Some populations of the coastal cutthroat trout (O. c. clarkii) are semi-anadromous. (source: https://en.wikipedia.org/wiki/Cutthroat_trout) + + Oncorhynchus clarkii clarkii + + + + + + + + Total number of recruits of age class 7.8. + Age class 7.8 recruits + 2021-07-15T19:35:36Z + + + + + + https://en.wikipedia.org/wiki/Coastal_cutthroat_trout, accessed 2021-06-18 +https://www.wikidata.org/wiki/Q5138345, accessed 2021-06-18 + 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. + + + + + + Fish length determination method + 2021-06-14T20:43:46Z + + + + + + http://orcid.org/0000-0002-5300-3075 + The gathering live or deceased fishes by hand. + + + + + + http://purl.dataone.org/odo/ECSO_00001225 + + Objective comparative measure of hot or cold of air. + Air temperature + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-14T22:18:45Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + date + 2019-01-14T23:28:39Z + + + + + + http://purl.dataone.org/odo/ECSO_00001226 + An objective measure of hot or cold of water in a marine (i.e. ocean or sea) environment. + Seawater temperature + 2021-04-22T04:05:29Z + + + + + + A tag which transmits information about a fish via an electronic receiver. + Biologger +Biotelemetry tag +Radio tag + Electronic tag + 2021-05-05T16:37:48Z + + + + + + A spatial region whose boundaries are typically defined against some material frame of reference (like the earth). + Region + 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. + 2021-06-22T22:51:02Z + + + + + + seconds elapsed + 2019-01-15T01:05:09Z + + + + + + https://en.wikipedia.org/wiki/Coded_wire_tag, accessed 2021-05-05 https://www.wikidata.org/wiki/Q23581650, accessed 2021-05-05 + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + A small metal pin which is inserted into the fish, usually into the cartilage of the snout. + + + + + + The degree of hotness or coldness of a body or environment (corresponding to its molecular activity). + temp +temperature + http://purl.dataone.org/odo/ECSO_00001104 + Temperature measurement type + 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. + 2021-04-14T22:18:17Z + + + + + + The proportion of males and females in a smolt population. + Sex ratio of smolts + 2021-05-11T00:02:35Z + + + + + + Place + 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. + 2021-06-22T22:51:00Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + The adipose fin is removed using scissors or a razor blade. + + + + + + Oncorhynchus clarkii clarkii (i.e. coastal cutthroat trout) is a subspecies of Oncorhynchus mykiss and one fo the Pacific trout species. The coastal cutthroat trout occurs in four distinct forms. A semi-anadromous or sea-run form is the most well known. Freshwater forms occur in both large and small rivers and streams and lake environments. The native range of the coastal cutthroat trout extends south from the southern coastline of the Kenai Peninsula in Alaska to the Eel River in Northern California. Coastal cutthroat trout are resident in tributary streams and rivers of the Pacific basin and are rarely found more than 100 miles (160 km) from the ocean. + +Physical Description: Freshwater forms of the coastal cutthroat trout are generally dark green to greenish-blue on back, olive-green on upper flank, silvery on lower flank and belly. They display more numerous flank spots below lateral line, irregular spots on dorsal, adipose and caudal fins and the anal, pectoral and pelvic fin bases. The gill covers are pinkish. Sea-run forms while in salt water and shortly after returning to fresh water are silvery with a bluish back, yellowish lower flanks and fins, and display sparse spots. Cutthroats usually display distinctive red, pink, or orange linear marks along the undersides of their mandibles in the lower folds of the gill plates. These markings are responsible for the common name "cutthroat" given to the trout by outdoor writer Charles Hallock in an 1884 article in The American Angler., although the red slashes are not unique to the cutthroat trout and some coastal rainbow trout and redband trout also display throat slashes. The sea-run forms of coastal cutthroat average 2 to 5 lb (0.9 to 2.3 kg), while stream-resident forms attain much smaller sizes 0.4 to 3.2 oz (11 to 91 g). + +Range: The native range of the coastal cutthroat trout extends south from the southern coastline of the Kenai Peninsula in Alaska to the Eel River in Northern California. Coastal cutthroat trout are resident in tributary streams and rivers of the Pacific basin and are rarely found more than 100 miles (160 km) from the ocean. Semi-anadromous, stream resident, fluvial and lake resident forms exist. The great majority of coastal cutthroat trout habitat coincides with the belt of Pacific coast coniferous rainforest that extends from Alaska southward into Northern California. + The class which contains all instances of Oncorhynchus clarkii clarkii. + 2021-06-16T16:26:35Z + + + + O. c. clarkii +Onchorhynchus c. clarkii +sea-run cutthroat trout +blueback trout +harvest trout + Oncorhynchus clarkii clarkii + + NCBI:txid69121 + + + Total number of recruits of age class 7.7. + Age class 7.7 recruits + 2021-07-15T19:35:30Z + + + + + + + The left pectoral fin of the fish is removed. + + + + + + + + + The parental year for a group of returning salmon, i.e. the calendar year when the majority of parents of these fish spawned. + Brood year + 2021-05-04T17:25:52Z + + + + + + http://purl.dataone.org/odo/ECSO_00001525 + The objective measure of hot or cold in freshwater (i.e. non-saline water). + Freshwater temperature + 2021-04-22T04:05:19Z + + + + + + http://purl.dataone.org/odo/ECSO_00001237 + Measurement types which pertain to any product of the condensation of atmospheric water vapor that falls under gravity. + + + + + + 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. + One of the pelvic fins is removed using scissors. + Pelvic fin clip + 2021-05-05T16:36:17Z + + + + + + part of season measurement made + 2019-01-15T00:16:39Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000029 + A flowing body of water. + + + + + + https://en.wikipedia.org/wiki/10th_edition_of_Systema_Naturae, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q4547210, 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. + + + + + + + A numeric value assigned to a scale gum card. + + + + + + + + + + + + Time Step + + time interval + Time Step + Time Step + duration + Interval of time representing duration of observation + + time interval + duration + Adapted from +http://en.wikipedia.org/wiki/Time + + + In biological taxonomy, Type generically refers to the official name applied to a taxon. This Class constrains Type members as belonging to family Salmonidae + Scientific name +Binomial name +Binomen +Latin name + Salmonid Type + 2021-04-26T20:17:29Z + + + + + + 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. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28421 + Fish sex measurement type + 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 + 2021-04-14T19:59:20Z + + + + + + A reference to a position on the Earth, by its name or by its geographical location. + Location + [NEEDS ALIGNMENT] + +http://purl.obolibrary.org/obo/GAZ_00000448 + 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. + 2021-06-22T22:50:56Z + + + + + + Sport fishery harvest count + Estimates of number of fish caught based on some sport harvest + 2022-06-10T21:46:57Z + + + + + + + Coastal cutthroat trout + 2021-06-16T16:10:16Z + + + + + + + + + Schiewe, MH (2013) Salmon. Encyclopedia of Biodiversity (Second Edition). pg. 522-531. https://doi.org/10.1016/B978-0-12-384719-5.00293-8 + 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. + + + + + + Total number of recruits of age class 7.6. + Age class 7.6 recruits + 2021-07-15T19:35:23Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-03-31 + A fish length measurement taken from the mid-orbit (i.e. eye) to the posterior insertion of the anal fin. + + + + + + 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://alaskasalmonandpeople.org/regions/, accessed 2021-04-16 + "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 + + + + + + + + + + https://en.wikipedia.org/wiki/Steelhead_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q64437771, accessed 2021-06-15 + Oncorhynchus mykiss irideus +Oncorhynchus m. irideus +O. m. irideus +"steelhead" @en + + + + + + The flap in the corner of the mouth is clipped away (the maxilla - sometimes also the supermaxilla). + Maxilla clip + 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. + 2021-05-05T16:35:46Z + + + + + + The ratio of males and females in a juvenile standing stock. + Sex ratio of juvenile standing stock + 2021-05-11T00:01:49Z + + + + + + longitude second component + 2019-01-28T21:59:23Z + + + + + + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25150 + The duration of time for which a fish has been alive. + + + + + + Total number of recruits of age class 1.4. + Age class 1.4 recruits + 2021-07-15T18:47:12Z + + + + + + + Oncorhynchus tshawytscha +O. tshawytscha +"king salmon" @en +"Quinnat salmon" @en +"spring salmon" @en +"chrome hog" @en +"Blackmouth" @en +"Tyee salmon" @en + "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 + Chinook salmon + 2021-04-16T18:10:30Z + + + + + + Geospatial information + 2021-06-22T22:50:49Z + + + + + + Oncorhynchus clarkii clarkii +Oncorhynchus c. clarkii +O. c. clarkii + Coastal cutthroat trout + 2021-06-16T16:09:57Z + + + + + + Total number of recruits of age class 7.5. + Age class 7.5 recruits + 2021-07-15T19:35:15Z + + + + + + https://www.fishbase.se/Glossary/Glossary.php?q=stock&language=english&sc=is, accessed 2021-06-15 + 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://en.wikipedia.org/wiki/Spearfishing, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q765706, accessed 2021-04-01 + A barbed pole, which is used to strike and collect a fish. Spearheads come in a variety of different shapes (e.g. arrow, trident), and can be thrown by hand or deployed using elastic-powered spearguns and slings or compressed gas pneumatic powered spearguns. + + + + + + A portion of the upper caudal fin lobe is removed. + Upper caudal fin clip + 2021-05-05T16:31:23Z + + + + + + The proportion of males and females in an adult spawning stock. + Sex ratio of adult spawning stock + 2021-05-11T00:01:35Z + + + + + + Salmonid species name or identifier + 2021-04-14T18:47:11Z + + + + + + https://www.solitudelakemanagement.com/blog/know-your-pond-life-fin-clipping-for-fisheries-management-success/, accessed 2021-05-05 + A portion of the lower caudal fin lobe is removed. + + + + + + https://en.wikipedia.org/wiki/Sex_ratio, accessed 10May2021 +https://www.wikidata.org/wiki/Q1068155, accessed 10May2021 + The ratio of males to females in a population. + + + + + + https://en.wikipedia.org/wiki/Radio-frequency_identification, accessed 2021-05-05 +https://www.wikidata.org/wiki/Q104954, accessed 2021-05-05 + A system which uses electromagnetic fields to automatically identify and track tags attached to objects. + + + + + + + + + + + + + + + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + http://purl.obolibrary.org/obo/PATO_0000383 + Female + 2021-04-15T20:51:08Z + + + + + + + + + + Total number of recruits of age class 1.3. + Age class 1.3 recruits + 2021-07-15T18:46:55Z + + + + + + A fish length measurement taken from the hind margin of the orbit to the tip of the median caudal fin rays. + POFK + + Post-orbit to fork of tail length + 2021-03-31T18:19:40Z + + + + + + Fish stock name + 2021-06-21T20:16:55Z + + + + + Subsistence fishery harvest count + Estimates of number of fish caught based on some subsistence harvest + 2022-06-10T21:46:57Z + + + + + + Semi-anadromous + 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. + 2021-06-16T16:03:41Z + + + + + + https://en.wikipedia.org/wiki/Sea_louse, accessed 2021-06-23 +https://www.wikidata.org/wiki/Q3808922, accessed 2021-06-23 + 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. + + + + + + A portion of the lower caudal fin lobe is removed. + Lower caudal fin clip + 2021-05-05T16:30:45Z + + + + + + + + + + + A measurement type taken of some non-living chemical or physical component of the environment. + Environmental measurement type + 2021-04-14T18:23:43Z + + + + + + Salmo spp. + NCBI:txid8028 + 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. + 2021-05-27T00:02:38Z + + + + + + Julian day + day of year + Julian day + 2019-01-15T18:26:54Z + + + + + + + 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. + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=fishingHatcheries.main, accessed 2021-04-02 + https://www.adfg.alaska.gov/static/fishing/PDFs/hatcheries/2013_ak_hatcheries.pdf, 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. + + + + + + + + + + Anadromous Waters Catalog water body code +State of Alaska's Anadromous Waters Stream Catalog + + + + + + https://www.pac.dfo-mpo.gc.ca/fm-gp/salmon-saumon/gloss-eng.html, accessed 2021-05-04 + 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.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31 + 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://en.wikipedia.org/wiki/Angling, accessed 2021-04-01 + 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. + + + + + + Total number of recruits of age class 1.2. + Age class 1.2 recruits + 2021-07-15T18:46:25Z + + + + + + 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). + FL +tip of snout to fork of tail + + Fork length + 2021-03-31T18:19:34Z + + + + + + Recruits per spawner + A count or other estimate of the number of fish returning to a breeding site from a spawning individual. + 2021-07-20T21:55:30Z + + + + + + + + + + + http://rs.tdwg.org/dwc/terms/lifeStage + The age class or life stage of the biological individual(s) at the time the occurrence was recorded. + + + + + + The removal of a portion or entirety of a fin or the maxilla of a fish, for identification purposes. + Fin or maxilla clip + 2021-05-05T16:29:24Z + + + + + + + + + + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + http://purl.obolibrary.org/obo/PATO_0000384 + Male + 2021-04-15T20:51:04Z + + + + + + + Linnaeus, 1758 + 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. + 2021-05-26T23:58:33Z + + + + + + The number of salmon which do not get caught by commercial or recreational fisheries and return to their freshwater spawning habitat. + Salmon escapement count + 2021-04-26T23:21:35Z + + + + + + https://www.fishbase.in/Glossary/Glossary.php?q=smolt&language=english&sc=is, accessed 2021-04-21 + 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. + + + + + + Total number of recruits of age class 1.1. + Age class 1.1 recruits + 2021-07-15T18:46:02Z + + + + + + End of a temporal entity. + + + + + 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. + + + + + + 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. + ID +Identity + Identifiers and Codes + 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. + 2021-06-21T20:12:18Z + + + + + Recruit abundance + 2021-07-20T21:55:15Z + + + + + + https://en.wikipedia.org/wiki/Notation, accessed 2021-06-14 +https://www.wikidata.org/wiki/Q2001982, accessed 2021-06-14 + + A series or system of written symbols used to represent numbers, amounts, or elements. + + + + + + The ratio of males to females in a population. + Sex ratio + 2021-05-10T22:51:40Z + + + + + + A numerical value which represents the length of a fish, typically in units of millimeters, centimeters, or inches. + http://purl.dataone.org/odo/ECSO_00000553 + Fish length measurement type + 2021-03-31T17:43:39Z + + + + + + Oncorhynchus spp. + NCBI:txid8016 + 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"). + 2021-05-26T23:57:17Z + + + + + + A series or system of written symbols used to represent numbers, amounts, or elements. + Notation type + [NEEDS ALIGNMENT] + +http://semanticscience.org/resource/SIO_001385 + 2021-04-26T23:10:08Z + + + + + Objective comparative measure of hot or cold of water temperature in an aquatic environment. + + Aquatic temperature + 2021-04-15T20:49:21Z + + + + + + https://en.wikipedia.org/wiki/Salvelinus, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q548682, accessed 2021-06-15 + 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. + + + + + + https://en.wikipedia.org/wiki/Body_of_water, accessed 2021-03-30 +https://www.wikidata.org/wiki/Q15324, accessed 2021-03-30 + An accumulation of water of varying size. + + + + + + https://alaskasalmonandpeople.org/working-group/governance-and-subsistence/, accessed 2021-04-02 + http://www.adfg.alaska.gov/index.cfm?adfg=fishingPersonalUse.main, accessed 2021-04-02 + 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)). + + + + + + + + + + Juvenile standing stock abundance + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-29T19:02:18Z + + + + + + site identifier + Identifier associated, in some context" with a "Site"-- i.e. a location where some research data have been or are being collected + 2019-05-23T19:30:55Z + + + + + + https://en.wikipedia.org/wiki/Coho_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q934874, 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. + + + + + + https://en.wikipedia.org/wiki/Atlantic_salmon, accessed 2021-06-01 +https://www.wikidata.org/wiki/Q188879, accessed 2021-06-01 + Salmo salar +S. salar + + + + + + + + + + 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 +Oncorhynchus c. clarkii +O. c. clarkii + + + + + + 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. + Fish stock type + 2021-06-14T23:05:05Z + + + + + Total number of recruits of age class 6.4. + Age class 6.4 recruits + 2021-07-15T18:57:59Z + + + + + + 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. + Anadromous + 2021-06-01T20:10:58Z + + + + + + Total number of recruits of age class 3.7. + Age class 3.7 recruits + 2021-07-15T18:52:32Z + + + + + + Total number of recruits of age class 1.5. + Age class 1.5 recruits + 2021-07-15T18:47:26Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000015 + A marine water body which is constitutes the majority of an astronomical body's hydrosphere. + Ocean + 2021-04-07T18:39:26Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + This identification type will last the entire lifetime of the fish, is used for group marking, and is most suitable for salmonids that are at least 10cm in length. + + + + + + + + + + + The number of recruits which survive to a legal age and/or size and are captured by a fishery. + + + + + + https://www.wikidata.org/wiki/Q833503, accessed 2021-04-16 + https://en.wikipedia.org/wiki/Chinook_salmon, accessed 2021-04-16 + Oncorhynchus tshawytscha +O. tshawytscha +"king salmon" @en +"Quinnat salmon" @en +"spring salmon" @en +"chrome hog" @en +"Blackmouth" @en +"Tyee salmon" @en + + + + + + https://orcid.org/0000-0002-5300-3075 + Objective comparative measure of hot or cold of water in a stream. + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + The total number of recruits which successfully return to spawn in freshwater habitats for a given brood year. + adult spawning stock abundance +adult spawning stock + Spawner 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.' + 2021-04-29T19:02:08Z + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-06 + 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. + + + + + + An identifier, which may be assigned to a physical sample taken from a fish (e.g. tissue, fin, otolith) or an entire fish specimen. + Fish sample code + 2021-05-04T21:55:17Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000016 + A large expanse of saline water usually connected with an ocean. + + + + + + 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. + + Total length measurement method + 2021-06-14T21:49:03Z + + + + + + Total number of recruits of age class 6.3. + Age class 6.3 recruits + 2021-07-15T18:57:51Z + + + + + + European System Age Designation + 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 + 2021-12-09T20:51:19Z + + + + + + 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 + A reference to a position on the Earth, by its name or by its geographical location. + + + + + + Migratory pattern + A broad category that may be useful for classifying fish based on patterns in migratory trajectories. + 2021-06-01T20:10:50Z + + + + + + + + + + A numeric or alphanumeric code which represents potential sources of error in determining the age of a fish specimen. + + + + + + Total number of recruits of age class 3.6. + Age class 3.6 recruits + 2021-07-15T18:52:26Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000020 + A body of water or other liquid of considerable size contained in a depression on a landmass. + Lake + 2021-04-07T18:39:22Z + + + + + + https://en.wikipedia.org/wiki/Bismarck_brown_Y, accessed 05May2021 + Bismarck brown +Machester brown +Phenylene brown +Bismarck brown Y +C.I. 21000 +C.I. Basic Brown 1 +Basic Brown 1 +Vesuvine BA + + + + + + + + + + Salmon abundance + A measurement or estimate of the number of salmon, based on counts, densities, weights, or other methods. + 2021-04-29T19:01:14Z + + + + + + + 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. + sample id + Sample code + 2021-05-04T21:54:57Z + + + + + + Subsurface sea temperature + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-22T17:20:03Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + The flap in the corner of the mouth is clipped away (the maxilla - sometimes also the supermaxilla). + + + + + + 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. + + Standard length measurement method + 2021-06-14T21:45:52Z + + + + + + 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 + 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). + + + + + + Total number of recruits of age class 6.2. + Age class 6.2 recruits + 2021-07-15T18:57:46Z + + + + + + Schiewe, MH (2013) Salmon. Encyclopedia of Biodiversity (Second Edition). pg. 522-531. https://doi.org/10.1016/B978-0-12-384719-5.00293-8 + Atlantic salmon are the only anadromous salmonid native to the Atlantic coast of North America. + + + + + + second of hour + second of measurement time + second of hour + 2019-01-16T00:29:24Z + + + + + + A reproductive strategy which is characterized by a single reproductive episode, typically before death. + Semelparity + 2021-06-01T20:04:35Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-06-14 +https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14 + 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. + + + + + + Total number of recruits of age class 3.5. + Age class 3.5 recruits + 2021-07-15T18:52:22Z + + + + + + European system Age designation recruits + 2021-12-09T20:48:48Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000022 + 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. + River + 2021-04-07T18:39:18Z + + + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=fishingPersonalUse.main, 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. + + + + + + Total number of recruits of age class 3.4. + Age class 3.4 recruits + 2021-07-15T18:52:16Z + + + + + + Geocoordinates + 2021-08-12T20:54:42Z + + + + + + + + + http://purl.obolibrary.org/obo/PCO_0000004 + A quality that inheres in a community. + Quality of an ecological community + 2021-04-29T18:48:45Z + + + + + + 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. + Alaska Department of Fish and Game gear code + ADF&G gear code + 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) + 2021-05-04T19:58:32Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000033 + A body of water, usually of smaller size than a lake. + + + + + + Places and Locations + 2022-01-27T20:37:47Z + + + + + Total number of recruits of age class 8.5. + Age class 8.5 recruits + 2021-07-15T19:36:20Z + + + + + + 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. + + Post-orbit to hypural plate measurement method + 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. + 2021-06-14T21:38:35Z + + + + + + Total number of recruits of age class 6.1. + Age class 6.1 recruits + 2021-07-15T18:57:39Z + + + + + + A reproductive strategy which is characterized by multiple reproductive cycles over the course of an organism's lifetime. + Iteroparity + 2021-06-01T20:04:29Z + + + + + + http://purl.obolibrary.org/obo/MMO_0000000 + 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. + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-27 + 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. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000476 + An opening of a lake into its shore. + + + + + + Pre-fishery abundance + [ADDRESS COMMENT, THEN DELETE] + +needs defintion + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-29T18:44:25Z + + + + + + Reproductive strategy + A general category for gathering traits (morphological, behavioral, and otherwise) that have some evolutionary basis for achieving reproductive success. + 2021-06-01T20:04:09Z + + + + + Total number of recruits of age class 3.3. + Age class 3.3 recruits + 2021-07-15T18:52:09Z + + + + + + A numeric or alphanumeric code, which represents a particular type of fishing gear or equipment. + Fishing gear code + 2021-05-04T19:58:20Z + + + + + + http://purl.dataone.org/odo/ECSO_00001658 + 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. + Sea surface salinity + Is also an Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-22T17:17:30Z + + + + + + + + + + + + The weight of a fish, typically taken when the specimen is still alive or freshly deceased, but before being frozen or further processed. + Wet weight + 2021-06-16T22:53:55Z + + + + + + year and day of measurement + 2019-01-16T00:44:09Z + + + + + + Total number of recruits of age class 8.4. + Age class 8.4 recruits + 2021-07-15T19:36:14Z + + + + + + 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. + + Post-orbit to fork of tail measurement method + 2021-06-14T21:30:14Z + + + + + + Total number of recruits of age class 5.5. + Age class 5.5 recruits + 2021-07-15T18:57:19Z + + + + + + + + + https://en.wikipedia.org/wiki/Recreational_fishing, accessed 2021-04-02 +https://www.wikidata.org/wiki/Q283534, accessed 2021-04-02 + A fishery in which fishes and other seafood are harvested for pleasure or competition. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000020 + A body of water or other liquid of considerable size contained in a depression on a landmass. + + + + + + Total number of recruits of age class 5.9. + Age class 5.9 recruits + 2021-07-15T18:56:26Z + + + + + + 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. + Alaska Department of Fish and Wildlife species code + ADF&G species code + ADF&G salmon species codes: + +410 salmon, chinook +420 salmon, sockeye +430 salmon, coho +440 salmon, pink +450 salmon, chum + 2021-05-04T19:44:10Z + + + + + + http://purl.dataone.org/odo/ECSO_00001164 + A measure of the saltiness or dissolved salt content of a body of water. + Water salinity measurement type + 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. + 2021-04-22T17:00:09Z + + + + + + A barbed plastic tag which is inserted under the dorsal fin of the fish using a cannula. + Dart 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. + 2021-05-05T16:43:07Z + + + + + + fish weight +weight of fish +fish mass +mass of fish + Fish weight measurement type + 2021-06-16T22:45:21Z + + + + + + Total number of recruits of age class 8.3. + Age class 8.3 recruits + 2021-07-15T19:36:09Z + + + + + + + + + Modeled salmon abundance + Abundance of salmon estimated from modeling techniques, rather than direct counts, weights, etc. + 2021-04-29T18:39:15Z + + + + + + 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. + + Mid-orbit to posterior insertion of anal fin measurement method + 2021-06-14T21:17:24Z + + + + + + https://www.adfg.alaska.gov/static/license/fishing/pdfs/coar_fish_codes.pdf, accessed 04May2021 + 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) + + + + + + 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. + + Mid-orbit to hypural plate measurement method + 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. + 2021-06-14T21:08:39Z + + + + + + The unique alphanumeric code or marking color(s) of a tagged fish. + Fish tag code or color + 2021-05-04T19:41:34Z + + + + + + Total number of recruits of age class 5.8. + Age class 5.8 recruits + 2021-07-15T18:56:21Z + + + + + + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-22T16:49:49Z + Sea surface temperature + SST +Ocean surface temperature + + + + http://purl.dataone.org/odo/ECSO_00001523 + 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. + + + + Carlin tag + 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. + A metal plate with a unique identifying code, which is attached to a fish below the dorsal fin via two stainless steel wires. + 2021-05-05T16:40:41Z + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=fishingsubsistence.main, accessed 2021-04-02 + 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. + + + + + + + + + https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14 + 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. + + + + + + year of measurement + 2019-01-14T23:23:43Z + + + + + + 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. + run reconstruction + Brood table + 2021-06-16T22:33:58Z + + + + + + Total number of recruits of age class 8.2. + Age class 8.2 recruits + 2021-07-15T19:36:04Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + + 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. + + + + + + + The weight of a specimen's stomach, taken after the stomach has been dissected from the fish and emptied of its contents. + + + + + + https://www.fisheries.noaa.gov/species/pacific-salmon-and-steelhead#overview, accessed 2021-06-01 + Schiewe, MH (2013) Salmon. Encyclopedia of Biodiversity (Second Edition). pg. 522-531. https://doi.org/10.1016/B978-0-12-384719-5.00293-8 + 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. + + + + + + http://purl.dataone.org/odo/ECSO_00001231 + Objective comparative measure of hot or cold of water in a lake. + Lake water temperature + 2021-04-22T16:36:05Z + + + + + + Total number of recruits of age class 8.1. + Age class 8.1 recruits + 2021-07-15T19:35:56Z + + + + + + 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). + External visual tag + 2021-05-05T16:40:28Z + + + + + + 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. + + Mid-orbit to fork of tail measurement method + 2021-06-14T20:58:33Z + + + + + + years elapsed + 2019-07-15T23:41:07Z + + + + + + Total number of recruits of age class 5.7. + Age class 5.7 recruits + 2021-07-15T18:56:12Z + + + + + + + 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). + + + + + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=egg&language=english&sc=is, accessed 2021-06-15 + In fish, the term egg usually refers to female haploid gametes. + + + + + + https://en.wikipedia.org/wiki/Abiotic_component, accessed 2021-04-14 +https://www.wikidata.org/wiki/Q461335, accessed 2021-06-14 + A measurement type taken of some non-living chemical or physical component of the environment. + + + + + + A numeric or alphanumeric code, which represents a particular species and may be recorded in place of a formal scientific or vernacular name. + Species code + [NEEDS ALIGNMENT] + +http://purl.dataone.org/odo/ECSO_00002490 + 2021-05-04T19:41:18Z + + + + + + Dataset type + Class intended to facilitate search by "dataset type" + 2021-06-16T22:33:55Z + + + + + + + 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 + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + The number of salmon from a given population that escape the fishery in a year. + 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? + 2021-04-26T23:24:51Z + + + + + + Total number of recruits of age class 0.9. + Age class 0.9 recruits + 2021-07-15T18:49:12Z + + + + + + https://en.wikipedia.org/wiki/Temperature, accessed 2021-04-22 +https://www.wikidata.org/wiki/Q11466, accessed 2021-04-22 + The objective measure of hot or cold of water in a river. + + + + + + estuary name + 2019-05-20T21:33:57Z + + + + + + + + + Beginning of a temporal entity. + + + + + + + + The gathering live or deceased fishes by hand. + Handpicked or carcass collection + 2021-04-01T18:02:25Z + + + + + + 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. + hand net +scoop net + Dip net + 2021-04-01T18:01:59Z + + + + + + + + + Chose not to assert owl:equivalentClass here, because all Steelhead trout are Oncorhynchus mykiss, but not all Oncorhynchus mykiss are considered Steelhead trout. + + + + + + + https://fishbio.com/field-notes/inside-fishbio/spray-on-tan, accessed 05May2021 + 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 + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + The use of a DNA sample to identify fish which have known biomarkers. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000015 + A marine water body which is constitutes the majority of an astronomical body's hydrosphere. + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + One of the pelvic fins is removed using scissors. + + + + + + Total number of recruits of age class 0.8. + Age class 0.8 recruits + 2021-07-15T18:49:01Z + + + + + + https://nceas.github.io/sasap-training/materials/reproducible_research_in_r_fairbanks/example-brood-table-analysis.html, accessed 2021-06-16 + 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://en.wikipedia.org/wiki/Taxonomy_(biology), accessed 2021-04-28 + The name of the scientist or scientists who first validly published the scientific name of a particular organism. + + + + + + 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 + + Beach seine + 2021-04-01T18:01:54Z + + + + + + + + + + https://en.wikipedia.org/wiki/Johann_Julius_Walbaum, accessed 2021-04-26 +https://www.wikidata.org/wiki/Q68096, accessed 2021-04-26 + Johann Julius Walbaum (30 June 1724, Wolfenbüttel, Brunswick-Wolfenbüttel – 21 August 1799, Lübeck) was a German physician, naturalist and fauna taxonomist. + + + + + + Total number of recruits of age class 0.7. + Age class 0.7 recruits + 2021-07-15T18:48:49Z + + + + + + 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 + Tag based on application of a dilution of diazo dye in which fish are immersed and which stains the fins a brown/tan color. + + + + + + milliseconds elapsed + 2019-05-07T21:18:21Z + + + + + + Aquaculture + + 2021-04-02T22:18:14Z + The culturing of fish, shellfish, aquatic plants, and/or other organisms in captivity or under controlled conditions in the near shore environment. + http://vocab.nerc.ac.uk/collection/M13/current/018/ + + Aquatic farming +Aquafarming + In Alaska, the aquaculture industry primarily produces Pacific oysters, littleneck clams, and mussels for commercial food production. + + + + + + + Keta salmon + 2022-03-24T19:58:28Z + + + + + + + A tag which transmits information about a fish via an electronic receiver. + + + + + + + + + + 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. + trap + Pot + 2021-04-01T18:01:50Z + + + + + + 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. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28421 + + + + + + https://en.wikipedia.org/wiki/Dolly_Varden_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q327067, accessed 2021-06-15 + Salvelinus malma +S. malma +"Dolly Varden" @en + + + + + + http://purl.dataone.org/odo/ECSO_00001104 + The degree of hotness or coldness of a body or environment (corresponding to its molecular activity). + + + + + + Total number of recruits of age class 4.3. + Age class 4.3 recruits + 2021-07-15T18:54:15Z + + + + + + + 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)). + Personal use fishery + 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. + 2021-04-02T22:17:54Z + + + + + + river or stream name + 2019-04-25T22:17:53Z + + + + + + Total number of recruits of age class 0.6. + Age class 0.6 recruits + 2021-07-15T18:48:30Z + + + + + + 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. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25150 + + + + + + + + + + https://en.wikipedia.org/wiki/Salmon_escapement, accessed 2021-04-26 +https://www.wikidata.org/wiki/Q23582242, accessed 2021-04-26 + The number of salmon which do not get caught by commercial or recreational fisheries and return to their freshwater spawning habitat. + + + + + + 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. + Hatchery + Oftentimes, hatchery-reared salmon will have their adipose fins removed (i.e. clipped) to mark that they come from a hatchery (versus a wild stock). + The 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. + 2021-04-02T20:00:45Z + + + + + + + + + http://calfish.ucdavis.edu/species/?uid=39&ds=698 + Sea-running, i.e. anadromous individuals of Rainbow Trout, are called Steelhead. + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + https://www.adfg.alaska.gov/fedaidpdfs/FRED.132.pdf, accessed 2021-04-15 + 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://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + reproductiveStrategyOf + 2021-06-01T20:30:32Z + + + + + + Total number of recruits of age class 4.2. + Age class 4.2 recruits + 2021-07-15T18:54:08Z + + + + + + Total number of recruits of age class 1.9. + Age class 1.9 recruits + 2021-07-15T18:48:13Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000033 + A body of water, usually of smaller size than a lake. + Pond + 2021-04-07T18:47:40Z + + + + + + + A mark or tag which is placed beneath the skin of a fish. + + + + + + http://purl.dataone.org/odo/ECSO_00001231 + Objective comparative measure of hot or cold of water in a lake. + + + + + + + + + + http://purl.obolibrary.org/obo/ENVO_01000618 + A water body in which the accumulated water, in its totality, is flowing. + Lotic water body + 2021-04-07T18:44:17Z + + + + + + 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. + artisinal fishery +traditional fishery + Subsistence fishery + In Alaska, subsistence fisheries may not operate in "nonsubsistence areas" as designated by the state (AS 16.05.258(c)). + 2021-04-02T20:00:36Z + + + + + + signal quality + 2019-03-26T17:39:32Z + + + + + + + + + + + + Oncorhynchus keta + + + + + + + 2021-04-30T17:44:51Z + + + + + hasReproductiveStrategy + 2021-06-01T20:27:15Z + + + + + + + + Total number of recruits of age class 4.1. + Age class 4.1 recruits + 2021-07-15T18:54:02Z + + + + + + http://purl.obolibrary.org/obo/ENVO_01000617 + A water body in which the accumulated water, in its totality, has very little to no directed flow. + Lentic water body + 2021-04-07T18:47:13Z + + + + + + Total number of recruits of age class 1.8. + Age class 1.8 recruits + 2021-07-15T18:48:00Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000495 + 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. + affluent + Tributary + 2021-04-07T18:40:15Z + + + + + + + The alteration of a physical bodily feature of a fish, either internally or externally, for identification purposes. + + + + + + "POHL" is an acronym used by Alaska Department of Fish & Game (ADF&G) + POHL + + + + + + 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 + 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. + + + + + + https://en.wikipedia.org/wiki/Oxygen_saturation, accessed 22April2021 +https://www.wikidata.org/wiki/Q6294669, accessed 22April2021 + 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 (%). + + + + + + + 2021-04-30T17:44:44Z + + Oncorhynchus gorbuscha + + + + + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + The appearance of the otoliths (located in the inner ear of the fish) are changed. + + + + + + hasMigratoryPattern + 2021-06-01T20:26:57Z + + + + + + + Total number of recruits of age class 3.9. + Age class 3.9 recruits + 2021-07-15T18:52:44Z + + + + + + Total number of recruits of age class 1.7. + Age class 1.7 recruits + 2021-07-15T18:47:48Z + + + + + + https://www.merriam-webster.com/dictionary/grilse + a young Atlantic salmon returning to its native river to spawn for the first time after one winter at sea + + + + + + A fishery in which fishes and other seafood are harvested for pleasure or competition. + sport fishery + Recreational (sport) fishery + 2021-04-02T20:00:25Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000023 + A watercourse which is linear and flows across the solid portion of a planetary surface. + Stream + 2021-04-07T18:40:11Z + + + + + + 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. + Juvenile + 2021-04-29T19:11:32Z + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=wildlifenews.view_article&articles_id=693, accessed 2021-06-15 + 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). + + + + + + Total number of recruits of age class 6.5. + Age class 6.5 recruits + 2021-07-15T18:58:05Z + + + + + + A classification of fishes which spawn in marine habitats, migrate to freshwater areas to forage and mature, then return to marine habitats to spawn. + Catadromous + 2021-06-01T20:11:04Z + + + + + + https://en.wikipedia.org/wiki/Gigging, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q4412590, accessed 2021-04-01 + A multi-pronged spear, typically ranging in length from 8 to 14 feet, which is used to spear (or "gig") fishes for harvest. + + + + + + Total number of recruits of age class 3.8. + Age class 3.8 recruits + 2021-07-15T18:52:37Z + + + + + + Total number of recruits of age class 1.6. + Age class 1.6 recruits + 2021-07-15T18:47:36Z + + + + + + Artisanal fishery + http://www.oceansatlas.org/subtopic/en/c/1303/ + 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. + 2021-07-22T05:58:02Z + + + + + + 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://alaskasalmonandpeople.org/regions/, accessed 2021-04-16 + "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 + + + + + + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + A small, electronic, sound-emitting device which is placed inside a fish and collects information on that fish's physiology and/or movement patterns. + + + + + + hour of day + hour of measurement time + hour of day + 2019-01-14T22:40:52Z + + + + + + https://www.adfg.alaska.gov/static/license/fishing/pdfs/coar_fish_codes.pdf, accessed 04May2021 + ADF&G salmon species codes: + +410 salmon, chinook +420 salmon, sockeye +430 salmon, coho +440 salmon, pink +450 salmon, chum + + + + + + https://en.wikipedia.org/wiki/Seawater +https://www.wikidata.org/wiki/Q184395 + On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/l, 35 ppt, 599 mM). + + + + + + + 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). + + + + + + http://purl.dataone.org/odo/ECSO_00001523 + 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. + + + + + + Whole fish weight + 2021-06-23T18:46:24Z + + + + + + https://en.wikipedia.org/wiki/Fishing_weir, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q1417573, accessed 2021-04-01 + An obstruction placed in tidal waters, or wholly or partially across a river, to direct the passage of, or trap fish. + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=fishingaquaticfarming.programinfo, accessed 2021-04-02 + In Alaska, the aquaculture industry primarily produces Pacific oysters, littleneck clams, and mussels for commercial food production. + + + + + + A system which uses electromagnetic fields to automatically identify and track tags attached to objects. + Radio Frequency Identification + RFID + 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. + 2021-05-05T16:47:51Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000137 + An opening of the sea into the land. + Coastal inlet + 2021-04-15T18:39:14Z + + + + + + + 2021-05-27T19:40:11Z + Some populations of the coastal cutthroat trout (O. c. clarkii) are semi-anadromous. (source: https://en.wikipedia.org/wiki/Cutthroat_trout) + + + Oncorhynchus clarkii + + + + + + + Sexual dimorphic characteristic + A method that uses the presence or other features of a trait ("characteristic") of an organism to differentiate or assign gender + 2021-04-28T00:02:33Z + + + + + + https://doi.org/10.1577/M02-143, 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. + + + + + + longitude 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. + 2019-01-17T18:58:37Z + + + + + + month of year + 2019-01-14T22:26:35Z + + + + + + + + + + A quality of an ecological community that reflects how close in abundance all species in a community are. + + + + + + + + + + http://www.fao.org/fishery/geartype/202/en, accessed 01April2021 + 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 + + + + + + Project name + The label, acronym, or other preferred way to refer to a Project + 2021-06-23T18:22:30Z + + + + + http://purl.obolibrary.org/obo/ENVO_00000475 + An opening of the sea into the land, or of a lake into its shore. + Inlet + 2021-04-15T18:37:33Z + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=fry&language=english&sc=is, accessed 2021-04-21 + 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. + + + + + + 2021-04-26T20:19:15Z + The class which contains all instances of Oncorhynchus tshawytscha. + + 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. + Oncorhynchus tshawytscha + 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) + + + + O. tshawytscha + + + https://en.wikipedia.org/wiki/Commercial_fishing, accessed 2021-04-02 +https://www.wikidata.org/wiki/Q11202642, accessed 2021-04-02 + A fishery in which fishes and other seafood are harvested for commercial profit, mostly from wild fisheries. + + + + + + Fishery type + 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." + 2021-04-01T17:33:14Z + + + + + Hermaphrodite + Used to designate that some individual or individuals in a group of organisms possessed functional qualities of more than one gender, simultaneously or sequentially. + 2021-04-27T23:59:24Z + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=juvenile&language=english&sc=is, accessed 2021-06-15 + 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. + + + + + + A numeric value assigned to a scale gum card. + Gum card number + Gum cards are used to mount and label the identity of sampled fish scales. + 2021-06-23T17:34:31Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + A barbed plastic tag which is inserted under the dorsal fin of the fish using a cannula. + + + + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + When done correctly, this identification type will remain visible for the entire lifetime of the fish and can be used for group or individual marking. Neon or fluorescent colors are often used, and best placement is in light areas and fin rays, though even semi-transparent and transparent tissue may be suitable for easy visual reading. + + + + + + + + + A numeric or alphanumeric code which represents potential sources of error in determining the age of a fish specimen. + Age error code + 2021-06-23T17:53:09Z + + + + + + An identifier which represents a region or location in and is used in place of the full name. + Region or location code + 2021-05-12T17:37:57Z + + + + + + + + 2021-04-26T20:19:04Z + The class which contains all instances of Oncorhynchus nerka. + 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 + O. nerka + + + hasADF&GCode + 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. + 2021-05-27T18:00:35Z + + + + + + + Genetic sexing + 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 + 2021-04-27T23:57:56Z + + + + + + https://doi.org/10.1186/2050-3385-1-18, accessed 2021-05-05 + A scar made on the dermal tissue using liquid nitrogen. + + + + + + + + + https://en.wikipedia.org/wiki/Alkalinity, accessed 2021-04-22 +https://www.wikidata.org/wiki/Q432016, accessed 2021-04-22 + A measure of the quantitative capacity of an aqueous solution to neutralize an acid. + + + + + + latitude second component + 2019-01-28T21:37:49Z + + + + + + http://calfish.ucdavis.edu/species/?uid=39&ds=698 + Sea-running, i.e. anadromous individuals of Rainbow Trout are called Steelhead. + + + + + + 2021-05-11T17:26:46Z + + + Steelhead trout + + + + Oncorhynchus mykiss irideus +Oncorhynchus m. irideus +O. m. irideus +"steelhead" @en + 540 + + + + + + The total number of recruits which successfully return to spawn in freshwater habitats for a given brood year. + + + + + + "hasDbXref' is used here to indicate the equivalence of this Class with its usage in a Darwin Core context + http://rs.tdwg.org/dwc/terms/Occurrence + + + + + + Measurement types which pertain to any product of the condensation of atmospheric water vapor that falls under gravity. + Precipitation measurement type + 2021-04-14T22:31:36Z + + + + + + Pacific salmon + 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. + 2021-05-11T17:26:55Z + + + + + + + 2021-04-26T20:18:52Z + O. kisutch + 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 (i.e. coho salmon) is one of the five species of Pacific salmon. + +Physical Description: During their ocean phase, coho salmon have silver sides and dark-blue backs. During their spawning phase, their jaws and teeth become hooked. After entering fresh water, they develop bright-red sides, bluish-green heads and backs, dark bellies and dark spots on their backs. Sexually maturing fish develop a light-pink or rose shading along the belly, and the males may show a slight arching of the back. Mature adults have a pronounced red skin color with darker backs and average 28 inches (71 cm) and 7 to 11 pounds (3.2 to 5.0 kg), occasionally reaching up to 36 pounds (16 kg). They also develop a large kype (hooked beak) during spawning. Mature females may be darker than males, with both showing a pronounced hook on the nose. + +Range: The traditional range of the coho salmon runs along both sides of the North Pacific Ocean, from Hokkaidō, Japan and eastern Russia, around the Bering Sea to mainland Alaska, and south to Monterey Bay, California. Coho salmon have also been introduced in all the Great Lakes, as well as many landlocked reservoirs throughout the United States. A number of specimens, (more than 20), were caught in waters surrounding Denmark and Norway in 2017. Their source is currently unknown, but the salmon species is farmed at several locations in Europe, making it probable that the animal has slipped the net at such a farm. + + The class which contains all instances of Oncorhynchus kisutch. + Oncorhynchus kisutch + + + + Richardson, 1836 + Sir John Richardson (5 ovember 1787 - 5 June 1865) was a Scottish naval surgeon, naturalist and arctic explorer. + 2021-05-27T00:09:04Z + + + + + + Internal sex determination method + Determination of fish gender based on internal examination, e.g. examination of gonads + 2021-04-27T23:57:03Z + + + + + + 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. + Electrofishing + 2021-04-01T18:02:48Z + + + + + + 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). + SL + + Standard length + 2021-03-31T18:21:24Z + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-27 + The number of annuli on a given otolith. + + + + + + cruise name + 2019-03-15T23:48:23Z + + + + + + Oncorhynchus gorbuscha + 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. + O. gorbuscha + + 2021-04-26T20:17:52Z + + The class which contains all instances of Oncorhynchus gorbuscha. + + + 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) + + + latitude minute component + 2019-01-17T19:36:39Z + + + + + + https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-gillnets + A gillnet which is attached to poles fixed in the substrate or an anchor system to prevent movement of the net. + + + + + + + The removal of a portion or entirety of a fin or the maxilla of a fish, for identification purposes. + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=alevin&language=english&sc=is, accessed 2021-04-21 + Larval salmon that have hatched but have not yet completely absorbed their yolk sacs and usually have not yet emerged from the gravel. + + + + + + The class which contains all instances of Oncorhynchus keta. + + + + 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. + 2021-04-26T20:18:47Z + 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) + O. keta + + + Oncorhynchus keta + + + http://www.adfg.alaska.gov/index.cfm%3Fadfg=dollyvarden.main + Some Dolly Varden individuals are anadromous + + + + + + 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. + TL + + Total length + 2021-03-31T18:21:18Z + + + + + + + + + + + 2021-05-27T00:08:33Z + + + The class which contains all instances of Oncorhynchus clarkii. + 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) + O. clarkii + Oncorhynchus clarkii + + + + External sex determination method + Sex determined on basis of organism's external morphology + 2021-04-27T23:56:52Z + + + + + + https://www.adfg.alaska.gov/static/license/fishing/pdfs/coar_fish_codes.pdf, accessed 04May2021 + 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. + + + + + + + Oncorhynchus kisutch +O. kisutch +"silver salmon" @en +"silvers" @en + "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 + Coho salmon + 2021-04-16T18:11:22Z + + + + + + https://en.wikipedia.org/wiki/Standard_weight_in_fish, accessed 2021-06-16 +https://www.wikidata.org/wiki/Q7598325, accessed 2021-06-16 + 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://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + A metal plate with a unique identifying code, which is attached to a fish below the dorsal fin via two stainless steel wires. + + + + + + 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. + + Purse seine + 2021-04-01T18:02:44Z + + + + + + https://en.wikipedia.org/wiki/Oxygen_saturation, accessed 22April2021 +https://www.wikidata.org/wiki/Q6294669, accessed 22April2021 + 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. + + + + + + Salvelinus spp. + 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. + 2021-05-27T00:07:24Z + + + + + + latitude and longitude coordinates + 2019-01-29T00:50:47Z + + + + + + + http://courses.washington.edu/fish450/Lecture%20PDFs/Salmon_age_and_size_at_maturity.pdf, accessed 2021-04-06 + The sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching. + + + + + + https://arcos.disl.org/main/whatisDO#:~:text=Dissolved%20Oxygen%20is%20the%20amount,can%20affect%20dissolved%20oxygen%20levels, accessed 2021-04-22 + The amount of gaseous oxygen (O2) dissolved in water. + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, 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. + + + + + + https://www.fws.gov/guidance/sites/default/files/documents/Calcein_%28SE%20Mark%29_Study_Protocol.pdf, accessed 2021-05-05 + SE-MARK + + + + + + + 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 + "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 + Sockeye salmon + 2021-04-16T18:11:02Z + + + + + + + + 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. + Salvelinus malma + + S. malma + 2021-05-27T00:07:31Z + 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) + The class which contains all instances of Salvelinus malma. + + + + 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 +Mid-eye to fork of tail + + Mid-orbit to fork of tail length + 2021-03-31T18:20:33Z + + + + + + 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. + Proxy measurement type + [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 + 2021-04-27T22:01:23Z + + + + + + A gillnet which is kept afloat at the proper depth using a system of weights and buoys attached to the headrope, footrope, or floatline. + Drift gillnet + 2021-04-01T18:02:38Z + + + + + + + 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) + + + O. mykiss + 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. + 2021-05-27T00:06:44Z + 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. + + + + Oncorhynchus keta +O. keta +"dog salmon" @en +"keta salmon" @en +"silverbrite salmon" @en + "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 + Chum salmon + 2021-04-16T18:10:52Z + + + + + + Bycatch abundance + Amount of Bycatch + 2021-04-26T23:38:07Z + + + + + + 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. + 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 number of annuli on a given otolith. + Number of otolith annuli + 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. + 2021-04-27T21:37:46Z + + + + + + A multi-pronged spear, typically ranging in length from 8 to 14 feet, which is used to spear (or "gig") fishes for harvest. + Gig + 2021-04-01T18:02:33Z + + + + + + + Oncorhynchus gorbuscha +O. gorbuscha +"humpback salmon" @en +"humpbacked salmon" @en + "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 + Pink salmon + 2021-04-16T18:10:57Z + + + + + + A fish length measurement taken from the mid-orbit (i.e. eye) to the posterior insertion of the anal fin. + Mid-eye to posterior insertion of anal fin + + Mid-orbit to posterior insertion of anal fin length + The insertion of a fin is the posterior-most point where the fin connects with the body. + 2021-03-31T18:20:26Z + + + + + + A fish length measurement taken from the hind margin of the orbit to the hypural plate. + POHL + + Post orbit to hypural plate length + 2021-03-31T18:19:49Z + + + + + + geographic position measurement type + 2019-01-17T18:54:57Z + + + + + + S. salar + 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 is the only species of Atlantic salmon. + +Physical Description: Atlantic salmon are the largest species in their genus, Salmo. After two years at sea, the fish average 71 to 76 cm (28 to 30 in) in length and 3.6 to 5.4 kg (7.9 to 11.9 lb) in weight. The colouration of young Atlantic salmon does not resemble the adult stage. While they live in fresh water, they have blue and red spots. At maturity, they take on a silver-blue sheen. The easiest way of identifying them as an adult is by the black spots predominantly above the lateral line, though the caudal fin is usually unspotted. When they reproduce, males take on a slight green or red colouration. The salmon has a fusiform body, and well-developed teeth. All fins, except the adipose fin, are bordered with black. + The class which contains all instances of Salmo salar. + + 2021-05-27T00:02:46Z + Salmo salar + + + + Total number of recruits of age class 2.1. + Age class 2.1 recruits + 2021-07-15T18:49:46Z + + + + + + The number of salmon from a given population that escape the fishery in a day. + Daily escapement count + 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? + 2021-04-26T23:24:56Z + + + + + + latitude degree component + 2019-01-28T21:57:42Z + + + + + + https://en.wikipedia.org/wiki/Chum_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q475211, 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. + + + + + + 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. + Troll + 2021-04-01T18:02:30Z + + + + + + A fish length measurement taken from the middle of the orbit (i.e. eye) to the hypural plate. + Mid-eye to hypural plate +MEHL +MEPS +Mid-eye to posterior scale + + Mid-orbit to hypural plate length + 2021-03-31T18:19:56Z + + + + + + https://en.wikipedia.org/wiki/Sockeye_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q44064, 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. + + + + + + + + + + + + + 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 (%). + http://purl.dataone.org/odo/ECSO_00002386 + Dissolved oxygen saturation + DOsat + 2021-04-22T18:13:22Z + + 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. + http://purl.dataone.org/odo/ECSO_00002386 + + + + Fish weight proxy measurement type + 2021-07-16T19:32:02Z + + + + + + 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. + Acoustic tag + 2021-05-05T23:05:51Z + + + + + + Rainbow trout + 2021-06-15T20:05:20Z + + + + + + + + Total number of recruits of age class 6.8. + Age class 6.8 recruits + 2021-07-15T18:58:23Z + + + + + + + + + + + + 2021-04-30T17:44:59Z + + Oncorhynchus kisutch + + + + + + time of measurement + 2019-01-14T20:43:43Z + + + + + + The age class or life stage of the biological individual(s) at the time the occurrence was recorded. + http://rs.tdwg.org/dwc/terms/lifeStage + Life history stage of salmonid fish + 2021-04-21T23:42:02Z + + + + + + A small, electronic, sound-emitting device which is placed inside a fish and collects information on that fish's physiology and/or movement patterns. + Internal acoustic tag + 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. + 2021-05-05T16:20:13Z + + + + + + Total number of recruits of age class three. + Age class 3.x recruits + 2021-06-17T16:30:49Z + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=adult&language=english&sc=is, accessed 2021-04-21 + Fish that have fully developed morphological and meristic characters and that have attained sexual maturity. + + + + + + https://en.wikipedia.org/wiki/Radio-frequency_identification, accessed 2021-05-05 +https://www.wikidata.org/wiki/Q104954, accessed 2021-05-05 + 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. + + + + + + The alteration of a physical bodily feature of a fish, either internally or externally, for identification purposes. + Fish body modification + 2021-05-05T17:26:06Z + + + + + + Total number of recruits of age class two. + Age class 2.x recruits + 2021-06-17T16:30:43Z + + + + + + + Oncorhychus mykiss +O. mykiss +"lake trout" @en +"rainbow" @en +"silver trout" @en +"steelhead" @en +"brook trout" @en + Rainbow trout + 2021-06-15T20:05:01Z + + + + + + Total number of recruits of age class 6.7. + Age class 6.7 recruits + 2021-07-15T18:58:16Z + + + + + + Taxon (name) + 2022-02-04T02:06:35Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1548, 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. + + + + + + Immature + 2021-04-21T21:15:55Z + + + + + + The use of a DNA sample to identify fish which have known biomarkers. + Genetic identification + 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. + 2021-05-04T23:17:57Z + + + + + + The amount of gaseous oxygen (O2) dissolved in water. + DO + Dissolved oxygen measurement type + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-22T18:12:58Z + + + + + + + Gum cards are used to mount and label the identity of sampled fish scales. + + + + + + hour and minute of measurement time + 2019-01-16T00:19:09Z + + + + + + station identifier + Identifier associated, in some context, with a "station", i.e. a location having some established facilities for doing scientific research + 2019-02-20T18:41:50Z + + + + + + longitude minute component + 2019-01-17T22:52:26Z + + + + + + + + Oncorhynchus kisutch +O. kisutch +"silver salmon" @en +"silvers" @en + + + + + + Total number of recruits of age class one. + Age class 1.x recruits + 2021-06-17T16:30:32Z + + + + + + 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. + Measurement method + 2021-04-12T23:21:32Z + + + + + Simultaneous 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. + 2022-02-03T22:55:07Z + + + + + + An integer, which represents the sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching. + Fish total age + 2021-06-15T19:26:05Z + + + + + + A stream that is usually smaller than a river. + Brook + Creek + Term not currently in ENVO, will be submitted for consideration to ENVO curation team. 03AUG2021 + 2021-04-15T18:50:11Z + + + + + + Total number of recruits of age class 6.6. + Age class 6.6 recruits + 2021-07-15T18:58:10Z + + + + + + + A colored marking, which is placed beneath the skin of a fish for identification. + + + + + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + + + + A small metal pin which is inserted into the fish, usually into the cartilage of the snout. + CWT + Coded wire tag + 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. + 2021-05-04T23:17:44Z + + + + + + + Alkalinity which is measured in seawater. + Seawater alkalinity + 2021-04-22T17:45:58Z + + + + + + A colored marking, which is placed beneath the skin of a fish for identification. + Subcutaneous color mark + 2021-05-05T17:00:38Z + + + + + + search for '[NEEDS ALIGNMENT]' to find terms that should have owl:equivalentClass assertions (but were removed for now b/c Protege was having issues) + 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 '[ADDRESS COMMENT, THEN DELETE]' to find terms that need further review + + + https://en.wikipedia.org/wiki/Cutthroat_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q2717060, accessed 2021-06-15 + 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. + + + + + + + Volume of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000476 + An opening of a lake into its shore. + Lake inlet + 2021-04-15T18:47:50Z + + + + + + The number of sea lice counted on an individual fish. + Sea lice count + 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. + 2021-06-23T18:54:56Z + + + + + + Total number of recruits of age class zero. + Age class 0.x recruits + 2021-06-17T16:30:26Z + + + + + + Total number of recruits of age class 8.9. + Age class 8.9 recruits + 2021-07-15T19:36:45Z + + + + + + 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://alaskasalmonandpeople.org/regions/, accessed 2021-04-16 + "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 + + + + + + http://www.fishbase.us/glossary/Glossary.php?q=parr&language=english&sc=is, accessed 2021-06-15 + A young salmonid (salmon or trout) with parr-marks before migration to the sea and after dispersal from the redd. + + + + + + + A stock that is sustained by natural spawning and rearing in the natural habitat, regardless of parentage or origin. + Wild stock + 2021-06-14T23:05:21Z + + + + + + Sequential hermaphrodite + 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. + 2022-02-03T22:54:57Z + + + + + + + A community species diversity that is the ratio between regional and local species diversity. + + + + + + http://purl.dataone.org/odo/ECSO_00002895 + Alkalinity which is measured in freshwater. + Freshwater alkalinity + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-04-22T17:45:49Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000016 + A large expanse of saline water usually connected with an ocean. + Sea + 2021-04-12T21:38:14Z + + + + + + station name + 2019-02-20T18:28:45Z + + + + + + An ink solution, which is injected into the skin. + Tattoo + 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. + 2021-05-05T17:00:08Z + + + + + + measurement start time + 2019-01-14T21:55:20Z + + + + + + elapsed time + 2019-01-16T00:27:36Z + + + + + + http://orcid.org/0000-0002-5300-3075 + A measurement type taken of some physical, biological, or ecological aspect of a fish or fishes. + + + + + + + The unique alphanumeric code or marking color(s) of a tagged fish. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000039 + A long and narrow sea inlet with high steeply sloped walled sides. A fjord is a landform created during a period of glaciation. + Fjord + 2021-04-15T18:40:03Z + + + + + + Fish parasite measurement type + 2021-06-23T18:53:19Z + + + + + + + + + The number of salmon which survive to reach legal age and/or size for harvest. Recruits include both individuals that are captured by a fishery and individuals that escape the fishery -- total recruitment is calculated as catch plus escapement. + Total recruit abundance + Recruits do not include individuals lost to predation. + 2021-06-17T16:16:10Z + + + + + + Total number of recruits of age class 8.8. + Age class 8.8 recruits + 2021-07-15T19:36:40Z + + + + + + 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 + A small, electronic, sound-emitting device which is attached externally to a fish and collects information on fish movement patterns and the physical environment. + + + + + + A marking which is used to differentiate individual fish or groups of fish(es). + Fish tag or identification type + 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 + 2021-05-04T22:55:08Z + + + + + A colored two-component plastic which is injected into the fish's epidermis or fins. + VIE + Visible implant elastomer + 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. + 2021-05-05T16:58:54Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00001999 + A significant accumulation of saline water which is part of a marine biome. + marine waterbody +body of marine water + Marine water body + On average, seawater in the world's oceans has a salinity of about 3.5% (35 g/l, 35 ppt, 599 mM). + 2021-04-12T21:36:50Z + + + + + + date and time of measurement + 2019-01-14T21:16:02Z + + + + + + Chose not to assert owl:equivalentClass here, because all Rainbow trout are Oncorhynchus mykiss, but not all Oncorhynchus mykiss are considered Rainbow trout. + + + + + + + https://en.wikipedia.org/wiki/Taxonomy_(biology), accessed 2021-04-28 + 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". + + + + + + https://www.fishbase.in/glossary/Glossary.php?q=standard+length, accessed 2021-03-31 + 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). + + + + + + "POFK" is an acronym used by Alaska Department of Fish & Game (ADF&G) + POFK + + + + + + hours elapsed + 2019-01-16T00:23:41Z + + + + + + http://purl.obolibrary.org/obo/ENVO_01000617 + A water body in which the accumulated water, in its totality, has very little to no directed flow. + + + + + + + + + The weight of a specimen's stomach, taken after the stomach has been dissected from the fish and emptied of its contents. + Weight of empty stomach + 2021-06-23T18:47:15Z + + + + + + https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-gillnets + A gillnet which is kept afloat at the proper depth using a system of weights and buoys attached to the headrope, footrope, or floatline. + + + + + + A group of individuals of the same species that have the same age. + Age class + For example, salmon of age class 2 include all individuals in a population of interest that are two years old. + 2021-06-17T16:11:34Z + + + + + + Total number of recruits of age class 8.7. + Age class 8.7 recruits + 2021-07-15T19:36:34Z + + + + + + http://purl.dataone.org/odo/ECSO_00001749 + A measure of the quantitative capacity of an aqueous solution to neutralize an acid. + Alkalinity measurement type + 2021-04-22T17:28:15Z + + + + + + The appearance of the otoliths (located in the inner ear of the fish) are changed. + Otolith marking + 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. + 2021-05-05T16:55:56Z + + + + + + A material entity which determines an environmental system. + http://purl.obolibrary.org/obo/ENVO_00002297 + Environmental feature + 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) + 2021-04-12T19:49:29Z + + + + + http://purl.obolibrary.org/obo/ENVO_00000393 + 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. + Sound + 2021-04-15T18:39:58Z + + + + + + https://en.wikipedia.org/wiki/Region + 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. + + + + + + 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 full stomach + 2021-06-23T18:47:09Z + + + + + + https://www.salmonography.com/Salmonid-Topic/Jack-Salmon/ + 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. + + + + + + https://www.seagrant.wisc.edu/our-work/focus-areas/fish-and-fisheries/fish-glossary/, accessed 2021-03-31 + The insertion of a fin is the posterior-most point where the fin connects with the body. + + + + + + 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. + Standard weight + 2021-06-16T22:57:49Z + + + + + + Total number of recruits of age class 8.6. + Age class 8.6 recruits + 2021-07-15T19:36:25Z + + + + + + An appearance that varies between individuals. + Natural pattern or unique marking + 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. + 2021-05-05T16:54:30Z + + + + + + 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. + G-R notation +G-R + Fish age (Gilbert-Rich notation) + 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'. + 2021-04-09T18:52:00Z + + + + + + https://en.wikipedia.org/wiki/Atlantic_Ocean, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q97, accessed 2021-06-15 + 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. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000138 + A circular or round inlet with a narrow entrance. + Cove + 2021-04-15T18:39:55Z + + + + + + + A marking which is used to differentiate individual fish or groups of fish(es). + + + + + + latitude coordinate + 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. + 2019-01-17T18:57:21Z + + + + + + https://en.wikipedia.org/wiki/Dolly_Varden_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q327067, 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. + + + + + + minute of hour + minute of measurement time + minute of hour + 2019-01-16T00:29:17Z + + + + + + measurement end time + 2019-01-14T21:55:34Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + A colored two-component plastic which is injected into the fish's epidermis or fins. + + + + + + https://en.wikipedia.org/wiki/Identifier, accessed 2021-06-22 +https://www.wikidata.org/wiki/Q853614, accessed 2021-06-22 + 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/Creek, accessed 2021-04-15 +https://www.wikidata.org/wiki/Q63565252, accessed 2021-04-15 + A stream that is usually smaller than a river. + + + + + + Stomach weight + 2021-06-23T18:46:59Z + + + + + + The weight of a fish, taken after the specimen has been frozen. + Frozen weight + 2021-06-16T22:54:03Z + + + + + + https://www.fishbase.se/Glossary/Glossary.php?q=wild+stock&language=english&sc=is, accessed 2021-06-15 + A stock that is sustained by natural spawning and rearing in the natural habitat, regardless of parentage or origin. + + + + + + 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. + 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. + Passive Integrated Transponder tag +Microchip + PIT tag + 2021-05-05T16:47:58Z + + + + + + 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). + Fish age (European notation) + 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 + 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'. + 2021-04-09T18:49:30Z + + + + + + An area of water bordered by land on three sides. + Bay + 2021-04-15T18:39:18Z + + + + + + Salmo salar + 2021-05-27T19:45:43Z + + + + + + + + + + https://www.fws.gov/guidance/sites/default/files/documents/Calcein_%28SE%20Mark%29_Study_Protocol.pdf, accessed 2021-05-05 + 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://en.wikipedia.org/wiki/Electrofishing, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q1249133, accessed 2021-04-01 + 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. + + + + + + Year of fish harvest + 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. + 2021-05-04T17:21:40Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-03-31 + A fish length measurement taken from the middle of the orbit (i.e. eye) to the hypural plate. + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-15 + 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). + + + + + + http://orcid.org/0000-0002-5300-3075 + Objective comparative measure of hot or cold of water temperature in an aquatic environment. + + + + + + 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 + The number of years or winters a salmon spends in a freshwater environment as a free-swimming fish. + + + + + + http://purl.obolibrary.org/obo/PCO_0000076 + 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. + γ-diversity + Gamma diversity + 2021-06-04T22:01:04Z + + + + + + + The right pectoral fin of the fish is removed. + + + + + + Total number of recruits of age class 5.1. + Age class 5.1 recruits + 2021-07-15T18:55:44Z + + + + + + + King salmon + 2021-10-07T01:05:10Z + + + + + + Cutthroat trout + 2021-05-27T19:58:56Z + + + + + + + + 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 + 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." + + + + + + Total number of recruits of age class 2.4. + Age class 2.4 recruits + 2021-07-15T18:50:08Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1551, accessed 2021-06-14 + 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://en.wikipedia.org/wiki/Coastal_cutthroat_trout, accessed 2021-06-18 +https://www.wikidata.org/wiki/Q5138345, accessed 2021-06-18 + O. c. clarkii +Onchorhynchus c. clarkii +sea-run cutthroat trout +blueback trout +harvest trout + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-06-14 + 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. + + + + + + creek name + 2019-03-15T23:46:34Z + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-15 + 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. + + + + + + + + Kokanee salmon + + 2021-08-03T22:40:10Z + + + + + + 2021-04-30T17:45:49Z + Sockeye salmon + + + + + + + 420 + + + + A standardized notation format for describing the age of a salmon. + Fish age notation type + 2021-04-22T00:00:42Z + + + + + + https://en.wikipedia.org/wiki/Atlantic_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q188879, 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. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000138 + A circular or round inlet with a narrow entrance. + + + + + + https://en.wikipedia.org/wiki/Chinook_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q833503, 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. + + + + + + Total number of recruits of age class 7.4. + Age class 7.4 recruits + 2021-07-15T19:35:09Z + + + + + + http://purl.obolibrary.org/obo/PCO_0000075 + A community species diversity that is the ratio between regional and local species diversity. + β-diversity + Beta diversity + 2021-06-04T22:00:59Z + + + + + + Total number of recruits of age class 4.9. + Age class 4.9 recruits + 2021-07-15T18:54:45Z + + + + + + 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 + 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'. + + + + + + Dolly Varden trout + 2021-05-27T19:58:43Z + + 531 + + + + + + + Total number of recruits of age class 2.3. + Age class 2.3 recruits + 2021-07-15T18:50:00Z + + + + + + https://en.wikipedia.org/wiki/Oncorhynchus, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q133325, accessed 2021-06-15 + 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"). + + + + + + "MEHL" is an acronym used by Alaska Department of Fish & Game (ADF&G) + Mid-eye to hypural plate +MEHL +MEPS +Mid-eye to posterior scale + + + + + + https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-03-31 +https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31 + A fish length measurement taken from the hind margin of the orbit to the tip of the median caudal fin rays. + + + + + + https://en.wikipedia.org/wiki/Fish_wheel, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q5454688, accessed 2021-04-01 + 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. + + + + + + + + + + Total number of recruits of age class 2.2. + Age class 2.2 recruits + 2021-07-15T18:49:54Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000039 + A long and narrow sea inlet with high steeply sloped walled sides. A fjord is a landform created during a period of glaciation. + + + + + + Pink salmon + + 440 + + + + + + + + + + + + + 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). + Numeric age of fish + 2021-04-22T00:00:18Z + + + + + + 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://alaskasalmonandpeople.org/regions/, accessed 2021-04-16 + "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 + + + + + + http://purl.dataone.org/odo/ECSO_00001164 + A measure of the saltiness or dissolved salt content of a body of water. + + + + + + A young salmonid (salmon or trout) with parr-marks before migration to the sea and after dispersal from the redd. + Parr + 2021-06-16T04:18:20Z + + + + + + https://en.wikipedia.org/wiki/Longitude + 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. + + + + + + Total number of recruits of age class 7.3. + Age class 7.3 recruits + 2021-07-15T19:35:00Z + + + + + + http://purl.obolibrary.org/obo/PCO_0000074 + A community species diversity that is the mean species diversity at a site or within a specific habitat. + α-diversity + Alpha diversity + 2021-06-04T22:00:56Z + + + + + + Total number of recruits of age class 4.8. + Age class 4.8 recruits + 2021-07-15T18:54:40Z + + + + + + Atlantic salmon + 2021-05-27T19:58:37Z + + + + + + + http://orcid.org/0000-0002-5300-3075 + Equipment which is used to harvest aquatic resources, and in particular fish(es). + + + + + + https://en.wikipedia.org/wiki/Body_of_water, accessed 2021-03-30 + 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. + + + + + + + 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. + + + + + + Salvelinus malma + Some Dolly Varden individuals are anadromous + 2021-05-27T19:45:59Z + + + + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + has scientific name + + + + + Coho salmon + + + + + + + 2021-04-30T17:45:43Z + + + 430 + + + + Fish that have fully developed morphological and meristic characters and that have attained sexual maturity. + Adult + 2021-04-21T23:42:40Z + + + + + + study location name + 2019-04-24T00:15:35Z + + + + + + 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. + Dye tag + [NEEDS ALIGHMENT] + +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C461 + 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 + 2021-05-05T16:26:27Z + + + + + + https://en.wikipedia.org/wiki/Rainbow_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q187986, 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. + + + + + + https://spo.nmfs.noaa.gov/sites/default/files/legacy-pdfs/leaflet488.pdf, accessed 2021-04-15 + 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. + + + + + + + + + 2021-06-15T23:43:41Z + Coastal rainbow trout + + + + + + + + Total number of recruits of age class 7.2. + Age class 7.2 recruits + 2021-07-15T19:34:51Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00002297 [DEPRECATED] + A material entity which determines an environmental system. + + + + + + http://purl.obolibrary.org/obo/PCO_0000019 + 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. + Species diversity + 2021-06-04T22:00:50Z + + + + + + Total number of recruits of age class 4.7. + Age class 4.7 recruits + 2021-07-15T18:54:35Z + + + + + + http://purl.obolibrary.org/obo/ENVO_01000618 + A water body in which the accumulated water, in its totality, is flowing. + + + + + + https://www.monitoringresources.org/Document/Method/Details/1551, accessed 2021-03-31 + 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://en.wikipedia.org/wiki/Semelparity_and_iteroparity#Semelparity, accessed 01June2021 +https://www.wikidata.org/wiki/Q522960, accessed 01June2021 + A reproductive strategy which is characterized by multiple reproductive cycles over the course of an organism's lifetime. + + + + + + has vernacular name + + + + + Total number of recruits of age class 4.6. + Age class 4.6 recruits + 2021-07-15T18:54:29Z + + + + + + + 2021-04-30T17:45:41Z + + 450 + + + + + + Chum salmon + + + 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. + Fry + 2021-04-21T23:42:38Z + + + + + + A scar made on the dermal tissue using liquid nitrogen. + Freeze brand + 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. + 2021-05-05T16:25:55Z + + + + + + 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://alaskasalmonandpeople.org/regions/, accessed 2021-04-16 + "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 + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + + + + Sea-running, i.e. anadromous individuals of Rainbow Trout are called Steelhead. + + Oncorhynchus mykiss irideus + + 2021-06-15T23:34:02Z + + + + + Total number of recruits of age class 7.1. + Age class 7.1 recruits + 2021-07-15T19:34:44Z + + + + + + http://purl.dataone.org/odo/ECSO_00001237 + Volume of precipitation, which is any product of the condensation of atmospheric water vapor that falls under gravity. + Precipitation volume + 2021-06-04T21:13:21Z + + + + + + + 410 + + + 2021-04-30T17:45:38Z + + + + Chinook salmon + + + + Egg abundance + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-06-01T22:28:19Z + + + + + + 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. + Smolt + 2021-04-21T23:42:21Z + + + + + + https://en.wikipedia.org/wiki/John_Richardson_(naturalist), accessed 2021-06-15 +https://www.wikidata.org/wiki/Q545944, accessed 2021-06-15 + Sir John Richardson (5 ovember 1787 - 5 June 1865) was a Scottish naval surgeon, naturalist and arctic explorer. + + + + + + Total number of recruits of age class 4.5. + Age class 4.5 recruits + 2021-07-15T18:54:24Z + + + + + + 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. + SE-MARK + Calcein dye tag + Though not well studied, this type of identification may last up to 3 years post-immersion, and is used for group marking. + 2021-05-05T16:24:43Z + + + + + + + Dog salmon + + + + + 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. + Measuring the girth of a fish + 2021-07-16T19:37:41Z + + + + + + + + + + Gibbons, 1855 + 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. + 2021-06-15T23:33:16Z + + + + + + Age class 8.x recruits + Total number of recruits of age class 8 + + + + + + + Oncorhynchus gorbuscha +O. gorbuscha +"humpback salmon" @en +"humpbacked salmon" @en + + + + + + https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-03-31 + A fish length measurement taken from the hind margin of the orbit to the hypural plate. + + + + + + + The weight of a fish, typically taken when the specimen is still alive or freshly deceased, but before being frozen or further processed. + + + + + + + An identifier, which may be assigned to a physical sample taken from a fish (e.g. tissue, fin, otolith) or an entire fish specimen. + + + + + + https://www.solitudelakemanagement.com/blog/know-your-pond-life-fin-clipping-for-fisheries-management-success/, accessed 2021-05-05 + A portion of the upper caudal fin lobe is removed. + + + + + + Larval salmon that have hatched but have not yet completely absorbed their yolk sacs and usually have not yet emerged from the gravel. + Alevin + 2021-04-21T23:42:13Z + + + + + + Age class 7.x recruits + Total number of recruits of age class 7 + + + + + Tag based on application of a dilution of diazo dye in which fish are immersed and which stains the fins a brown/tan color. + Bismarck brown +Machester brown +Phenylene brown +Bismarck brown Y +C.I. 21000 +C.I. Basic Brown 1 +Basic Brown 1 +Vesuvine BA + Bismarck brown dye tag + 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 + 2021-05-05T16:23:36Z + + + + + + Smolt abundance + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 2021-06-01T22:27:09Z + + + + + + Total number of recruits of age class 4.4. + Age class 4.4 recruits + 2021-07-15T18:54:20Z + + + + + + + A standardized notation format for describing the age of a salmon. + + + + + + Total number of recruits of age class five. + Age class 5.x recruits + 2021-06-17T16:31:10Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, 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. + + + + + + Fish weight determination method + 2021-07-16T19:37:18Z + + + + + + + + + 2021-04-30T17:45:30Z + + + Oncorhynchus tshawytscha + + + + + + + + + + + data quality flag + 2018-11-30T05:06:08Z + + + + + + https://en.wikipedia.org/wiki/Temperature, accessed 2021-04-22 +https://www.wikidata.org/wiki/Q11466, accessed 2021-04-22 + The objective measure of hot or cold in freshwater (i.e. non-saline water). + + + + + + 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 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 adipose fin is removed using scissors or a razor blade. + Adipose fin clip + When done correctly, this identification type will last the entire life of the fish, and is used for group marking. + 2021-05-05T16:20:22Z + + + + + + Oncorhynchus mykiss irideus + + + + + Total number of recruits of age class 6.9. + Age class 6.9 recruits + 2021-07-15T18:58:29Z + + + + + + A concentration of the amount of oxygen present in water. + DO concentration + Dissolved oxygen concentration + http://purl.dataone.org/odo/ECSO_00001669 + 2021-04-22T18:13:32Z + + + + + + migratoryPatternOf + 2021-06-01T20:31:46Z + + + + + + https://en.wikipedia.org/wiki/Trolling_(fishing), accessed 2021-04-01 + 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. + + + + + + Subcutaneous tag + A mark or tag which is placed beneath the skin of a fish. + 2021-05-05T23:07:11Z + + + + + + Julian day fractional + fractional day of year + Julian day fractional + 2019-01-15T18:52:39Z + + + + + + Total number of recruits of age class four. + Age class 4.x recruits + 2021-06-17T16:31:03Z + + + + + + + + + + + + + Oncorhynchus nerka + + + + + + 2021-04-30T17:45:08Z + + + In fish, the term egg usually refers to female haploid gametes. + Egg + 2021-04-21T23:42:09Z + + + + + + A measurement taken around the thickest portion of the midsection of a fish. + Girth of fish + 2021-07-16T19:32:26Z + + + + + + + The number of sea lice counted on an individual fish. + + + + + + Organism name or identifier + 2021-08-12T17:29:30Z + + + + + Commercial harvest count + Estimates of number of fish caught based on some commerical harvest + 2021-04-28T18:15:54Z + + + + + + Unknown sex + 2021-04-19T18:26:55Z + + + + + + minutes elapsed + 2019-05-04T00:30:14Z + + + + + + + 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). + + + + + + https://www.fishbase.in/glossary/Glossary.php?q=standard+length, accessed 2021-03-31 + 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. + + + + + + Jack + 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. + 2021-07-22T02:55:24Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 05May2021 + 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://en.wikipedia.org/wiki/Hand_net, accessed 2021-04-01 +https://www.wikidata.org/wiki/Q640082, accessed 2021-04-01 + 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. + + + + + + Fishing gear type + [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. + Equipment which is used to harvest aquatic resources, and in particular fish(es). + 2021-04-01T18:00:22Z + + + + + + 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. + + + + + + https://en.wikipedia.org/wiki/Rainbow_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q187986, accessed 2021-06-15 + Oncorhychus mykiss +O. mykiss +"lake trout" @en +"rainbow" @en +"silver trout" @en +"steelhead" @en +"brook trout" @en + + + + + + + + + + The number of recruits which survive to a legal age and/or size and are captured by a fishery. + Salmon harvest count + 2021-04-28T18:15:41Z + + + + + + Total number of recruits of age class 3.2. + Age class 3.2 recruits + 2021-07-15T18:52:05Z + + + + + + + + + + https://en.wikipedia.org/wiki/Stream, accessed 2021-04-07 +https://www.wikidata.org/wiki/Q47521, accessed 2021-04-07 + http://purl.obolibrary.org/obo/ENVO_00000023 + A watercourse which is linear and flows across the solid portion of a planetary surface. + + + + + + contains occurrence data about + Object property to enable linking an information-bearing object such as a dataset, to its assertion of some organismal occurrence (sensu Darwin Core) + 2021-08-12T01:42:16Z + + + + + + + The number of years or winters a salmon spends in a saltwater environment. + Saltwater age + 2021-04-06T23:14:20Z + + + + + + King salmon + 2021-07-21T23:27:40Z + + + + + + + + + + + + + Netting + 2021-04-01T18:46:07Z + + + + + + 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 'Salmon specimen and occurrence' to be the domain and 'Author citation' to be the range. + + + + + https://en.wikipedia.org/wiki/Salmo, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q310436, 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. + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + When done correctly, this identification type will last the entire life of the fish, and is used for group marking. + + + + + + Occurrence record(s) + http://rs.tdwg.org/dwc/terms/Occurrence + 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." + 2021-08-12T01:31:25Z + + + + + + The number of years or winters a salmon spends in a freshwater environment as a free-swimming fish. + Freshwater age + 2021-04-06T23:10:05Z + + + + + + Total number of recruits of age class 3.1. + Age class 3.1 recruits + 2021-07-15T18:51:54Z + + + + + + Red salmon + 2021-07-21T23:26:30Z + + + + + + + + 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). + Hand collection + 2021-04-01T18:47:27Z + + + + + + 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. + + + + 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. + + Seine + 2021-04-01T18:32:41Z + + + + + + lake name + 2019-03-26T22:54:25Z + + + + + + longitude degree component + 2019-01-28T21:35:36Z + + + + + + + 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. + + + + + + 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 + http://purl.obolibrary.org/obo/ENVO_00001999 + + + + + + Total number of recruits of age class 2.9. + Age class 2.9 recruits + 2021-07-15T18:50:43Z + + + + + + The sum of freshwater and marine annuli plus one to account for time spent in the gravel before hatching. + Total age + 2021-04-06T22:51:22Z + + + + + + Silver salmon + 2021-07-21T23:15:02Z + + + + + + + https://en.wikipedia.org/wiki/Fish_hatchery, accessed 2021-04-02 +https://www.wikidata.org/wiki/Q15615109, accessed 2021-04-02 + 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. + + + + + + The way in which age is determined for a given individual. + http://purl.dataone.org/odo/ECSO_00001602 + Fish age determination method + 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. + 2021-04-06T22:49:05Z + + + + + + + + + + Duration of a temporal entity. + + + + The way in which sex is determined for a given individual. + http://purl.dataone.org/odo/ECSO_00001601 + Fish sex determination method + 2021-04-06T22:50:14Z + + + + + + Total number of recruits of age class 2.8. + Age class 2.8 recruits + 2021-07-15T18:50:39Z + + + + + + Bristol Bay + 2021-08-10T22:44:31Z + + + + + + Dog salmon + 2021-07-21T23:13:40Z + + + + + + + https://en.wikipedia.org/wiki/Subregion + 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. + + + + + + https://www.adfg.alaska.gov/static/license/fishing/pdfs/coar_fish_codes.pdf, accessed 04May2021 + 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. + + + + + + The duration of time for which a fish has been alive. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25150 + Fish age measurement type + 2021-04-06T22:46:36Z + + + + + + + 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. + Gillnet + 2021-04-01T18:31:54Z + + + + + + + A numeric or alphanumeric code, which represents a particular species and may be recorded in place of a formal scientific or vernacular name. + + + + + + + + + + http://www.touchngo.com/lglcntr/akstats/statutes/title16/chapter05/section258.htm, accessed 2021-04-27 + In Alaska, subsistence fisheries may not operate in "nonsubsistence areas" as designated by the state (AS 16.05.258(c)). + + + + + + https://github.com/DataONEorg/sem-prov-ontologies + Salmon Ontology + 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 + https://creativecommons.org/publicdomain/zero/1.0/ + + https://orcid.org/0000-0002-5300-3075 +https://orcid.org/0000-0002-0381-3766 +https://orcid.org/0000-0003-0632-7576 +https://orcid.org/0000-0003-0077-4738 + + SALMON + 2021-04-12T11:02:10-07:00 + + + 0.3.1 + + 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. + https://github.com/DataONEorg/sem-prov-ontologies/issues + + + + In biological taxonomy, Type generically refers to the official name applied to a taxon. This Class constrains Type members as belonging to family Salmonidae + + + + + + https://en.wikipedia.org/wiki/Rainbow_trout, accessed 2021-06-16 +https://www.wikidata.org/wiki/Q187986, accessed 20212-06-16 + 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. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000475 + An opening of the sea into the land, or of a lake into its shore. + + + + + + Total number of recruits of age class 5.4. + Age class 5.4 recruits + 2021-07-15T18:56:01Z + + + + + + + The weight of a fish, taken after the specimen has been frozen. + + + + + + Total number of recruits of age class 2.7. + Age class 2.7 recruits + 2021-07-15T18:50:32Z + + + + + + Humpback salmon + 2021-07-21T23:13:14Z + + + + + + http://vocab.nerc.ac.uk/collection/M13/current/018/, accessed 2021-04-02 + https://en.wikipedia.org/wiki/Aquaculture, accessed 2021-04-02 +https://www.wikidata.org/wiki/Q188989, accessed 2021-04-02 + The culturing of fish, shellfish, aquatic plants, and/or other organisms in captivity or under controlled conditions in the near shore environment. + + + + + + + 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. + + + + + + valley name + 2019-03-25T22:43:37Z + + + + + + https://risaa.org/newsletter/0516/0516_09.pdf, accessed 2021-05-06 + A pectoral fin is removed, typically as close to the body as possible, using scissors or a razor blade. + + + + + + http://purl.obolibrary.org/obo/PCO_0000010 + The number of different species represented in an ecological community. + Species richness + 2021-06-04T22:06:09Z + + + + + + Total number of recruits of age class 5.3. + Age class 5.3 recruits + 2021-07-15T18:55:54Z + + + + + + + Humpback salmon + 2021-10-07T01:18:28Z + + + + + + Total number of recruits of age class 2.6. + Age class 2.6 recruits + 2021-07-15T18:50:27Z + + + + + + non-anadromous + Fish belonging to a taxon that is typically anadromous, that do not migrate seaward at some time in their life-cycle. + 2021-08-06T06:33:41Z + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + 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 measurement method + 2021-04-05T21:55:12Z + + + + + + http://purl.obolibrary.org/obo/MMO_0000000 + 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. + + + + + + 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 + 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://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + An ink solution, which is injected into the skin. + + + + + + http://purl.dataone.org/odo/ECSO_00000553 + A numerical value which represents the length of a fish, typically in units of millimeters, centimeters, or inches. + + + + + + + + + + + Year of commercial fish harvest + 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. + 2021-05-04T17:21:48Z + + + + + + http://purl.obolibrary.org/obo/PCO_0000023 + A quality of an ecological community that reflects how close in abundance all species in a community are. + Species evenness + 2021-06-04T22:05:10Z + + + + + + Total number of recruits of age class 5.2. + Age class 5.2 recruits + 2021-07-15T18:55:50Z + + + + + + + A quality that inheres in a population of organisms. + + + + + + + Silver salmon + 2021-10-07T01:15:21Z + + + + + + Total number of recruits of age class 2.5. + Age class 2.5 recruits + 2021-07-15T18:50:22Z + + + + + + https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-traps-and-pots, accessed 2021-04-01 + 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. + + + + + + year and season + 2019-01-22T22:55:13Z + + + + + + + + + + + + + http://purl.dataone.org/odo/ECSO_00001104 + 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. + + + + + + A body of structured information describing some topic(s) of interest. (schema.org) + + + + Total number of recruits of age class 0.5. + Age class 0.5 recruits + 2021-07-15T18:45:39Z + + + + + + A numeric or alphanumeric code, which represents a particular salmon stock and may be recorded in place of a formal scientific or vernacular name. + Fish stock code + 2021-06-17T17:12:48Z + + + + + + Anadromous Waters Catalog water body code +State of Alaska's Anadromous Waters Stream Catalog + AWC water body code + 2021-07-19T20:55:57Z + + + + + + https://en.wikipedia.org/wiki/Seine_fishing, accessed 01April2021 +https://www.wikidata.org/wiki/Q600580, accessed 01April2021 + 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. + + + + + + + A quality that inheres in a community. + + + + + + Pacific trout and char + 2021-03-30T21:00:02Z + + + + + + 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. + Distance between scale circuli + An Essential Salmon Variable (ESV) from the working list being developed by Graeme Diack et al. at the Atlantic Salmon Trust. + 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. + 2021-04-15T19:38:49Z + + + + + + + Salmo salar +S. salar + Atlantic salmon + Atlantic salmon are the only anadromous salmonid native to the Atlantic coast of North America. + 2021-05-26T23:51:30Z + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + 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. + + + + + + https://en.wikipedia.org/wiki/Fish_migration, accessed 01June2021 +https://www.wikidata.org/wiki/Q852569, accessed 01June2021 + A classification of fishes which spawn in marine habitats, migrate to freshwater areas to forage and mature, then return to marine habitats to spawn. + + + + + + + + + Total number of recruits of age class 0.4. + Age class 0.4 recruits + 2021-07-15T18:45:17Z + + + + + + Total number of recruits of age class six. + Age class 6.x recruits + 2021-06-17T16:31:20Z + + + + + + The right pectoral fin of the fish is removed. + Right pectoral fin clip + 2021-05-06T16:58:12Z + + + + + + A quality that inheres in a population of organisms. + Quality of a population measurement type + [NEEDS ALIGNMENT] + +http://purl.obolibrary.org/obo/PCO_0000003 + 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. + 2021-04-26T22:37:24Z + + + + + + Fish age proxy measurement type + Fish ages are often estimated using proxy measurements, such as the space or distance between scale circuli. + 2021-04-15T19:38:17Z + + + + + + data quality assessment measurement type + 2018-11-30T05:06:00Z + + + + + + + + Oncorhynchus keta +O. keta +"dog salmon" @en +"keta salmon" @en +"silverbrite salmon" @en + + + + + + https://www.monitoringresources.org/Document/Method/Details/1548, accessed 2021-06-14 +https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-06-14 + 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. + + + + + + http://purl.obolibrary.org/obo/ENVO_00000063 + An accumulation of water of varying size. + waterbody +body of water +aquatic feature + Water body + 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. + 2021-03-30T20:59:53Z + + + + + + observer confidence + 2019-03-19T21:55:20Z + + + + + + https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-gillnets, accessed 01April2021 + 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. + + + + + + days elapsed + 2019-01-16T21:22:28Z + + + + + + + + + + https://en.wikipedia.org/wiki/Semelparity_and_iteroparity#Semelparity, accessed 01June2021 +https://www.wikidata.org/wiki/Q522960, accessed 01June2021 + A reproductive strategy which is characterized by a single reproductive episode, typically before death. + + + + + + https://code.iczn.org/authorship/article-51-citation-of-names-of-authors/?frame=1, 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. + + + + + + https://en.wikipedia.org/wiki/Tributary, accessed 2021-04-07 +https://www.wikidata.org/wiki/Q159675, accessed 2021-04-07 + http://purl.obolibrary.org/obo/ENVO_00000495 + 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://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.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. + + + + + + Total number of recruits of age class 0.3. + Age class 0.3 recruits + 2021-07-15T18:44:58Z + + + + + + A pectoral fin is removed, typically as close to the body as possible, using scissors or a razor blade. + Pectoral fin clip + 2021-05-06T16:58:02Z + + + + + + https://www.geonames.org/3373405/atlantic-ocean.html + http://purl.obolibrary.org/obo/GAZ_0000034 + 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. + Atlantic Ocean + 2021-05-26T22:07:26Z + + + + + + Walbaum, 1792 + Johann Julius Walbaum (30 June 1724, Wolfenbüttel, Brunswick-Wolfenbüttel – 21 August 1799, Lübeck) was a German physician, naturalist and fauna taxonomist. + 2021-04-26T22:06:58Z + + + + + + An obstruction placed in tidal waters, or wholly or partially across a river, to direct the passage of, or trap fish. + fish weir +fishing weir +fishgarth +kiddle + Weir + 2021-04-01T18:01:41Z + + + + + + Fish abundance + 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. + 2021-04-28T21:29:53Z + + + + + + Place or location or region + Union of Place and Location to enable searching over both less and more precise named designations of Regions + 2021-03-30T20:59:48Z + + + + + + + day of month + 2019-01-16T21:15:01Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000032 + An area of water bordered by land on three sides. + + + + + + Total number of recruits of age class 0.1. + Age class 0.1 recruits + 2021-07-15T18:43:45Z + + + + + + Note that this ENVO term, 'environmental feature' is deprecated + http://purl.obolibrary.org/obo/ENVO_00002297 + + + + + + Temporal Measurement Type + temporal_MeasurementType + temporal_MeasurementType + + + + + Total number of recruits of age class 0.2. + Age class 0.2 recruits + 2021-07-15T18:44:37Z + + + + + + https://www.geonames.org/2363254/pacific-ocean.html + http://purl.obolibrary.org/obo/GAZ_00000360 + 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. + Pacific Ocean + 2021-05-26T22:07:09Z + + + + + + https://www.monitoringresources.org/Document/Method/Details/1549, accessed 2021-03-31 +https://www.monitoringresources.org/Document/Method/Details/4041, accessed 2021-03-31 + A fish length measurement taken from the middle of the orbit (i.e. eye) to the tip of the median caudal fin rays (i.e. fork). + + + + + + A 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). + Counting otolith annuli + 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 + 2021-04-15T19:27:37Z + + + + + + A gillnet which is attached to poles fixed in the substrate or an anchor system to prevent movement of the net. + set net + Set gillnet + 2021-04-01T18:01:36Z + + + + + + Traditional fishery + http://www.oceansatlas.org/subtopic/en/c/1303/ + 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. + 2021-07-22T05:57:23Z + + + + + + hasNativeWaterbody + 2021-05-26T21:41:26Z + + + + + + http://purl.dataone.org/odo/ECSO_00001225 + Objective comparative measure of hot or cold of air. + + + + + + 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). + Measuring the distance between scale circuli + 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 + 2021-04-15T19:25:23Z + + + + + + + Oncorhynchus clarkii +O. clarkii + Cutthroat trout + 2021-05-26T21:45:56Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000137 + An opening of the sea into the land. + + + + + + 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. + Spear + 2021-04-01T18:01:30Z + + + + + + https://en.wikipedia.org/wiki/Pink_salmon, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q673380, accessed 2021-06-15 + 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. + + + + + + + + + + + + + Sea-running, i.e. anadromous individuals of Rainbow Trout, are called Steelhead. + + + + + + Oncorhynchus mykiss + + 2021-05-26T21:27:02Z + + + 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 + The number of years or winters a salmon spends in a saltwater environment. + + + + + + Industrial Fishery + http://www.oceansatlas.org/subtopic/en/c/1303/ + 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). + 2021-07-22T05:53:20Z + + + + + + season + 2019-05-17T22:41:45Z + + + + + + http://semanticscience.org/resource/SIO_000414 + A spatial region whose boundaries are typically defined against some material frame of reference (like the earth). + + + + + + http://purl.obolibrary.org/obo/ENVO_00001999 + A significant accumulation of saline water which is part of a marine biome. + + + + + + + + + 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. + salmon wheel + Fish wheel + 2021-04-01T18:01:23Z + + + + + + http://purl.obolibrary.org/obo/ENVO_00000029 + A flowing body of water. + Watercourse + 2021-04-15T18:52:49Z + + + + + + A fishery in which fishes and other seafood are harvested for commercial profit, mostly from wild fisheries. + Commercial fishery + 2021-04-02T19:59:17Z + + + + + + https://en.wikipedia.org/wiki/Cutthroat_trout, accessed 2021-06-15 +https://www.wikidata.org/wiki/Q2717060, accessed 2021-06-15 + Oncorhynchus clarkii +O. clarkii + + + + + + Small-scale fishery + http://www.oceansatlas.org/subtopic/en/c/1303/ + 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. + 2021-07-22T05:52:51Z + + + + + + "MEFK" is an acronym used by Alaska Department of Fish & Game (ADF&G) + MEFK +Mid-eye to fork of tail + + + + + + https://jordbruksverket.se/download/18.38d764e9177375620998e232/1611738582157/Rapport-Fish-identification-marking-and-tagging-methods.pdf, accessed 2021-05-05 + An appearance that varies between individuals. + + + + + + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28421 + 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. + + + + + + + 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. + + + + + + + The number of different species represented in an ecological community. + + + + + + + + + + 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. + hook and line + Angling + 2021-04-01T18:01:18Z + + + + + + The name of the scientist or scientists who first validly published the scientific name of a particular organism. + taxonomic authority +authority + Author citation + For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758". + The 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. + 2021-04-28T20:18:16Z + + + + + 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 + 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/4041, accessed 2021-06-14 + 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. + + + + + + Fish biomass + A measurement of the weight of a fish, or of a sample of fish/fishes + 2021-04-28T18:42:51Z + + + + + + + + + + http://purl.obolibrary.org/obo/ENVO_00000393 + 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. + + + + + + http://vocab.nerc.ac.uk/collection/M13/current/015/, accessed 01April2021 + https://www.fisheries.noaa.gov/national/bycatch/fishing-gear-purse-seines, accessed 01April2021 + 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://en.wikipedia.org/wiki/Location + 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. + + + + + + https://en.wikipedia.org/wiki/River, accessed 2021-04-07 +https://www.wikidata.org/wiki/Q4022, accessed 2021-04-07 + http://purl.obolibrary.org/obo/ENVO_00000022 + A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. + + + + + + + + + A reference which is made to a taxon name along with a publication which explains how the author intends for the name to be applied. + taxonomic concept + Taxon concept + 2021-04-28T19:23:01Z + + + + + + + A measurement type taken of some physical, biological, or ecological aspect of a fish or fishes. + Fish measurement type + 2021-04-01T21:37:39Z + + + + + + Grilse + a young Atlantic salmon returning to its native river to spawn for the first time after one winter at sea + 2021-07-22T02:58:24Z + + + + + + https://en.wikipedia.org/wiki/Location + 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. + + + + + diff --git a/src/main/resources/ontologies/SALMON_alignment.owl b/src/main/resources/ontologies/SALMON_alignment.owl new file mode 100644 index 00000000..c6c4c76b --- /dev/null +++ b/src/main/resources/ontologies/SALMON_alignment.owl @@ -0,0 +1,639 @@ + + + + true + Age class 4.2 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000728. Existing uses should be updated where possible. + + + + + + true + Wet weight + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000659. Existing uses should be updated where possible. + + + + + + true + Oncorhynchus mykiss irideus + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000647. Existing uses should be updated where possible. + + + + + + true + Age class 2.4 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000712. Existing uses should be updated where possible. + + + + + + true + Age class 1.5 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000700. Existing uses should be updated where possible. + + + + + + true + Age class 3.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000667. Existing uses should be updated where possible. + + + + + + true + Age class 1.4 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000699. Existing uses should be updated where possible. + + + + + + true + Age class 3.3 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000720. Existing uses should be updated where possible. + + + + + + true + Total recruit abundance + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000663. Existing uses should be updated where possible. + + + + + + true + Age class 0.5 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000695. Existing uses should be updated where possible. + + + + + + true + Annual escapement count + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000480. Existing uses should be updated where possible. + + + + + term replaced by + + + + + true + Commercial harvest count + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000492. Existing uses should be updated where possible. + + + + + + true + Fish stock code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000671. Existing uses should be updated where possible. + + + + + + true + AWC water body code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000780. Existing uses should be updated where possible. + + + + + + true + Cutthroat trout + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000582. Existing uses should be updated where possible. + + + + + + true + Fish sex determination method + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000186. Existing uses should be updated where possible. + + + + + + true + Fishing gear type + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000142. Existing uses should be updated where possible. + + + + + + true + Coho salmon + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000243. Existing uses should be updated where possible. + + + + + + true + Distance between scale circuli + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000235. Existing uses should be updated where possible. + + + + + + true + Chinook salmon + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000239. Existing uses should be updated where possible. + + + + + + true + Age class 4.1 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000727. Existing uses should be updated where possible. + + + + + + true + Age class 8.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000755. Existing uses should be updated where possible. + + + + + 0.1 + Alignment ontology for The Salmon Ontology (SALMON) + + + + + This ontology contains a set of classes (and their alignments) for deprecated terms from The Salmon Ontology (SALMON). While patterns for deprecating terms in ontologies commonly involve retaining the deprecated term(s) in the main ontology, we've opted to move the deprecated terms into an alignment ontology. Our main justification for this choice is (1) that all publicly-accessible instances of deprecated terms were created before the first published release of SALMON and (2) we have sufficient authorship access to update these instances to use published terms. + 2022-07-18 + + + + true + Age class 2.3 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000711. Existing uses should be updated where possible. + + + + + + true + Age class 2.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000666. Existing uses should be updated where possible. + + + + + + true + Age class 1.3 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000698. Existing uses should be updated where possible. + + + + + + true + Rainbow trout + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000642. Existing uses should be updated where possible. + + + + + + true + Fish length determination method + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000630. Existing uses should be updated where possible. + + + + + + true + Subsistence fishery harvest count + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000783. Existing uses should be updated where possible. + + + + + + true + Age class 0.4 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000694. Existing uses should be updated where possible. + + + + + + true + Age class 6.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000670. Existing uses should be updated where possible. + + + + + + true + Sockeye salmon + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000242. Existing uses should be updated where possible. + + + + + + true + Mid-orbit to fork of tail length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000133. Existing uses should be updated where possible. + + + + + + true + Saltwater age + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000189. Existing uses should be updated where possible. + + + + + + true + ADF&G species code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000525. Existing uses should be updated where possible. + + + + + + true + Dolly Varden trout + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000569. Existing uses should be updated where possible. + + + + + + true + Post-orbit to fork of tail length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000129. Existing uses should be updated where possible. + + + + + + true + Fish sample code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000529. Existing uses should be updated where possible. + + + + + + true + Age class 3.2 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000719. Existing uses should be updated where possible. + + + + + + true + Age class 3.1 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000718. Existing uses should be updated where possible. + + + + + + true + Age class 5.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000669. Existing uses should be updated where possible. + + + + + + true + Age class 7.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000754. Existing uses should be updated where possible. + + + + + + true + Age class 2.2 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000710. Existing uses should be updated where possible. + + + + + + true + Age class 1.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000665. Existing uses should be updated where possible. + + + + + + true + Age class 1.2 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000697. Existing uses should be updated where possible. + + + + + + true + Recruits per spawner + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000782. Existing uses should be updated where possible. + + + + + + true + Chum salmon + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000240. Existing uses should be updated where possible. + + + + + + true + Age class 0.3 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000693. Existing uses should be updated where possible. + + + + + + true + Age error code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000681. Existing uses should be updated where possible. + + + + + + true + Gum card number + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000680. Existing uses should be updated where possible. + + + + + + true + Pink salmon + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000241. Existing uses should be updated where possible. + + + + + + true + Freshwater age + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000188. Existing uses should be updated where possible. + + + + + + true + Mid-orbit to posterior insertion of anal fin length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000132. Existing uses should be updated where possible. + + + + + + true + Brood year + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000520. Existing uses should be updated where possible. + + + + + + true + Fork length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000128. Existing uses should be updated where possible. + + + + + + true + Salmon abundance + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000504. Existing uses should be updated where possible. + + + + + + true + Age class 4.3 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000729. Existing uses should be updated where possible. + + + + + + true + Age class 0.6 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000705. Existing uses should be updated where possible. + + + + + + true + Age class 2.5 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000713. Existing uses should be updated where possible. + + + + + + true + Age class 4.x recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000668. Existing uses should be updated where possible. + + + + + + true + Age class 1.6 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000701. Existing uses should be updated where possible. + + + + + + true + Girth of fish + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000777. Existing uses should be updated where possible. + + + + + + true + Age class 3.4 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000721. Existing uses should be updated where possible. + + + + + + true + Sport fishery harvest count + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000785. Existing uses should be updated where possible. + + + + + + true + Age class 1.1 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000696. Existing uses should be updated where possible. + + + + + + true + Post orbit to hypural plate length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000130. Existing uses should be updated where possible. + + + + + + true + Daily escapement count + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000481. Existing uses should be updated where possible. + + + + + + true + Steelhead trout + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000570. Existing uses should be updated where possible. + + + + + + true + Fish biomass + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000493. Existing uses should be updated where possible. + + + + + + true + Age class 0.2 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000692. Existing uses should be updated where possible. + + + + + + true + Total age + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000187. Existing uses should be updated where possible. + + + + + + true + Age class 0.1 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000691. Existing uses should be updated where possible. + + + + + + true + Fish age (European notation) + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000200. Existing uses should be updated where possible. + + + + + + true + Mid-orbit to hypural plate length + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000131. Existing uses should be updated where possible. + + + + + + true + Fish length measurement type + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000127. Existing uses should be updated where possible. + + + + + + true + Fish sex measurement type + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000216. Existing uses should be updated where possible. + + + + + + true + ADF&G gear code + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000527. Existing uses should be updated where possible. + + + + + + true + Age class 2.1 recruits + This term is deprecated in favor of http://purl.dataone.org/odo/SALMON_00000709. Existing uses should be updated where possible. + + + + diff --git a/src/main/resources/ontologies/SASAP.owl b/src/main/resources/ontologies/SASAP.owl new file mode 100644 index 00000000..cbe7bd5d --- /dev/null +++ b/src/main/resources/ontologies/SASAP.owl @@ -0,0 +1,3592 @@ + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#arctic +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + In the Arctic region of Alaska, connections between salmon and people are in their infancy. Salmon are just one harbinger of change in this region. + +The bounding coordinates for this SASAP region are: +North: 71.4396 degrees +South: 67.7408 degrees +East: -136.684 degrees +West: -166.311 degrees + + + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.sfmission + A department within the government of Alaska with a mission to protect and improve the state's sport fishery resources. + + + + + + Working Group + SASAP working group and project support + Beginning in 2016, nine SASAP working groups formed – each composed of between 12 and 24 knowledge experts from a range of disciplines, backgrounds, and regions. Each participant brought his or her data and experiences for synthesis and analysis, while NCEAS provided logistical and technical support to facilitate each group’s innovative work. + +Each of the nine groups focused on specific issues related to salmon and people in Alaska: + +Four SASAP groups were tasked with integrating knowledge across multiple disciplines to understand the fundamental state of knowledge of Alaska’s salmon systems. The work of each group is presented for each of the major watersheds in Alaska in the Region section (https://alaskasalmonandpeople.org/regions/). + +An additional five working groups were selected to focus on specific research questions that provide insight into the pressures on salmon and salmon communities, as well as options for response to those pressures. Their work is presented in the Special Topics section (https://alaskasalmonandpeople.org/topics/). + 2021-03-25T18:45:38Z + + + + + Greg Roscicza + 2021-04-20T15:49:34Z + + + + + + + + + https://schema.org/affiliation + + 2021-03-25T19:00:26Z + An organization that this person is affiliated with. For example, a school/university, a club, or a team. + + isAffiliateOf + The SASAP project and its associated working groups were made up of researchers from a variety of academic, govenmental, etc. organizations from across the United States. The 'affiliateOf' object property connects SASAP researchers with their respective employer(s)/home institution(s) (at least what was considered to be their employer/home institution during the time when they worked on the SASAP project). + + + + + Matthew Catalano + 2021-04-20T15:32:36Z + + + + + + + + American-based college or university + 2021-04-21T17:33:35Z + + + + + + https://orcid.org/0000-0002-4244-2865 + Jorge Cornejo-Donoso + 2021-03-25T20:08:09Z + + + + + + + + Erika Gavenus + 2021-04-19T23:48:58Z + + + + + + + + + UC Berkeley +Berkeley + https://ror.org/01an7q238 + University of California, Berkeley + UC Berkeley's website is accessible at: https://www.berkeley.edu/ + 2021-04-21T16:38:19Z + + + + + + A department within the government of Alaska which manages commercial, subsistence, and personal use fisheries within the jurisdiction of the State of Alaska. + Alaska Department of Fish and Game, Division of Commercial Fisheries + The Division of Commercial Fisheries website is accessible at: https://www.adfg.alaska.gov/index.cfm?adfg=fishingcommercial.main + 2021-03-25T18:03:36Z + + + + + + + + A community-based nonprofit organization that combines advocacy, education and science toward its mission to protect Alaska’s Cook Inlet watershed and the life it sustains. Inletkeeper’s monitoring and science work builds credibility with scientists and resource managers, its education and advocacy efforts enhance stewardship and citizen participation, and together, these efforts translate into Inletkeeper’s ability to effectively ensure a vibrant and healthy Cook Inlet watershed. + Cook Inletkeeper + The Cook Inletkeeper's website is accessible at: https://inletkeeper.org/ + 2021-03-25T18:04:51Z + + + + + + + https://orcid.org/0000-0002-6689-9392 + Madeline Javonovich + 2021-04-20T16:09:17Z + + + + + + + + https://en.wikipedia.org/wiki/North_Slope_Borough,_Alaska +https://www.wikidata.org/wiki/Q511806 + The North Slope Borough is the northernmost borough in the US state of Alaska. + + + + + + + + + + + + + + + + + Peter Westley + 2021-03-25T18:58:18Z + + + + + + + + + + An institution of higher education and research, which grants academic degrees in a variety of subjects, and provides both undergraduate education and postgraduate education. + College or university + 2021-04-02T20:22:02Z + + + + + + + https://orcid.org/0000-0002-5415-3534 + Krista Oke + 2021-04-20T16:08:39Z + + + + + + + + https://orcid.org/0000-0003-4703-1974 + Jeanette Clark + 2021-03-25T20:08:02Z + + + + + + + + Lamont Albertson + 2021-04-20T15:48:56Z + + + + + + + + https://orcid.org/0000-0002-0258-9264 + Kristen B. Gorman + 2021-03-25T20:09:26Z + + + + + + + + Lewis Coggins + 2021-04-20T15:29:14Z + + + + + + + + McGill + https://ror.org/01pxwe438 + McGill University + McGill University's website is accessible at: https://www.mcgill.ca/ + 2021-04-21T17:32:35Z + + + + + + UCSC + https://ror.org/03s65by71 + University of California, Santa Cruz + UCSC's website is accessible at: https://www.ucsc.edu/ + 2021-04-21T16:34:58Z + + + + + + https://www.fws.gov/ + A bureau of the United States Department of the Interior whose mission is to work with others to conserve, protect and enhance fish, wildlife and plants and their habitats for the continuing benefit of the American people. + + + + + + A department within the government of Alaska which provides non-partisan budgetary and fiscal analysis to the Alaska Legislature. + LFD + Alaska Department of Legislative Finance + LFD's webpage is accessible at: https://www.legfin.akleg.gov/ + 2021-03-25T18:04:43Z + + + + + + + + + + + + + + + https://www.nhgis.org/ + The National Historical Geographic Information System (NHGIS) provides easy access to summary tables and time series of population, housing, agriculture, and economic data, along with GIS-compatible boundary files, for years from 1790 through the present and for all levels of U.S. census geography, including states, counties, tracts, and blocks. + + + + + + https://orcid.org/0000-0001-5923-4133 + Patricial M. Clay + 2021-04-19T23:53:46Z + + + + + + + + + UBC + https://ror.org/03rmrcq20 + The University of British Columbia + UBC's website is accessible at: https://www.ubc.ca/ + 2021-04-21T16:40:45Z + + + + + + A department within the government of Alaska and a sub-division of the Alaska Department of Fish and Wildlife, Division of Commercial Fisheries which manages the Central Region. + Alaska Department of Fish and Game, Division of Commercial Fisheries, Central Region + Central Region Alaska commercial fisheries are composed of four distinct management areas that include Bristol Bay, Prince William Sound and Copper River, Upper Cook Inlet, and Lower Cook Inlet. Although all 5 species of salmon are harvested in each area, sockeye and pink salmon are the most abundant and most valuable. This area encompasses some of the largest and most valuable salmon fisheries in the world. From Bristol Bay, home of the largest sockeye salmon fishery in the world, to the Copper River where sockeye and Chinook salmon fetch some of the highest prices per pound paid to commercial fishermen. Cook Inlet commercial fisheries occur near the largest population center in Alaska, providing salmon to numerous niche and local markets, as well as fresh salmon to markets in other states. Prince William Sound adds productive healthy pink, chum, and sockeye salmon fisheries to the region. Southcentral groundfish fisheries are small, yet diverse, targeting pollock, Pacific cod, rockfish, sablefish, lingcod, and skate while small shrimp and scallop fisheries in Prince William Sound cater predominately to local markets. Southcentral commercial fisheries are of tremendous importance and an integral part of many communities and local economies in the state. + 2021-03-25T18:04:02Z + + + + + + + + DFO + Fisheries and Oceans Canada + DFO's website is accessible at: https://www.dfo-mpo.gc.ca/index-eng.html + 2021-04-20T23:04:01Z + + + + + + https://ror.org/01qn7cs15 + A principle agency of the U.S. Federal Satistical System, whose responsibility and mission is to serve as the nation's leading provider of quality data about its people and economy. + United States Census Bureau + The U.S. Census Bureau's website is accessible at: https://www.census.gov/ + 2021-03-25T18:05:22Z + + + + + + + Sociocultural working group + Social and cultural dimensions of salmon systems working group + Learn more about the Social and Cultural Dimensions of Salmon Systems Working Group here: https://alaskasalmonandpeople.org/working-group/social-and-cultural-dimensions-of-salmon-systems/ + The topics explored by the Sociocultural working group are (1) social and cultural values and relationships between people and salmon, (2) trends in human populations and communities and uses of salmon, and (3) key threads to salmon-dependent communities + 2021-03-25T18:47:05Z + + + + + + Dan Rinella + 2021-03-25T19:07:18Z + + + + + + + + + + + + https://alaskasalmonandpeople.org/about/process-people/ + A research center of the University of California, Santa Barbara which fosters collaborative synthesis research by assembling interdisciplinary teams to distill existing data, ideas, theories, or methods drawn from many sources, across multiple fields of inquiry, in order to accelerate the generation of new knowledge on a broad scale. + + + + + + Steve Munch + 2021-04-20T16:11:15Z + + + + + + + + Kevin Whitworth + The SASAP website lists Kevin Whitworth's affiliation as 'Up-River Stakeholder', but I've been unable to find information about that online to include as an 'Organization' instance. + 2021-04-20T15:50:25Z + + + + + + + Steve Fleischman + 2021-04-20T15:34:26Z + + + + + + + + McGill Biology + Department of Biology + McGill's Department of Biology's website is accessible at: https://www.mcgill.ca/biology/ + 2021-04-21T17:36:24Z + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#kotzebue +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Straddling the Arctic Circle, the Kotzebue region is twice the size of West Virginia and categorized as among the driest areas of Alaska. Chum salmon is the primary species in this region and is harvested by local users in both subsistence and commercial fisheries. + +The bounding coordinates for this SASAP region are: +North: 68.9178 degrees +South: 65.3082 degrees +East: 65.3082 degrees +West: -169.0513 degrees + + + + + + 2021-03-25T18:04:57Z + National Park Service + + An agency of the federal government of the United States that manages all national parks, many national monuments, and other conservation and hisotrical properties with various title designations. + + + + Visit the National Park Service's website at: https://www.nps.gov/index.htm + NPS + https://ror.org/044zqqy65 + + + https://orcid.org/0000-0002-2342-3482 + Ben Staton + 2021-04-20T15:33:36Z + + + + + + + Canadian-based college or university + 2021-04-21T17:33:46Z + + + + + + http://dnr.alaska.gov/ssd/irm/ + A division within the government of Alaska's Department of Natural Resources (DNR) which maintains the department's land records repository and oversees DNR's computer systems and networks services. It provides for the department's data processing functions including development, training, operations, and maintenance. The Department of Natural Resources' (DNR) systems include the Land Administration System (LAS), the Geographic Information System, the Revenue and Billing System, and others. The section also produces and maintains the state's land status maps. + + + + + + Biophysical working group + Learn more about the Biophysical Working Group here: https://alaskasalmonandpeople.org/working-group/biophysical-information-on-salmon-distribution-and-habitat/ + The goal of the to Biophysical working group is to compare and contrast the status of Alaska salmon and their habitats across regions. + 2021-03-25T18:46:55Z + + + + + + Caroline Brown + 2021-04-19T23:51:22Z + + + + + + + + + MSU + https://ror.org/05hs6h993 + Michigan State University + MSU's website is accessible at: https://msu.edu/ + 2021-04-21T16:39:46Z + + + + + + isLeadResearcherOf + Each SASAP working group has an affiliated researcher(s) leading the working group's research efforts. The 'isLeadResearcherOf' object property connects lead researchers to their respective working groups. + 2021-03-25T19:00:44Z + + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.sfmission + The Division of Sport Fisheries provides the following core services: (a) fisheries management, (b) fisheries research, (c) fisheries enhancement, (d) protection and restoration of fish habitats for the ebefit of fish and sport anglers, (e) communication and outreach, and (f) providing leadership and administrative support for the Division's core functions. + + + + + + NOAA Fisheries Northwest Fisheries Science Center + NOAA Fisheries Northwest Fisheries Science Center's website is accessible at: https://www.fisheries.noaa.gov/about/northwest-fisheries-science-center + 2021-04-20T22:59:58Z + + + + + + + https://orcid.org/0000-0002-1513-9078 + Courtney Carothers + 2021-03-25T20:08:16Z + + + + + + + + + + + + + Neala Kendall + 2021-04-20T16:10:15Z + + + + + + + + + + A department within the government of Alaska and a sub-division of the Alaska Department of Fish and Wildlife, Division of Commercial Fisheries which manages the Arctic-Yukon-Kuskokwim Region. + 2021-03-25T18:03:57Z + + Alaska Department of Fish and Game, Division of Commercial Fisheries, Arctic-Yukon-Kuskokwim Region + + AYK + + The Arctic-Yukon-Kuskokwim (AYK) Region encompasses the coastal waters of Alaska and includes the rivers and streams that drain into the Bering, Chukchi, and Beaufort Seas. It stretches from its boundary at Cape Newenham with the Bristol Bay area to the border with Canada on the Arctic Ocean. The Yukon River, with the fifth largest drainage in North America, lies within this management region, as do many other major rivers; the Kuskokwim being second in size next to the Yukon. With the exception of Fairbanks, Bethel, and Nome, this is a region of villages. Salmon and herring are the most important fisheries resources in this region. Large numbers of salmon are taken for subsistence and subsistence harvests can equal or surpass the numbers of fish harvested in commercial fisheries, especially Chinook salmon. King crab is harvested near Nome in both commercial and subsistence fisheries. Whitefish are also important to the residents of this region. + + + Nick Kameroff + 2021-04-20T15:50:03Z + + + + + + + + http://nativecouncil.org/welcome/ + A federally recognized governing body for the community of Bethel, Alaska whose mission is to promote the general welfare, enhance independence, encourage self-sufficiency/self-motivation, enhance quality of life, and preserve cultural and traditional values of the Tribe, and to exercise tribal authority over resources through educational, economic, and social development opportunities. + + + + + + + Organization + 2021-03-25T21:14:05Z + + + + + Consulting firm + Consultancy + 2021-04-06T17:24:47Z + + + + + + Holly Kindsvter + 2021-04-20T15:55:31Z + + + + + + + + + + + Zach Liller + 2021-04-20T15:46:53Z + + + + + + + + A federally recognized governing body for the community of Bethel, Alaska whose mission is to promote the general welfare, enhance independence, encourage self-sufficiency/self-motivation, enhance quality of life, and preserve cultural and traditional values of the Tribe, and to exercise tribal authority over resources through educational, economic, and social development opportunities. + ONC + Orutsararmiut Traditional Native Council + The ONC website is accessible at: http://nativecouncil.org/welcome/ + 2021-03-25T18:06:45Z + + + + + + + Kenai lowlands working group + 2021-03-25T18:47:37Z + + + + + + https://orcid.org/0000-0001-5722-5073 + Ian Dutton + 2021-03-25T20:07:45Z + + + + + + + + + Rachel Donkersloot + 2021-03-25T20:09:04Z + + + + + + + + + + + + + + + + https://orcid.org/0000-0002-4807-6667 + Andrew P. Hendry + 2021-04-20T15:54:54Z + + + + + + + + + Community engagement working group +Community based monitoring working group + Comunity monitoring working group + Community based monitoring working group + 2021-03-25T18:47:30Z + + + + + + https://orcid.org/0000-0002-5496-7263 + Eric P. Palkovacs + 2021-03-25T20:08:54Z + + + + + + + + Indigenous-led organization + 2021-03-25T21:04:36Z + + + + + + http://en.wikipedia.org/wiki/Kodiak_Island +https://www.wikidata.org/wiki/Q514093 + A large island on the south coast of the State of Alaska, separated from the Alaska mainland by the Shelikof Strait. + + + + + + + + + + https://alaskasalmonandpeople.org/about/process-people/ + An essential component of the SASAP working group process is the support each group received from a stellar group of “data wranglers”, a team of geospatial analysis experts from NCEAS known as the Data Task Force. + +The Task Force coordinated hundreds of data requests from Alaska Department of Fish and Game and other agencies and organizations, then worked to reformat, integrate, and run quality control on millions of lines of data in over 125 data sets. + +The graphs, figures, and infograms generated by the Task Force greatly enhanced the ability of users to visualize often complex information about Alaska salmon. + + + + + + + + + https://orcid.org/0000-0001-8874-7595 + Jared Kibele + 2021-03-25T20:07:56Z + + + + + + + + Robert W. Campbell + 2021-03-25T20:09:14Z + + + + + + + + https://orcid.org/0000-0002-8900-9479 + Katie Kobayashi + 2021-04-20T16:07:08Z + + + + + + + + Stephanie Quinn-Davidson + 2021-04-20T15:48:32Z + + + + + + + + + + + + Redpath Museum + The Redpath Museum's website is accessible at: https://www.mcgill.ca/redpath/ + 2021-04-21T17:31:49Z + + + + + + + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54073 + An organization whose primary objective is to support some issue or matter of private interest or public concern for non-commercial purposes. Nonprofits generally do not operate to generate profit, and this characteristic is popularly considered to be the defining characterisitic of such organizations. However, a non-profit organization may accept, hold and disburse money and other things of value. It may also legally and ethically trade at a profit. The extent to which it can generate income may be constrained, or the use of those profits may be restricted. + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=about.cfec#:~:text=Department%20of%20Fish%20and%20Game%3B%20Commercial%20Fisheries%20Entry%20Commission,the%20number%20of%20participating%20fishers. + A department within the government of Alaska which helps to conserve and maintain the economic health of Alaska’s commercial fisheries by limiting the number of participating fishers. The Commission issues permits and vessel licenses to qualified individuals in both limited and unlimited fisheries, and provides due process hearings and appeal processes for disputes related to limitations on fishery participation. + + + + + + A division wihtin Alaska's Department of Public Safety with a mission to protect Alaska's Natural Resources through the enfrocement wildlife statutes and regulations. + AWT + Alaska Department of Public Safety, Division of Alaska Wildlife Troopers + 2021-03-25T18:04:39Z + + + + + + + + Person + 2021-03-25T18:48:44Z + + + + + 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%23C54073, to ensure findability. + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/About + The State of Alaska's Salmon and People (SASAP) project is a collaboration of researchers, cultural leaders, and others working to bring together integrated, accurate, and up-to-date information that will help to support better salmon decision-making. + + + + + + Peter S. Rand + 2021-03-25T20:09:09Z + + + + + + + + John Reynolds + 2021-04-20T16:06:12Z + + + + + + + + Nick Smith + 2021-04-20T15:47:30Z + + + + + + + + Smithsonian +SI + Smithsonian Institution + The Smithsonian's website is accessible at: https://www.si.edu/ + 2021-04-21T17:30:23Z + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=fishingcommercialbyarea.interior + The Arctic-Yukon-Kuskokwim (AYK) Region encompasses the coastal waters of Alaska and includes the rivers and streams that drain into the Bering, Chukchi, and Beaufort Seas. It stretches from its boundary at Cape Newenham with the Bristol Bay area to the border with Canada on the Arctic Ocean. The Yukon River, with the fifth largest drainage in North America, lies within this management region, as do many other major rivers; the Kuskokwim being second in size next to the Yukon. With the exception of Fairbanks, Bethel, and Nome, this is a region of villages. Salmon and herring are the most important fisheries resources in this region. Large numbers of salmon are taken for subsistence and subsistence harvests can equal or surpass the numbers of fish harvested in commercial fisheries, especially Chinook salmon. King crab is harvested near Nome in both commercial and subsistence fisheries. Whitefish are also important to the residents of this region. + + + + + + https://en.wikipedia.org/wiki/National_Park_Service + An agency of the federal government of the United States that manages all national parks, many national monuments, and other conservation and hisotrical properties with various title designations. + + + + + + https://en.wikipedia.org/wiki/Intergovernmental_organization +https://www.wikidata.org/wiki/Q245065 + https://hls.harvard.edu/dept/opia/what-is-public-interest-law/public-service-practice-settings/public-international-law/intergovernmental-organizations-igos/ + An entity created by treaty, involving two or more nations, to work in good faith, on issues of common interest. + + + + + + Well-being working group + Well-being and salmon systems working group + 2021-03-25T18:47:41Z + + + + + + https://orcid.org/0000-0003-0077-4738 + Matthew Jones + 2021-03-25T20:07:50Z + + + + + + + + + + + + https://schema.org/Project + An enterprise (potentially individual but typically collaborative), planned to achieve a particular aim. + + + + + + + + + http://en.wikipedia.org/wiki/Bristol_Bay +https://www.wikidata.org/wiki/Q917872 + The eastern-most arm of the Bering Sea. It is located between the southwest part of the Alaska mainland to its north, and the Alaska Peninsula to its south and east. Bristol Bay is 400 km long and 290 km wide at its mouth. A number of rivers flow into the bay, including the Cinder, Igushik, Kvichak, Meshik, Nushagak, Naknek, Togiak, and Ugashik. + + + + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.subsoverview + A department within the government of Alaska with a mission to scientifically gather, quantify, evaluate, and report information about customary and traditional uses of Alaska's fish and wildlife resources. + + + + + + https://en.wikipedia.org/wiki/Category:Independent_research_institutes#:~:text=From%20Wikipedia%2C%20the%20free%20encyclopedia,operate%20under%20their%20own%20authority. + A research institute which is not part of a university, government, hospital or corporation. An independent research institute may have a close relationship with a larger institution such as a university, but is not part of the larger insitution and operates under its own authority. + + + + + + + + + + Steven J. Langdon + 2021-03-25T20:08:34Z + + + + + + + + + https://orcid.org/0000-0001-8384-3385 + Charles A. Simenstad + 2021-03-25T20:09:56Z + + + + + + + + Willy Dunne + 2021-04-20T16:21:59Z + + + + + + + + + Tobias Schworer + 2021-03-25T20:08:28Z + + + + + + + + https://orcid.org/0000-0002-8103-475X + Mark Rains + 2021-03-25T20:09:48Z + + + + + + + + + + + + + contributedDataTo + 2021-04-22T03:47:22Z + + + + + + + + Using skos:closeMatch rather than skos:exactMatch because schema.org does not provide an inverse property to https://schema.org/affiliation. We define the inverse of 'affiliateOf' as 'hasAffiliate'. + https://schema.org/affiliation + + + + + + http://en.wikipedia.org/wiki/Alaska_panhandle +https://www.wikidata.org/wiki/Q198710 + The southeastern portion of the coast of the State of Alaska, which lies just west of the northern half of the Canadian province of British Columbia. The majority of the panhandle's area is part of the Tongass National Forest, the United States's largest national forest. In many places, the international border runs along the crest of the Boundary Ranges of the Coast Mountains. + + + + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#yukon +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Larger than the state of Texas and home to the third longest river in the United States, the Yukon region is a governance mosaic of state and federal fisheries management. + +The bounding coordinates for this SASAP region are: +North: 69.0792 degrees +South: 58.8686 degrees +East: -129.1775 degrees +West: -166.281 degrees + + + + + + http://en.wikipedia.org/wiki/Alaska_Peninsula +https://www.wikidata.org/wiki/Q119285 + A peninsula extending about 800 km to the southwest from the mainland of Alaska and ending in the Aleutian Islands. The peninsula separates the Pacific Ocean from Bristol Bay, an arm of the Bering Sea. + + + + + + http://en.wikipedia.org/wiki/Norton_Sound +https://www.wikidata.org/wiki/Q1973692 + An inlet of the Bering Sea on the western coast of the State of Alaska, south of the Seward Peninsula. It is about 240 km long and 200 km wide. The Yukon River delta forms a portion of the south shore and water from the Yukon influences this body of water. + + + + + + The National Historical Geographic Information System (NHGIS) provides easy access to summary tables and time series of population, housing, agriculture, and economic data, along with GIS-compatible boundary files, for years from 1790 through the present and for all levels of U.S. census geography, including states, counties, tracts, and blocks. + + A historical GIS project to create and freely disseminate a database incorporating all available aggregate census information for the United States between 1790 and 2010. + NHGIS + **Unsure how to classify this** + 2021-04-05T20:19:55Z + + + + National Historic Geographic Information System + + + Stephanie M. Carlson + 2021-04-20T15:54:16Z + + + + + + + + Ocean climate working group + Changing ocean working group + 2021-03-25T18:47:23Z + + + + + + https://orcid.org/0000-0002-4643-5718 + Frank Davis + 2021-03-25T19:55:01Z + + + + + + + + James Fall + 2021-03-25T20:08:46Z + + + + + + + + An Organization (or ProgramMembership) to which this Person or Organization belongs. + memberOf + + + + + + + + + + https://en.wikipedia.org/wiki/Tribe_(Native_American) +https://www.wikidata.org/wiki/Q7840353 + In the United States, an American Indian tribe, Native American tribe, Alaska Native village, tribal nation, or similar concept is any extant or historical clan, tribe, band, nation, or other group or community of Native Americans in the United States. + + + + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=about.mission + A department within the government of Alaska which manages approximately 750 active fisheries, 26 game management units, and 32 special areas, with a mission, "To protect, maintain, and improve the fish, game, and aquatic plant resources of the state, and manage their use and development in the best interest of the economy and the well-being of the people of the state, consistent with the sustained yield principle." + + + + + + https://firstalaskans.org/Alaska-Native-Policy-Center/overview/ + The Alaska Native Policy Center (Policy Center) is a project of the First Alaskans Institute created to support the Native voice and perspective in the public policy-making process. The Policy Center connects people and ideas producing knowledge that can be used to understand and improve the lives of Alaska Natives and all Alaskans. The Policy Center uses a proactive and forward- thinking approach, a focus that is statewide, and a relationship with the Native community that helps Alaska Native leaders and other policy makers access information they can use to help achieve healthy, thriving communities. + + + + + + http://www.chistochinaenterprises.com/ + Chistochina Enterprises is a wholly owned Section 17 Corporation authorized by the 1934 Indian Reorganization Act, formed under a Federal charter to represent the business interests of Cheesh'na and as a means of investing in the future of the Tribe. Chistochina Enterprises is governed by a five member Board of Director initially appointed by Cheesh'na Tribal Council. The main office is located in Chistochina, Alaska, and the enterprise is licensed to conduct business in the State of Alaska and nationally as outlined in its Federal charter. + + + + + + SALMoN + + + A community-based ecological monitoring program initiated by the Stika Conservation Society and the Sitka Sound Science Center, and with close coordination with the USFS Tongass National Forest, and whose purpose is to engage community members in credible ecological monitoring and adaptive management that supports both the health of the environment of Southeast Alaska and the communities living there. This program implements ecological monitoring projects that provide substantive opportunities for community members, especially students, to practice natural resource stewardship, supports management needs, and informs decision-making. + Southeast Alaska Long-term Monitoring Network + The SALMoN website is accessible at: http://www.seakecology.org/ + 2021-04-05T20:06:49Z + + + **Unsure how to classify this** + + + https://en.wikipedia.org/wiki/Arctic_Alaska +https://www.wikidata.org/wiki/Q3245148 + Arctic Alaska or Far North Alaska is a region of the U.S. state of Alaska generally referring to the northern areas on or close to the Arctic Ocean. + + + + + + hasLeadResearcher + 2021-03-25T19:45:52Z + + + + + + + Taylor Brelsford + 2021-03-25T20:08:42Z + + + + + + + + https://orcid.org/0000-0003-1488-820X + Dennis Whigham + 2021-03-25T20:10:04Z + + + + + + + + Greg Ruggerone + 2021-04-20T16:32:58Z + + + + + + + + + Ginny Litchfield + 2021-04-20T16:19:46Z + + + + + + + + + + + + + + + + http://www.mstc.org/ + Mt. Sanford Tribal Consortium (Kelt’aeni) is a tribal consortium of two federally recognized Tribal Councils of Chistochina and Mentasta Lake. The consortium was established on June 26, 1992 under a joint effort by Chistochina Village and Mentasta Village to advance and protect common interests of the descendants of the Upper Ahtna indigenous people. + + + + + + Michael L. Jones + 2021-03-25T20:09:31Z + + + + + + + + https://mtalab.adfg.alaska.gov/ + A department within the government of Alaska, which aims to provide fisheries managers and researchers with timely, current, and historical biological data to help them manage, preserve, protect, and perpetuate Alaska's fishery resources. The MTA lab refines and develops diverse methods and means for providing critical data, develops new applications to address management issues and fosters a broad information exchange. + + + + + + Andrea Akalleq Sanders + 2021-04-20T17:06:17Z + + + + + + + + Ed Farley + 2021-04-20T16:30:47Z + + + + + + + + + Steve Baird + 2021-04-20T16:18:46Z + + + + + + + + + + + + + http://orcid.org/0000-0002-5300-3075 + A collection of datasets. + + + + + + https://schema.org/affiliation + An organization that this person is affiliated with. For example, a school/university, a club, or a team. + + + + + + + + + + + + + https://inletkeeper.org/about/ + A community-based nonprofit organization that combines advocacy, education and science toward its mission to protect Alaska’s Cook Inlet watershed and the life it sustains. Inletkeeper’s monitoring and science work builds credibility with scientists and resource managers, its education and advocacy efforts enhance stewardship and citizen participation, and together, these efforts translate into Inletkeeper’s ability to effectively ensure a vibrant and healthy Cook Inlet watershed. + + + + + + Karyn DeCino + 2021-04-20T16:21:17Z + + + + + + + + + + + + Jessica Black + 2021-03-25T20:08:20Z + + + + + + + + + + + + Ryan King + 2021-03-25T20:09:43Z + + + + + + + + + 2021-04-20T16:33:31Z + + + + + + + Brendan Connors + + + + Brian Blossom + 2021-04-20T16:20:28Z + + + + + + + + + https://en.wikipedia.org/wiki/Investment_company +https://www.wikidata.org/wiki/Q1752459 + A financial institution principally engaged in investing in securites (i.e. a tradable financial asset). + + + + + + https://dps.alaska.gov/AWT/Home + A division wihtin Alaska's Department of Public Safety with a mission to protect Alaska's Natural Resources through the enfrocement wildlife statutes and regulations. + + + + + + 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%23C54073, to ensure findability. + + + + + + + + + + + https://en.wikipedia.org/wiki/Government_agency +https://www.wikidata.org/wiki/Q327333 + A permanent or semi-permanent federal govenrment organization which is responsible for the oversight and administration of specific functions. + + + + + + + + + + Coowe Walker + 2021-03-25T20:09:38Z + + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#cookinlet +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Home to over 60% of Alaska’s residents, the Cook Inlet region may provide a glimpse of the future. Issues of urbanization, road building, and the rise of invasive species are increasingly prominent here. These changes are set within a context of a changing climate and increased conflict among user groups for limited salmon resources. + +The bounding coordinates for this SASAP region are: +North: 63.638 degrees +South: 58.6157 degrees +East: -146.1503 degrees +West: -154.7415 degrees + + + + + + http://www.ccthita.org/ + The Central Council of the Tlingit and Haida Indian Tribes of Alaska (Tlingit & Haida) is a tribal government representing over 32,000 Tlingit and Haida Indians worldwide. The are a sovereign entity and have a government to government relationship with the United States. + +Tlingit & Haida's headquarters are in Juneau, Alaska but their commitment to serving the Tlingit and Haida people extends throughout the United States. + + + + + + + + + + The NMFS website is accessible at: https://www.fisheries.noaa.gov/ + NMFS +NOAA Fisheries + National Marine Fisheries Service + 2021-04-20T17:24:33Z + + + + + + + Ann Fienup Riordon + 2021-04-20T17:03:34Z + + + + + + + + https://ror.org/032a13752 + Smithsonian Environmental Research Center + **Unsure how to classify this** + The Smithsonian Environmental Research Center website is accessible at: https://serc.si.edu/ + 2021-03-29T22:59:15Z + + + + + + + + + + + + + + https://www.oldharbornativecorp.com/ + Old Harbor Native Corporation (OHNC) was established in 1971 under the terms of the Alaska Native Claims Settlement Act (ANCSA). + +OHNC’s mission is to preserve and protect the culture, values and traditions of its community, shareholders and descendants; and to work together to create economic and educational opportunities while promoting self-determination and pride. + + + + + + Christian Zimmerman + 2021-04-20T16:41:34Z + + + + + + + + + Mandy Bernard + 2021-04-20T16:26:12Z + + + + + + + + + Rich Brenner + 2021-04-20T16:13:20Z + + + + + + + + containsDataFrom + 2021-04-22T03:47:36Z + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#nortonsound +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + An average of two million pink salmon and 250,000 chum salmon return to the sub-Arctic region of Norton Sound, an area approximately twice the size of Massachusetts. + +The bounding coordinates of this SASAP region are: +North: 65.8544 degrees +South: 62.8268 degrees +East: -159.1906 degrees +West: -171.9762 degrees + + + + + + Bechtol Research + Some information about Bechtol Research may be found at: https://www.alaskabids.us/alaska-contractors/contractor-5277895-BECHTOL-RESEARCH.htm + 2021-04-20T20:04:29Z + + + + + + IRES + The IRES webpage is accessible at: http://ires.ubc.ca/about-ires/ + Institute for Resources, Environment and Sustainability + 2021-04-20T17:21:43Z + + + + + + + https://earthlab.uw.edu/2018/09/center-for-creative-conservation-transitions-to-earthlab/ + Since its establishment, the Center has been a member of UW EarthLab—a new environmental institute housing other groups such as the Climate Impacts Group, the Center for Health and the Global Environment, and the Washington Ocean Acidification Center. EarthLab’s inaugural Executive Director, Ben Packard, has been working over the past year to clarify the vision, priorities and strategic outcomes for EarthLab. As this vision has taken shape, it has become clear that the activities of the Center are a key element of EarthLab. Rather than duplicating the efforts of C3 at the EarthLab level, we have decided to integrate the Center for Creative Conservation into EarthLab. + + + + + + School of Aquatic and Fishery Sciences + The UW School of Aquatic and Fishery Science webpage is accessible at: https://fish.uw.edu/ + 2021-03-29T22:58:06Z + + + + + + + + + + + https://www.usgs.gov/about/about-us + A bureau of the United Sates Departement of the Interior, which provides science about the natural hazards that threaten lives and livelihoods, the water, energy, minerals, and other natural resources we rely on, the health of our ecosystems and environment, and the impacts of climate and land-use change. + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#kuskokwim +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + The Kuskokwim region is the 4th largest of Alaska, and at 154,168 km² is comparable in size to the state of Georgia. The region drains the Kuskokwim – one of the great rivers of the world. The salmon-producing habitat of the Kuskokwim region is diverse and productive. Drier than the neighboring Bristol Bay region, the Kuskokwim region has a larger amount of burn area from forest fires than all other regions but the Yukon. + +The bounding coordinates for this SASAP region are: +North: 64.4166 degrees +South: 58.6262 degrees +East: -151.5105 degrees +West: -173.2164 degrees + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#kodiak +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + The abundance of salmon returning to the largest island in Alaska remain high, though sociocultural challenges loom as large as the 925 glaciers that cling to the island’s coastal and interior mountains. + +The bounding coordinates for this SASAP region are: +North: 59.0261 degrees +South: 56.3492 degrees +East: -151.6884 degrees +West: -156.7838 degrees + + + + + + https://ror.org/01j7nq853 + University of Alaska Fairbanks + UAF + The University of Alaska Fairbanks website is accessible at: https://www.uaf.edu/uaf/ + 2021-04-20T17:17:00Z + + + + + + + + + + + + + + Trent Sutton + 2021-04-20T16:40:42Z + + + + + + + + + Michael Opheim + 2021-04-20T16:25:39Z + + + + + + + + + https://orcid.org/0000-0001-7112-8069 + Vadim Karatayev + 2021-04-20T16:12:35Z + + + + + + + + + + http://vivoweb.org/ontology/core#AcademicDepartment + A distinct, usually specialized educational unit within an educational organization. + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#alaskapeninsulaandaleutianislands +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Although relatively small in landmass (4th smallest region) the total expanse of the Alaska Peninsula and Aleutian Island region is enormous, spanning over 1600 km (1000 miles) and 10 degrees of longitude. + +The bounding coordinates for this SASAP region are: +North: 57.2997 degrees +South: 51.1568 degrees +East: -153.6282 degrees +West: 179.8567 degrees + + + + + + Melissa Poe + 2021-04-20T17:05:18Z + + + + + + + + + + + + + A distinct, usually specialized educational unit within an educational organization. + Academic department + 2021-04-12T23:49:48Z + + + + + + + Andrew Gray + 2021-04-20T16:30:06Z + + + + + + + + + Chris Guo + 2021-04-20T16:17:58Z + + + + + + + + + + SASAP + 0.1.1 + The State of Alaska's Salmon and People Ontology + + https://orcid.org/0000-0002-5300-3075 +https://orcid.org/0000-0002-0381-3766 +https://orcid.org/0000-0003-0632-7576 +https://orcid.org/0000-0003-0077-4738 + https://creativecommons.org/publicdomain/zero/1.0/ + https://github.com/DataONEorg/sem-prov-ontologies + https://github.com/DataONEorg/sem-prov-ontologies/issues + 2021-04-19T12:45:10-07:00 + An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. + + + https://www.commerce.alaska.gov/web/ + A department within the government of Alaska whose mission is to "Promote a healthy economy, strong communities, and protect consumers in Alaska." + + + + + + https://npafc.org/ + An international inter-governmental organization established by the Convention for the Conservation of Anadromous Stocks in the North Pacific Ocean whose primary objective is to promote the conservation of anadromous stocks in the Convention Area. The Convention Area is the international waters of the North Pacific Ocean and its adjacent seas north of 33° North beyond the 200-mile zones (exclusive economic zones) of the coastal States. + + + + + + + + + + Syverine Bentz + 2021-04-20T16:17:09Z + + + + + + + + + Kawerak, Inc. + Kawerak Inc.'s website is accessible at: https://kawerak.org/ + 2021-04-20T17:45:08Z + + + + + + https://orcid.org/0000-0001-8842-4884 + Sara Jo Breslow + 2021-04-20T17:04:16Z + + + + + + + + Jacob Argueta + 2021-04-20T16:27:25Z + + + + + + + + + http://en.wikipedia.org/wiki/Prince_William_Sound +https://www.wikidata.org/wiki/Q631282 + A sound of the Gulf of Alaska on the south coast of the State of Alaska. It is located on the east side of the Kenai Peninsula. + + + + + + Quatitative Fisheries Center + Department of Fisheries and Wildlife Quantitative Fisheries Center + The Department of Fisheries and Wildlife Quantitative Fisheries Center webpage is accessible at: https://www.canr.msu.edu/qfc/ + 2021-03-29T22:59:25Z + + + + + + + Alice Rademacher + 2021-04-20T16:26:39Z + + + + + + + + + Gale Vick + 2021-04-20T16:14:25Z + + + + + + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#princewilliamsound +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Prince William Sound is a region of rain, icefields, and glaciers. Only two (Whittier and Valdez) of Prince William Sound’s largest human communities are connected via road. The terminus of the Alaska oil pipeline ends in this region and results in a fairly high footprint of human activity in a relatively small region. Pink salmon, chum salmon, and sockeye salmon fisheries are current mainstays of local communities with hatchery enhancement of these species (particularly pink salmon) a fundamental dynamic in the region. + +The bounding coordinates of this SASAP region are: +North: 61.5189 degrees +South: 59.357 degrees +East: -145.1013 degrees +West: -149.1761 degrees + + + + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=fishingcommercialbyarea.southcentral + Central Region Alaska commercial fisheries are composed of four distinct management areas that include Bristol Bay, Prince William Sound and Copper River, Upper Cook Inlet, and Lower Cook Inlet. Although all 5 species of salmon are harvested in each area, sockeye and pink salmon are the most abundant and most valuable. This area encompasses some of the largest and most valuable salmon fisheries in the world. From Bristol Bay, home of the largest sockeye salmon fishery in the world, to the Copper River where sockeye and Chinook salmon fetch some of the highest prices per pound paid to commercial fishermen. Cook Inlet commercial fisheries occur near the largest population center in Alaska, providing salmon to numerous niche and local markets, as well as fresh salmon to markets in other states. Prince William Sound adds productive healthy pink, chum, and sockeye salmon fisheries to the region. Southcentral groundfish fisheries are small, yet diverse, targeting pollock, Pacific cod, rockfish, sablefish, lingcod, and skate while small shrimp and scallop fisheries in Prince William Sound cater predominately to local markets. Southcentral commercial fisheries are of tremendous importance and an integral part of many communities and local economies in the state. + + + + + + A river in south-central Alaska in the United States. It drains a large region of the Wrangell Mountains and Chugach Mountains into the Gulf of Alaska. The Copper River rises out of the Copper Glacier, which lies on the northeast side of Mount Wrangell, in the Wrangell Mountains, within Wrangell-Saint Elias National Park. It begins by flowing almost due north in a valley that lies on the east side of Mount Sanford, and then turns west, forming the northwest edge of the Wrangell Mountains and separating them from the Mentasta Mountains to the northeast. It continues to turn southeast, through a wide marshy plain to Chitina, where it is joined from the southeast by the Chitina River. Downstream from its confluence with the Chitina it flows southwest, passing through a narrow glacier-lined gap in the Chugach Mountains east of Cordova Peak. There is an extensive area of sand dunes between the Copper and Bremner Rivers. Both Miles Glacier and Child's Glacier calve directly into the river. + http://purl.obolibrary.org/obo/GAZ_00197403 + Copper River + Fewer than 2500 people live permanently in the Copper River region, an area comparable in size to the state of West Virginia. Sockeye salmon are dominant here, given the multiple large lakes available for rearing juvenile salmon. Though less abundant than sockeye, king salmon are deeply important to all salmon-connected people. Kings have declined in number since 2007. + +The bounding coordinates for this SASAP region are: +North: 63.3227 degrees +South: 59.7112 degrees +East: -139.6942 degrees +West: -147.8251 degrees + 2021-03-24T21:28:12Z + + + + + + + + + + Data Task Force + An essential component of the SASAP working group process is the support each group received from a stellar group of “data wranglers”, a team of geospatial analysis experts from NCEAS known as the Data Task Force. + +The Task Force coordinated hundreds of data requests from Alaska Department of Fish and Game and other agencies and organizations, then worked to reformat, integrate, and run quality control on millions of lines of data in over 125 data sets. + +The graphs, figures, and infograms generated by the Task Force greatly enhanced the ability of users to visualize often complex information about Alaska salmon. + 2021-03-29T18:12:03Z + + + + + + Department of Anthropology + The UAA Department of Anthropology webpage is accessible at: https://www.uaa.alaska.edu/academics/college-of-arts-and-sciences/departments/anthropology/ + 2021-03-29T23:00:42Z + + + + + + + A large estuary stretching 180 miles from the Gulf of Alaska to Anchorage in south-central Alaska. It separates the Kenai Peninsula from mainland Alaska and branches into the Knik Arm and Turnagain Arm at its northern end, almost surrounding Anchorage. The watershed covers about 100,000 km2 of southern Alaska, east of the Aleutian Range and south of the Alaska Range, receiving water from its tributaries the Knik River, the Little Susitna River, and the Susitna and Matanuska rivers. The watershed includes the drainage areas of Mount McKinley. Within the watershed there are several national parks and four historically active volcanoes. + http://purl.obolibrary.org/obo/GAZ_00051076 + Cook Inlet + Home to over 60% of Alaska’s residents, the Cook Inlet region may provide a glimpse of the future. Issues of urbanization, road building, and the rise of invasive species are increasingly prominent here. These changes are set within a context of a changing climate and increased conflict among user groups for limited salmon resources. + +The bounding coordinates for this SASAP region are: +North: 63.638 degrees +South: 58.6157 degrees +East: -146.1503 degrees +West: -154.7415 degrees + 2021-03-24T21:28:08Z + + + + + + The North Slope Borough is the northernmost borough in the US state of Alaska. + North Slope Borough + The North Slope Borough's website is accessible at: https://www.north-slope.org/ + 2021-04-20T22:56:53Z + + + + + + Kuskokwim River Salmon Management Working Group + **Unsure how to classify this** + The Kuskokwim River Salmon Management Working Group (KRSMWG) was formed in 1988 by the Alaska Board of Fisheries (BOF) in response to requests from stakeholders in the Kuskokwim Area who sought a more active role in the management of salmon fishery resources. + +The Working Group is made up of 14 member seats representing elders, subsistence fishermen, processors, commercial fishermen, sport fishermen, Kuskokwim River Inter-Tribal Fish Commission, member at large, federal subsistence regional advisory committees, and the Alaska Department of Fish and Game. Non-agency members participate on a voluntary basis and receive no compensation. Participation in the Working Group process requires a great deal of time from its members and agency staff. + +The relationship among Working Group members, research planners, project leaders, and policy makers is fostered, and these interactions are critical to the aim of the Working Group. This relationship ensures that participants remain up-to-date on new information and maintain their direct involvement in management of Kuskokwim River salmon fisheries. + 2021-04-20T21:05:05Z + + + + + + ESSA Technologies, Ltd. + ESSA Technologies website is accessible at: https://essa.com/ + 2021-04-20T19:34:57Z + + + + + + https://www.legfin.akleg.gov/AgencyInfo/AboutLFD.php + A department within the government of Alaska which provides non-partisan budgetary and fiscal analysis to the Alaska Legislature. + + + + + + + + + + Freddie Christiansen + 2021-04-20T17:09:25Z + + + + + + + + Karen Dunmall + 2021-04-20T16:35:58Z + + + + + + + + + https://en.wikipedia.org/wiki/Kenai_Peninsula_Borough,_Alaska +https://www.wikidata.org/wiki/Q512713 + Kenai Peninsula Borough (Russian: Кенай боро, Kenay boro) is a borough of the U.S. state of Alaska. + + + + + + Populates the SASAP Data Portal (https://knb.ecoinformatics.org/portals/SASAP/Data) faceted search field, 'Working Group' + Working Group + + + + + + https://alaskasalmonandpeople.org/working-group/social-and-cultural-dimensions-of-salmon-systems/ + The topics explored by the Sociocultural working group are (1) social and cultural values and relationships between people and salmon, (2) trends in human populations and communities and uses of salmon, and (3) key threads to salmon-dependent communities + + + + + + https://en.wikipedia.org/wiki/Government_agency +https://www.wikidata.org/wiki/Q327333 + A permanent or semi-permanent state govenrment organization which is responsible for the oversight and administration of specific functions. + + + + + + https://www.adfg.alaska.gov/index.cfm?adfg=commercialbyareasoutheast.main + The Southeast Alaska/Yakutat Region (Region I) consists of Alaska waters between Cape Suckling on the north and Dixon Entrance on the south. Salmon are commercially harvested in Southeast Alaska with purse seines and drift gillnets; in Yakutat with set gillnets; and in both areas with hand and power troll gear. Herring are harvested in winter bait, sac roe, spawn-on-kelp, and bait pound fisheries. Miscellaneous shellfish (sea cucumber, sea urchins, and geoduck clams) are harvested in dive fisheries in the region. The Alaska Department of Fish and Game (ADF&G) has management jurisdiction over all groundfish resources within state waters in Region I. In addition, the State has management authority for Demersal Shelf Rockfish, ling cod, and black and blue rock fish in both state and federal waters. There are several commercially important shellfish species in Southeast Alaska. They include golden and red king crab, Dungeness crab, Tanner crab, and pandalid shrimp. + + + + + + A collection of datasets and their metadata which were curated in support of the State of Alaska's Salmon and People (SASAP) Project and accessible at the URL, https://knb.ecoinformatics.org/portals/SASAP/Data + SASAP Data Portal + State of Alaska's Salmon and People Data Portal + The State of Alaska's Salmon and People (SASAP) project is a collaboration of researchers, cultural leaders, and others working to bring together integrated, accurate, and up-to-date information that will help to support better salmon decision-making. + 2021-03-29T17:34:06Z + + + + + + EEB +UCSC EEB + Department of Ecology and Evolutionary Biology + The UCSC Department of Ecology and Evolutionary Biology webpage is accessible at: https://www.eeb.ucsc.edu/ + 2021-03-29T23:00:02Z + + + + + + + http://purl.obolibrary.org/obo/GAZ_00197745 +http://purl.obolibrary.org/obo/GAZ_00197347 +http://purl.obolibrary.org/obo/GAZ_00262790 + Chignik + Despite being the smallest salmon-people region of Alaska (6,587 km²), Chignik is remarkably rich in habitat diversity–which translates into biological diversity of its salmon. The Chignik region is home to multiple dispersed communities such as Chignik Lake, Chignik Lagoon, Chignik Bay, Perryville, and Ivanof Bay. + +The bounding coordinates for this SASAP region are: +North: 57.142 degrees +South: 55.5261 degrees +East: -155.4645 degrees +West: -159.6479 degrees + 2021-03-24T21:27:57Z + + + + + + Danielle Ringer + 2021-04-19T23:48:38Z + + + + + + + + + + + + + Calista Education and Culture, Inc. + Calista Elders Council + The Calista Elders Council was established in 1991 as a non-profit organization representing 1,300 Yup'ik traditional bearers of the Yukon-Kuskokwim Delta in Southwest Alaska. The Calista Elders Council was formed to help protect and preserve the Yup’ik, Cup’ik and Athabascan cultures. + +In 2014, after a 20 year history of interacting and working together, the Calista Elders Council, Inc. merged with the former Calista Heritage Foundation to form what is now Calista Education and Culture, Inc. + 2021-04-20T22:49:17Z + + + + + + Rutgers University +Rutgers +RU + https://ror.org/05vt9qd57 + Rutgers, The State University of New Jersey + RU's website is accessible at: https://www.rutgers.edu/ + 2021-04-20T20:32:34Z + + + + + + Mike Williams + 2021-04-20T17:08:50Z + + + + + + + + + https://orcid.org/0000-0002-5314-0109 + Jim Irvine + 2021-04-20T16:34:39Z + + + + + + + + + UW + https://ror.org/00cvxb145 + University of Washington + Learn more about UW at their website: https://www.washington.edu/ + 2021-04-20T19:46:36Z + + + + + + School of Geosciences + The USF School of Geosciences webpage is accessible at: http://hennarot.forest.usf.edu/main/depts/geosci/ + 2021-03-29T22:57:58Z + + + + + + + Nautilus Impact Investing, LLC + 2021-03-29T23:05:25Z + + + + + + http://purl.obolibrary.org/obo/GAZ_22223765 +http://purl.obolibrary.org/obo/GAZ_00132744 +http://purl.obolibrary.org/obo/GAZ_00198349 + Kotzebue + Straddling the Arctic Circle, the Kotzebue region is twice the size of West Virginia and categorized as among the driest areas of Alaska. Chum salmon is the primary species in this region and is harvested by local users in both subsistence and commercial fisheries. + +The bounding coordinates for this SASAP region are: +North: 68.9178 degrees +South: 65.3082 degrees +East: 65.3082 degrees +West: -169.0513 degrees + 2021-03-24T21:28:35Z + + + + + + https://ror.org/005781934 + Baylor University + The Baylor University website is accessible at: https://www.baylor.edu/ + 2021-03-29T22:57:21Z + + + + + + AYK SSI +AYK Sustainable Salmon Initiative + Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative + In response to salmon declines, Bering Sea Fishermen’s Association and regional Native organizations (Association of Village Council Presidents, Kawerak, Inc., and Tanana Chiefs Conference) joined with state and federal agencies to create the AYK SSI, a proactive science-based program working cooperatively to identify and address the critical salmon research needs facing this region. The AYK SSI is the largest example of co-management of research-funding addressing salmon within the Pacific Rim and one of the largest, most successful programs of its kind in North America. + +The AYK SSI website is accessible at: https://www.aykssi.org/ + 2021-04-20T19:43:45Z + + + + + + + + + + Carrie Stevens + 2021-04-20T17:11:42Z + + + + + + + + https://orcid.org/0000-0003-4833-2007 + Todd Sformo + 2021-04-20T16:39:25Z + + + + + + + + + Katie McCafferty + 2021-04-20T16:24:20Z + + + + + + + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#chignik +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Despite being the smallest salmon-people region of Alaska (6,587 km²), Chignik is remarkably rich in habitat diversity–which translates into biological diversity of its salmon. The Chignik region is home to multiple dispersed communities such as Chignik Lake, Chignik Lagoon, Chignik Bay, Perryville, and Ivanof Bay. + +The bounding coordinates for this SASAP region are: +North: 57.142 degrees +South: 55.5261 degrees +East: -155.4645 degrees +West: -159.6479 degrees + + + + + + DESP + Department of Environmental Science & Policy + DESP's webpage is accessible at: https://desp.ucdavis.edu/ + 2021-04-20T21:10:29Z + + + + + + + Institute of Social and Economic Research + The UAA Institute of Social and Economic Research webpage is accessible at: https://www.uaa.alaska.edu/research/institute-social-economic-research/ + 2021-03-29T23:01:04Z + + + + + + + A large island on the south coast of the State of Alaska, separated from the Alaska mainland by the Shelikof Strait. + http://purl.obolibrary.org/obo/GAZ_00050020 + Kodiak + The abundance of salmon returning to the largest island in Alaska remain high, though sociocultural challenges loom as large as the 925 glaciers that cling to the island’s coastal and interior mountains. + +The bounding coordinates for this SASAP region are: +North: 59.0261 degrees +South: 56.3492 degrees +East: -151.6884 degrees +West: -156.7838 degrees + 2021-03-24T21:28:29Z + + + + + + https://alaskasalmonandpeople.org/working-group/biophysical-information-on-salmon-distribution-and-habitat/ + The goal of the to Biophysical working group is to compare and contrast the status of Alaska salmon and their habitats across regions. + + + + + + https://en.wikipedia.org/wiki/National_Historical_Geographic_Information_System + A historical GIS project to create and freely disseminate a database incorporating all available aggregate census information for the United States between 1790 and 2010. + + + + + + https://alaskasalmonandpeople.org/about/process-people/ + Beginning in 2016, nine SASAP working groups formed – each composed of between 12 and 24 knowledge experts from a range of disciplines, backgrounds, and regions. Each participant brought his or her data and experiences for synthesis and analysis, while NCEAS provided logistical and technical support to facilitate each group’s innovative work. + +Each of the nine groups focused on specific issues related to salmon and people in Alaska: + +Four SASAP groups were tasked with integrating knowledge across multiple disciplines to understand the fundamental state of knowledge of Alaska’s salmon systems. The work of each group is presented for each of the major watersheds in Alaska in the Region section (https://alaskasalmonandpeople.org/regions/). + +An additional five working groups were selected to focus on specific research questions that provide insight into the pressures on salmon and salmon communities, as well as options for response to those pressures. Their work is presented in the Special Topics section (https://alaskasalmonandpeople.org/topics/). + + + + + + http://vivoweb.org/ontology/core#University + An institution of higher education and research, which grants academic degrees in a variety of subjects, and provides both undergraduate education and postgraduate education. + + + + + + + + + KBNERR + Kachemak Bay National Estuarine Research Reserve + The KBNERR website is accessbile at: https://accs.uaa.alaska.edu/kbnerr/ + 2021-03-29T22:57:11Z + + + + + + UAA + https://ror.org/03k3c2t50 + University of Alaska Anchorage + The UAA website is accessible at: https://www.uaa.alaska.edu/ + 2021-03-29T23:00:51Z + + + + + + KRITFC + Kuskokwim River Inter-Tribal Fish Commission + KRITFC's website is accessible at: https://www.kuskosalmon.org/ + 2021-04-20T21:07:27Z + + + + + + FAAS + School of Fisheries, Aquaculture & Aquatic Sciences + The FAAS webpage is accessible at: https://agriculture.auburn.edu/research/faas/ + 2021-04-20T19:38:05Z + + + + + + + William Voinot-Baron + 2021-04-20T17:10:53Z + + + + + + + + Mike Malick + 2021-04-20T16:36:53Z + + + + + + + + + Sue Mauger + 2021-04-20T16:22:44Z + + + + + + + + + https://alaskasalmonandpeople.org/regions/ + The thirteen SASAP regions were determined based on their geography, and in many cases represent large watersheds where all precipitation melts and flows into the same part of the ocean. Regions tend to also be grouped by Indigenous cultures and languages, evidence of the deep-time ties between Alaska’s salmon and people. Some regions align with current Alaska Department of Fish & Game (ADF&G) statistical areas; some do not. + +The bounding coordinates and shapefiles for each region are accessible at: https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + + + + + + + + + + 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%23C54073, to ensure findability. + + + + + + + http://www.seakecology.org/about-us/ + A community-based ecological monitoring program initiated by the Stika Conservation Society and the Sitka Sound Science Center, and with close coordination with the USFS Tongass National Forest, and whose purpose is to engage community members in credible ecological monitoring and adaptive management that supports both the health of the environment of Southeast Alaska and the communities living there. This program implements ecological monitoring projects that provide substantive opportunities for community members, especially students, to practice natural resource stewardship, supports management needs, and informs decision-making. + + + + + + Coastal Cultures Research + **Unsure how to classify this** + The Coastal Cultures Research website is accessible at: https://www.coastalculturesresearch.com/ + 2021-03-29T22:59:44Z + + + + + + A peninsula extending about 800 km to the southwest from the mainland of Alaska and ending in the Aleutian Islands. The peninsula separates the Pacific Ocean from Bristol Bay, an arm of the Bering Sea. + http://purl.obolibrary.org/obo/GAZ_00055133 + Alaska Peninsula/Aleutian Islands + Although relatively small in landmass (4th smallest region) the total expanse of the Alaska Peninsula and Aleutian Island region is enormous, spanning over 1600 km (1000 miles) and 10 degrees of longitude. + +The bounding coordinates for this SASAP region are: +North: 57.2997 degrees +South: 51.1568 degrees +East: -153.6282 degrees +West: 179.8567 degrees + 2021-03-24T21:27:29Z + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/GAZ_00069437 + Yukon + Larger than the state of Texas and home to the third longest river in the United States, the Yukon region is a governance mosaic of state and federal fisheries management. + +The bounding coordinates for this SASAP region are: +North: 69.0792 degrees +South: 58.8686 degrees +East: -129.1775 degrees +West: -166.281 degrees + 2021-03-24T21:29:06Z + + + + + + + An organization whose primary objective is to support some issue or matter of private interest or public concern for non-commercial purposes. Nonprofits generally do not operate to generate profit, and this characteristic is popularly considered to be the defining characterisitic of such organizations. However, a non-profit organization may accept, hold and disburse money and other things of value. It may also legally and ethically trade at a profit. The extent to which it can generate income may be constrained, or the use of those profits may be restricted. + Nonprofit +Non-profit +Nonprofit organization +NPO +Nonprofit group +Non-profit organization +Not for profit organization + Nonprofit organization + 2021-03-25T18:01:44Z + + + + + + The Alaska Department of Labor and Workforce Development (DOLWD) is a department within the govenrment of Alaska which handles most of the state's labor and workforce issues, primarily at the administrative level. + https://ror.org/05pc4pd06 + Alaska Department of Labor and Workforce Development + 2021-03-25T18:04:28Z + + + + + + + Alex Whiting + 2021-04-20T00:00:12Z + + + + + + + + Museum + 2021-04-21T17:30:14Z + + + + + + hasAdvisor + 2021-04-19T23:40:58Z + + + + + + + + A member of an Organization or a ProgramMembership. Organizations can be members of organizations; ProgramMembership is typically for individuals. + member + + + + + + + USACE +US Army Corps of Engineers + United States Army Corps of Engineers + UCACE's website is accessible at: https://www.usace.army.mil/ + 2021-04-20T23:28:01Z + + + + + + The Mt. Sanford Tribal Consortium's website is accessible at: http://www.mstc.org/ + Mt. Sanford Tribal Consortium (Kelt’aeni) is a tribal consortium of two federally recognized Tribal Councils of Chistochina and Mentasta Lake. The consortium was established on June 26, 1992 under a joint effort by Chistochina Village and Mentasta Village to advance and protect common interests of the descendants of the Upper Ahtna indigenous people. + Mt. Sanford Tribal Consortium + 2021-04-20T22:26:16Z + + + + + + WSG +Sea Grant Washington + Washington Sea Grant + WSG's website is accessible at: https://wsg.washington.edu/ + 2021-04-20T20:14:57Z + + + + + + + In the United States, an American Indian tribe, Native American tribe, Alaska Native village, tribal nation, or similar concept is any extant or historical clan, tribe, band, nation, or other group or community of Native Americans in the United States. + American Indian tribe +Native American tribe +Alaska Native village +Native village + Tribal nation + 2021-04-20T17:59:45Z + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#bristolbay +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Bristol Bay is sockeye salmon country. The region is a land of great inland lakes, ideally suited to the juvenile life of sockeye salmon. The habitats here are virtually pristine and intact with a notable absence of mining and offshore oil and gas exploration in the region. The long proposed Pebble Mine, situated at the intersection between the Nushagak River and Kvichak River watersheds, would unquestionably and permanently change this salmon landscape. + +The bounding coordinates for this SASAP region are: +North: 60.9278 degrees +South: 56.8716 degrees +East: -152.7319 degrees +West: -162.2713 degrees + + + + + + https://mtalab.adfg.alaska.gov/ + The Mark Lab (https://mtalab.adfg.alaska.gov/OTO/Default.aspx) tracks Alaska's salmon populations by deciphering thermal marks induced in fish otoliths. The Tag Lab (https://mtalab.adfg.alaska.gov/CWT/Default.aspx) is the centralized state resoruce for tracking salmon using microsopic coded wire tags. The Age Determination Lab (https://mtalab.adfg.alaska.gov/ADU/Default.aspx) is a statewide age reading service which produces data for fish and invertebrates sampled during commercial, population survey, and research harvests. + + + + + + + + + https://en.wikipedia.org/wiki/United_States_Census_Bureau + A principle agency of the U.S. Federal Satistical System, whose responsibility and mission is to serve as the nation's leading provider of quality data about its people and economy. + + + + + + http://en.wikipedia.org/wiki/Copper_River_(Alaska) +https://www.wikidata.org/wiki/Q1131444 + A river in south-central Alaska in the United States. It drains a large region of the Wrangell Mountains and Chugach Mountains into the Gulf of Alaska. The Copper River rises out of the Copper Glacier, which lies on the northeast side of Mount Wrangell, in the Wrangell Mountains, within Wrangell-Saint Elias National Park. It begins by flowing almost due north in a valley that lies on the east side of Mount Sanford, and then turns west, forming the northwest edge of the Wrangell Mountains and separating them from the Mentasta Mountains to the northeast. It continues to turn southeast, through a wide marshy plain to Chitina, where it is joined from the southeast by the Chitina River. Downstream from its confluence with the Chitina it flows southwest, passing through a narrow glacier-lined gap in the Chugach Mountains east of Cordova Peak. There is an extensive area of sand dunes between the Copper and Bremner Rivers. Both Miles Glacier and Child's Glacier calve directly into the river. + + + + + + + + + https://ror.org/0551hes90 + Prince William Sound Science Center + The Prince William Sound Center website is accessible at: https://pwssc.org/ + 2021-03-29T22:59:33Z + + + + + + SASAP Region + Populates the SASAP Data Portal (https://knb.ecoinformatics.org/portals/SASAP/Data) faceted search field, 'SASAP Region' + The thirteen SASAP regions were determined based on their geography, and in many cases represent large watersheds where all precipitation melts and flows into the same part of the ocean. Regions tend to also be grouped by Indigenous cultures and languages, evidence of the deep-time ties between Alaska’s salmon and people. Some regions align with current Alaska Department of Fish & Game (ADF&G) statistical areas; some do not. + +The bounding coordinates and shapefiles for each region are accessible at: https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + 2021-03-24T21:24:20Z + + + + + A collaborative project which seeks to provide a holistic, statewide overview of the status and characteristics of Alaska's coupled human-salmon system. + SASAP +SASAP Project + The State of Alaska's Salmon and People Project + The SASAP project is a deep assessment of the state of knowledge of the biological, sociocultural, economic and governance dimensions of Alaska's salmon and the people who depend upon them. The SASAP project shares this knowledge with Alaska salmon users through comprehensive watershed-level summaries (Regions), focused research on specific salmon issues (Topics), and suppported links to SASAP's free, open-source datasets, accessible through the SASAP Data Portal (https://knb.ecoinformatics.org/portals/SASAP/Data). + 2021-03-30T20:31:38Z + + + + + + The southeastern portion of the coast of the State of Alaska, which lies just west of the northern half of the Canadian province of British Columbia. The majority of the panhandle's area is part of the Tongass National Forest, the United States's largest national forest. In many places, the international border runs along the crest of the Boundary Ranges of the Coast Mountains. + http://purl.obolibrary.org/obo/GAZ_00055328 + Southeast Alaska +Alaska Panhandle +Alaskan Panhandle + Southeast + Approximately the size of the state of Kansas, the Southeast region is categorized by thousands of small coastal watersheds that provide ideal spawning habitat for pink salmon and chum salmon in particular. All five species are caught and return to this region. In terms of total abundance of salmon, Southeast Alaska dominates the state. Managing and conserving salmon populations that move beyond international borders is a key challenge here as many of the Chinook salmon caught in Southeast were hatched outside Alaska. + +The bounding coordinates for this SASAP region are: +North: 61.6887 degrees +South: 54.2508 degrees +East: -126.7735 degrees +West: -143.8874 degrees + 2021-03-24T21:29:03Z + + + + + + + + + + http://purl.bioontology.org/ontology/MESH/D035082 + + A permanent or semi-permanent federal govenrment organization which is responsible for the oversight and administration of specific functions. + Federal government department, division, or agency + 2021-03-25T18:01:18Z + + + + + + The Mark Lab (https://mtalab.adfg.alaska.gov/OTO/Default.aspx) tracks Alaska's salmon populations by deciphering thermal marks induced in fish otoliths. The Tag Lab (https://mtalab.adfg.alaska.gov/CWT/Default.aspx) is the centralized state resoruce for tracking salmon using microsopic coded wire tags. The Age Determination Lab (https://mtalab.adfg.alaska.gov/ADU/Default.aspx) is a statewide age reading service which produces data for fish and invertebrates sampled during commercial, population survey, and research harvests. + MTA +MTA Lab + + + Alaska Department of Fish and Game, Mark, Tag and Age Laboratory + + + + A department within the government of Alaska, which aims to provide fisheries managers and researchers with timely, current, and historical biological data to help them manage, preserve, protect, and perpetuate Alaska's fishery resources. The MTA lab refines and develops diverse methods and means for providing critical data, develops new applications to address management issues and fosters a broad information exchange. + 2021-03-25T18:04:24Z + + + An international inter-governmental organization established by the Convention for the Conservation of Anadromous Stocks in the North Pacific Ocean whose primary objective is to promote the conservation of anadromous stocks in the Convention Area. The Convention Area is the international waters of the North Pacific Ocean and its adjacent seas north of 33° North beyond the 200-mile zones (exclusive economic zones) of the coastal States. + NPAFC + North Pacific Anadromous Fish Commission + The North Pacific Anadrmous Fish Commission's website is accessbile at: https://npafc.org/ + 2021-03-25T18:06:17Z + + + + + + + Janessa Esquible + 2021-04-20T15:46:03Z + + + + + + + + TCC + Tanana Chiefs Conference + The Tanana Chiefs Conference website is accessible at: https://www.tananachiefs.org/ + 2021-04-21T17:25:34Z + + + + + + Ben Stevens + 2021-04-19T23:59:58Z + + + + + + + + SVT's website is accessible at: https://svt.org/ + SVT + Seldovia Village Tribe + 2021-04-20T23:26:20Z + + + + + + hasSupportingResearcher + 2021-04-19T21:20:01Z + + + + + + + Georgetown Tribe + Native Village of Georgetown + Find more information about the Native Village of Georgetown at: https://www.bia.gov/tribal-leaders/georgetown + 2021-04-20T21:34:02Z + + + + + + Federal/state partnerships and programs + 2021-04-20T20:14:46Z + + + + + + YRITFC + Yukon River Inter-Tribal Fish Commission + https://salmonlife.org/yellow/stewardship/one-voice-one-river/ + 2021-04-20T17:50:28Z + + + + + + https://labor.alaska.gov/ + https://en.wikipedia.org/wiki/Alaska_Department_of_Labor_and_Workforce_Development + The Alaska Department of Labor and Workforce Development (DOLWD) is a department within the govenrment of Alaska which handles most of the state's labor and workforce issues, primarily at the administrative level. + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.cfoverview + A department within the government of Alaska which manages commercial, subsistence, and personal use fisheries within the jurisdiction of the State of Alaska. + + + + + + https://alaskasalmonandpeople.org/working-group/economic-dimensions-of-salmon-systems/ + The goals of the Economic working group are to (1) identify important trends in the historical relationships between salmon and salmon users which may have been overlooked, (2) inform and support evidence-based policy aimed at sustainable and equitable decision making, and (3) compile, archive, and share relevant historical socioeconomic data about Alaska's salmon systems. + + + + + + A department within the government of Alaska which helps to conserve and maintain the economic health of Alaska’s commercial fisheries by limiting the number of participating fishers. The Commission issues permits and vessel licenses to qualified individuals in both limited and unlimited fisheries, and provides due process hearings and appeal processes for disputes related to limitations on fishery participation. + Alaska Department of Fish and Game, Commercial Fisheries Entry Commission + + + + + + CFEC + 2021-03-25T18:03:30Z + The CFEC website is accessible at: https://cfec.state.ak.us/ + + + https://alaskasalmonandpeople.org/ + A collaborative project which seeks to provide a holistic, statewide overview of the status and characteristics of Alaska's coupled human-salmon system. + + + + + + + + + + + + + A collection of datasets. + Data corpus + 2021-03-29T17:33:25Z + + + + + College of Fisheries & Ocean Sciences + The UAF College of Fisheries & Ocean Sciences webpage is accessible at: https://www.uaf.edu/cfos/ + 2021-03-29T22:59:55Z + + + + + + + The eastern-most arm of the Bering Sea. It is located between the southwest part of the Alaska mainland to its north, and the Alaska Peninsula to its south and east. Bristol Bay is 400 km long and 290 km wide at its mouth. A number of rivers flow into the bay, including the Cinder, Igushik, Kvichak, Meshik, Nushagak, Naknek, Togiak, and Ugashik. + http://purl.obolibrary.org/obo/GAZ_00055147 + Bristol Bay + Bristol Bay is sockeye salmon country. The region is a land of great inland lakes, ideally suited to the juvenile life of sockeye salmon. The habitats here are virtually pristine and intact with a notable absence of mining and offshore oil and gas exploration in the region. The long proposed Pebble Mine, situated at the intersection between the Nushagak River and Kvichak River watersheds, would unquestionably and permanently change this salmon landscape. + +The bounding coordinates for this SASAP region are: +North: 60.9278 degrees +South: 56.8716 degrees +East: -152.7319 degrees +West: -162.2713 degrees + 2021-03-24T21:27:48Z + + + + + + + + + + A department within the government of Alaska which manages approximately 750 active fisheries, 26 game management units, and 32 special areas, with a mission, "To protect, maintain, and improve the fish, game, and aquatic plant resources of the state, and manage their use and development in the best interest of the economy and the well-being of the people of the state, consistent with the sustained yield principle." + https://ror.org/02rh7vj17 + Alaska Department of Fish and Game + 2021-03-25T18:03:25Z + + + + + + + Jesse Coleman + 2021-04-19T23:46:33Z + + + + + + + + + Alaska Fisheries Science Center + The Alaska Fisheries Science Center's website is accessible at: https://www.fisheries.noaa.gov/about/alaska-fisheries-science-center + 2021-04-21T16:03:29Z + + + + + + + The Alaska Native Policy Center (Policy Center) is a project of the First Alaskans Institute created to support the Native voice and perspective in the public policy-making process. The Policy Center connects people and ideas producing knowledge that can be used to understand and improve the lives of Alaska Natives and all Alaskans. The Policy Center uses a proactive and forward- thinking approach, a focus that is statewide, and a relationship with the Native community that helps Alaska Native leaders and other policy makers access information they can use to help achieve healthy, thriving communities. + Alaska Native Policy Center + The Alaska Native Policy Center at the First Alaskans Institute's website is accessible at: https://firstalaskans.org/Alaska-Native-Policy-Center/overview/ + 2021-04-20T22:31:05Z + + + + + + SFU + https://ror.org/0213rcc28 + Simon Fraser University + SFU's website is accessible at: https://www.sfu.ca/ + 2021-04-20T20:29:55Z + + + + + + The Central Council of the Tlingit and Haida Indian Tribes of Alaska (Tlingit & Haida) is a tribal government representing over 32,000 Tlingit and Haida Indians worldwide. The are a sovereign entity and have a government to government relationship with the United States. + +Tlingit & Haida's headquarters are in Juneau, Alaska but their commitment to serving the Tlingit and Haida people extends throughout the United States. + Central Council of the Tlingit & Haida Indian Tribes of Alaska + The Central Council of the Tlingit and Haida Indian Tribes of Alaska website is accessbile at: http://www.ccthita.org/ + 2021-04-20T18:49:58Z + + + + + + Jonathan Samuelson + 2021-04-20T17:07:36Z + + + + + + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=commercialbyareakuskokwim.kswg + The Kuskokwim River Salmon Management Working Group (KRSMWG) was formed in 1988 by the Alaska Board of Fisheries (BOF) in response to requests from stakeholders in the Kuskokwim Area who sought a more active role in the management of salmon fishery resources. + +The Working Group is made up of 14 member seats representing elders, subsistence fishermen, processors, commercial fishermen, sport fishermen, Kuskokwim River Inter-Tribal Fish Commission, member at large, federal subsistence regional advisory committees, and the Alaska Department of Fish and Game. Non-agency members participate on a voluntary basis and receive no compensation. Participation in the Working Group process requires a great deal of time from its members and agency staff. + +The relationship among Working Group members, research planners, project leaders, and policy makers is fostered, and these interactions are critical to the aim of the Working Group. This relationship ensures that participants remain up-to-date on new information and maintain their direct involvement in management of Kuskokwim River salmon fisheries. + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.subsmission + The Subsistence Section provides the following core services: (a) Compile and analyze existing data; conduct research to gather information on the role of hunting and fishing by Alaskans for customary and traditional uses, (b) Disseminate current subsistence use information to the public; appropriate agencies and organizations; and fisheries and wildlife management divisions, (c) Assist the Board of Fisheries, the Board of Game, and the Joint Board of Fisheries and Game to evaluate customary and traditional uses of Alaska's fish and wildlife resources and amounts reasonably necessary for subsistence uses (ANS) of those resources, and (d) Assist fisheries and wildlife managers in preparing management plans to ensure information on customary and traditional uses and fish and wildlife harvests is incorporated. + + + + + + https://ror.org/0146z4r19 + A research center of the University of California, Santa Barbara which fosters collaborative synthesis research by assembling interdisciplinary teams to distill existing data, ideas, theories, or methods drawn from many sources, across multiple fields of inquiry, in order to accelerate the generation of new knowledge on a broad scale. + National Center for Ecological Analysis & Synthesis +NCEAS + National Center for Ecological Analysis and Synthesis + The NCEAS website is accessible at: https://www.nceas.ucsb.edu/ + 2021-03-27T00:18:57Z + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#southeast +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Approximately the size of the state of Kansas, the Southeast region is categorized by thousands of small coastal watersheds that provide ideal spawning habitat for pink salmon and chum salmon in particular. All five species are caught and return to this region. In terms of total abundance of salmon, Southeast Alaska dominates the state. Managing and conserving salmon populations that move beyond international borders is a key challenge here as many of the Chinook salmon caught in Southeast were hatched outside Alaska. + +The bounding coordinates for this SASAP region are: +North: 61.6887 degrees +South: 54.2508 degrees +East: -126.7735 degrees +West: -143.8874 degrees + + + + + + DANSRD + Department of Alaska Native Studies and Rural Development + The UAF Alaska Native Studies and Rural Development webpage is accessible at: https://www.uaf.edu/dansrd/ + 2021-03-29T22:59:49Z + + + + + + + Arctic Alaska or Far North Alaska is a region of the U.S. state of Alaska generally referring to the northern areas on or close to the Arctic Ocean. + Far North Alaska + Arctic + In the Arctic region of Alaska, connections between salmon and people are in their infancy. Salmon are just one harbinger of change in this region. + +The bounding coordinates for this SASAP region are: +North: 71.4396 degrees +South: 67.7408 degrees +East: -136.684 degrees +West: -166.311 degrees + 2021-03-24T21:27:43Z + + + + + + A department within the government of Alaska whose mission is to "Promote a healthy economy, strong communities, and protect consumers in Alaska." + https://ror.org/0580q1236 + Alaska Department of Commerce, Community, and Economic Development + 2021-03-25T18:03:19Z + + + + + + + A division within the government of Alaska's Department of Natural Resources (DNR) which maintains the department's land records repository and oversees DNR's computer systems and networks services. It provides for the department's data processing functions including development, training, operations, and maintenance. The Department of Natural Resources' (DNR) systems include the Land Administration System (LAS), the Geographic Information System, the Revenue and Billing System, and others. The section also produces and maintains the state's land status maps. + Alaska Department of Natural Resources, IRM + Alaska Department of Natural Resources, Support Services Division, Information Resource Management + 2021-03-25T18:04:32Z + + + + + + + Sam Truesdell + 2021-04-20T15:27:23Z + + + + + + + + isAdvisorTo + In addition to a lead researcher, some SASAP working groups have an additional advisor(s) to assist in the research efforts. The 'isAdvisorTo' object property connects advisors to their respective working groups. + 2021-04-19T23:41:09Z + + + + + + + Kenai Peninsula Borough (Russian: Кенай боро, Kenay boro) is a borough of the U.S. state of Alaska. + KPB + Kenai Peninsula Borough + The Kenai Peninsula Borough's website is accessible at: https://www.kpb.us/ + 2021-04-20T23:33:12Z + + + + + + Chistochina Enterprises is a wholly owned Section 17 Corporation authorized by the 1934 Indian Reorganization Act, formed under a Federal charter to represent the business interests of Cheesh'na and as a means of investing in the future of the Tribe. Chistochina Enterprises is governed by a five member Board of Director initially appointed by Cheesh'na Tribal Council. The main office is located in Chistochina, Alaska, and the enterprise is licensed to conduct business in the State of Alaska and nationally as outlined in its Federal charter. + Christochina Enterprises + Christochina Enterprises' website is accessible at: http://www.chistochinaenterprises.com + 2021-04-20T22:28:28Z + + + + + + UC Davis + https://ror.org/05rrcem69 + University of California, Davis + UC Davis's website is accessible at: https://www.ucdavis.edu/ + 2021-04-20T20:18:20Z + + + + + + Native Village of Kotzebue + More information about the Native Village of Kotzebue can be found at: https://www.nwabor.org/village/kotzebue/ + 2021-04-20T18:02:31Z + + + + + + Wilson Justin + 2021-04-20T17:06:54Z + + + + + + + + + + + + + + + + + http://purl.obolibrary.org/obo/GAZ_00147944 +http://purl.obolibrary.org/obo/GAZ_00197646 +http://purl.obolibrary.org/obo/GAZ_00055346 + Kuskokwim + The Kuskokwim region is the 4th largest of Alaska, and at 154,168 km² is comparable in size to the state of Georgia. The region drains the Kuskokwim – one of the great rivers of the world. The salmon-producing habitat of the Kuskokwim region is diverse and productive. Drier than the neighboring Bristol Bay region, the Kuskokwim region has a larger amount of burn area from forest fires than all other regions but the Yukon. + +The bounding coordinates for this SASAP region are: +North: 64.4166 degrees +South: 58.6262 degrees +East: -151.5105 degrees +West: -173.2164 degrees + 2021-03-24T21:28:48Z + + + + + + A department within the government of Alaska which (a) has the specific statutory responsibility of protecting freshwater habitat for anadromous fish and providing free passage for all fish in freshwater bodies, (b) develops management plans and oversees activities (excluding trapping, hunting, fishing, and wildlife viewing) in legislatively designated refuges, critical habitat areas, and sanctuaries known collectively as Special Areas, (c) works with the Division of Sport Fish to update the “Catalog of Waters Important for the Spawning, Rearing, or Migration of Anadromous Fishes,” (d) coordinates the ADF&G review of large and complex projects important to the State, and (e) works closely with the ADNR Division of Forestry to survey State and private forestry operations and evaluate implementation of Alaska’s Forest Resources and Practices Act (FRPA). + Alaska Department of Fish and Game, Division of Habitat + 2021-03-25T18:04:11Z + + + + + + + + 2021-03-25T18:05:35Z + + + + + United States Geologic Survey + https://ror.org/035a68863 + A bureau of the United Sates Departement of the Interior, which provides science about the natural hazards that threaten lives and livelihoods, the water, energy, minerals, and other natural resources we rely on, the health of our ecosystems and environment, and the impacts of climate and land-use change. + The USGS website is accessible at: https://www.usgs.gov/ + USGS + + + Governance working group + Governance and subsistence working group + Learn more about the Governance and Subsistence Working Group here: https://alaskasalmonandpeople.org/working-group/governance-and-subsistence/ + 2021-03-25T18:47:12Z + + + + + + A financial institution principally engaged in investing in securites (i.e. a tradable financial asset). + Investing firm + 2021-04-05T20:05:34Z + + + + + + Bert A. Lewis + 2021-04-20T15:51:45Z + + + + + + + Daniel Schindler + 2021-04-20T15:43:57Z + + + + + + + + Academic degree program + 2021-04-21T18:08:49Z + + + + + + + Liza Mack + 2021-04-19T23:55:55Z + + + + + + + + USF + https://ror.org/032db5x82 + University of South Florida + USF's website is accessible at: https://www.usf.edu/ + 2021-04-21T16:44:47Z + + + + + + Auke Bay Laboratories + Auke Bay Laboratories' website is accessible at: https://www.fisheries.noaa.gov/about/auke-bay-laboratories + 2021-04-20T23:09:04Z + + + + + + + https://alaskasalmonandpeople.org/ + The SASAP project is a deep assessment of the state of knowledge of the biological, sociocultural, economic and governance dimensions of Alaska's salmon and the people who depend upon them. The SASAP project shares this knowledge with Alaska salmon users through comprehensive watershed-level summaries (Regions), focused research on specific salmon issues (Topics), and suppported links to SASAP's free, open-source datasets, accessible through the SASAP Data Portal (https://knb.ecoinformatics.org/portals/SASAP/Data). + + + + + + https://wdfw.wa.gov/about + A department within the government of Washington which is dedicated to preserving, protecting, and perpetuating the state's fish, wildlife, and ecosystems while providing sustainable fish and wildlife recreational and commercial opportunities. + + + + + + NRC + Natural Resources Consultants, Inc. + NRC's website is accessible at: https://nrccorp.com/ + 2021-04-20T23:05:50Z + + + + + + The Southeast Alaska/Yakutat Region (Region I) consists of Alaska waters between Cape Suckling on the north and Dixon Entrance on the south. Salmon are commercially harvested in Southeast Alaska with purse seines and drift gillnets; in Yakutat with set gillnets; and in both areas with hand and power troll gear. Herring are harvested in winter bait, sac roe, spawn-on-kelp, and bait pound fisheries. Miscellaneous shellfish (sea cucumber, sea urchins, and geoduck clams) are harvested in dive fisheries in the region. The Alaska Department of Fish and Game (ADF&G) has management jurisdiction over all groundfish resources within state waters in Region I. In addition, the State has management authority for Demersal Shelf Rockfish, ling cod, and black and blue rock fish in both state and federal waters. There are several commercially important shellfish species in Southeast Alaska. They include golden and red king crab, Dungeness crab, Tanner crab, and pandalid shrimp. + Alaska Department of Fish and Game, Division of Commercial Fisheries, Southeast Region + + + 2021-03-25T18:04:07Z + + + Region I + + A department within the government of Alaska and a sub-division of the Alaska Department of Fish and Wildlife, Division of Commercial Fisheries which manages the Southeast Region. + + + ESPM +ESPM UC Berkeley + Department of Environmental Science, Policy, and Management + ESPM's webpage is accessible at: https://ourenvironment.berkeley.edu/ + 2021-04-20T21:12:55Z + + + + + + + + 2021-03-25T18:05:30Z + https://ror.org/04k7dar27 + + A bureau of the United States Department of the Interior whose mission is to work with others to conserve, protect and enhance fish, wildlife and plants and their habitats for the continuing benefit of the American people. + + USFWS + + + United States Fish and Wildlife Service + + + Economic working group + Socioeconomic working group + Learn more about the Socioeconomic Working Group here: https://alaskasalmonandpeople.org/working-group/economic-dimensions-of-salmon-systems/ + The goals of the Economic working group are to (1) identify important trends in the historical relationships between salmon and salmon users which may have been overlooked, (2) inform and support evidence-based policy aimed at sustainable and equitable decision making, and (3) compile, archive, and share relevant historical socioeconomic data about Alaska's salmon systems. + 2021-03-25T18:47:08Z + + + + + + hasAffiliate + 2021-03-25T19:11:36Z + + + + + + + http://www.adfg.alaska.gov/index.cfm?adfg=divisions.haboverview + A department within the government of Alaska which (a) has the specific statutory responsibility of protecting freshwater habitat for anadromous fish and providing free passage for all fish in freshwater bodies, (b) develops management plans and oversees activities (excluding trapping, hunting, fishing, and wildlife viewing) in legislatively designated refuges, critical habitat areas, and sanctuaries known collectively as Special Areas, (c) works with the Division of Sport Fish to update the “Catalog of Waters Important for the Spawning, Rearing, or Migration of Anadromous Fishes,” (d) coordinates the ADF&G review of large and complex projects important to the State, and (e) works closely with the ADNR Division of Forestry to survey State and private forestry operations and evaluate implementation of Alaska’s Forest Resources and Practices Act (FRPA). + + + + + + + + + http://www.calistaeducation.org/about-us.html + The Calista Elders Council was established in 1991 as a non-profit organization representing 1,300 Yup'ik traditional bearers of the Yukon-Kuskokwim Delta in Southwest Alaska. The Calista Elders Council was formed to help protect and preserve the Yup’ik, Cup’ik and Athabascan cultures. + +In 2014, after a 20 year history of interacting and working together, the Calista Elders Council, Inc. merged with the former Calista Heritage Foundation to form what is now Calista Education and Culture, Inc. + + + + + + + + + + + A research institute which is not part of a university, government, hospital or corporation. An independent research institute may have a close relationship with a larger institution such as a university, but is not part of the larger insitution and operates under its own authority. + Independent research institute + 2021-04-05T19:57:33Z + + + + + + https://orcid.org/0000-0002-1234-1297 + Curry Cunningham + 2021-04-20T16:11:48Z + + + + + + + + Laura Loucks + 2021-04-20T15:50:50Z + + + + + + + + Joe Spaeder + 2021-04-20T15:40:25Z + + + + + + + + UW EarthLab +University of Washington EarthLab +Center for Creative Conservation +C3 + EarthLab + Since its establishment, the Center has been a member of UW EarthLab—a new environmental institute housing other groups such as the Climate Impacts Group, the Center for Health and the Global Environment, and the Washington Ocean Acidification Center. EarthLab’s inaugural Executive Director, Ben Packard, has been working over the past year to clarify the vision, priorities and strategic outcomes for EarthLab. As this vision has taken shape, it has become clear that the activities of the Center are a key element of EarthLab. Rather than duplicating the efforts of C3 at the EarthLab level, we have decided to integrate the Center for Creative Conservation into EarthLab. + 2021-04-21T17:48:10Z + + + + + + + Jim Fall + 2021-04-19T23:54:56Z + + + + + + + + + Auburn + https://ror.org/02v80fc35 + Auburn University + Auburn's website is accessible at: https://www.auburn.edu/ + 2021-04-21T16:43:47Z + + + + + + https://knb.ecoinformatics.org/portals/SASAP/Regions#copperriver +https://knb.ecoinformatics.org/view/doi%3A10.5063%2FF1WH2N8W + Fewer than 2500 people live permanently in the Copper River region, an area comparable in size to the state of West Virginia. Sockeye salmon are dominant here, given the multiple large lakes available for rearing juvenile salmon. Though less abundant than sockeye, king salmon are deeply important to all salmon-connected people. Kings have declined in number since 2007. + +The bounding coordinates for this SASAP region are: +North: 63.3227 degrees +South: 59.7112 degrees +East: -139.6942 degrees +West: -147.8251 degrees + + + + + + + An enterprise (potentially individual but typically collaborative), planned to achieve a particular aim. + Project + 2021-03-30T20:31:09Z + + + + + + An inlet of the Bering Sea on the western coast of the State of Alaska, south of the Seward Peninsula. It is about 240 km long and 200 km wide. The Yukon River delta forms a portion of the south shore and water from the Yukon influences this body of water. + http://purl.obolibrary.org/obo/GAZ_00051068 + Norton Sound + An average of two million pink salmon and 250,000 chum salmon return to the sub-Arctic region of Norton Sound, an area approximately twice the size of Massachusetts. + +The bounding coordinates of this SASAP region are: +North: 65.8544 degrees +South: 62.8268 degrees +East: -159.1906 degrees +West: -171.9762 degrees + 2021-03-24T21:28:59Z + + + + + + + + A permanent or semi-permanent state govenrment organization which is responsible for the oversight and administration of specific functions. + State government department, division, or agency + 2021-03-25T18:01:09Z + + + + + + A department within the government of Alaska with a mission to scientifically gather, quantify, evaluate, and report information about customary and traditional uses of Alaska's fish and wildlife resources. + Alaska Department of Fish and Game, Division of Subsistence + The Subsistence Section provides the following core services: (a) Compile and analyze existing data; conduct research to gather information on the role of hunting and fishing by Alaskans for customary and traditional uses, (b) Disseminate current subsistence use information to the public; appropriate agencies and organizations; and fisheries and wildlife management divisions, (c) Assist the Board of Fisheries, the Board of Game, and the Joint Board of Fisheries and Game to evaluate customary and traditional uses of Alaska's fish and wildlife resources and amounts reasonably necessary for subsistence uses (ANS) of those resources, and (d) Assist fisheries and wildlife managers in preparing management plans to ensure information on customary and traditional uses and fish and wildlife harvests is incorporated. + 2021-03-25T18:04:20Z + + + + + + + + An entity created by treaty, involving two or more nations, to work in good faith, on issues of common interest. + Intergovernmental organization + 2021-03-25T18:06:04Z + + + + + + + + + Bill Bechtol + 2021-04-20T15:45:26Z + + + + + + + + Indigenous Studies Program + 2021-04-21T18:09:34Z + + + + + + + Rob Sanderson Jr. + 2021-04-19T23:58:18Z + + + + + + + + CBT + Clayoquot Biosphere Trust + CBT's website is accessible at: https://clayoquotbiosphere.org/about-us/overview + 2021-04-21T17:21:37Z + + + + + + isSupportingResearcherOf + In addition to a lead researcher, some SASAP working groups have an additional affiliated researcher(s) to assist in the research efforts. The 'isSupportingResearcherOf' object property connects supporting researchers to their respective working groups. + 2021-04-19T21:19:32Z + + + + + + + + Mountains to Sea + Kenai Mountains to Sea + Kenai Mountains to Sea's website is accessible at: https://kenaiwatershed.org/science-in-action/mountains-to-sea/ + 2021-04-20T23:24:55Z + + + + + + Akiak Native Community + The Akiak Native Community's website is accessible at: https://akiaknativecommunity.org/ + 2021-04-20T21:31:20Z + + + + + + NOAA + https://ror.org/02z5nhe81 + National Oceanic and Atmospheric Administration + NOAA's website is accessible at: https://www.noaa.gov/ + 2021-04-20T20:10:56Z + + + + + + UW + https://ror.org/01y2jtd41 + University of Wisconsin-Madison + UW's website is accessible at: https://www.wisc.edu/ + 2021-04-20T20:08:29Z + + + + + + A sound of the Gulf of Alaska on the south coast of the State of Alaska. It is located on the east side of the Kenai Peninsula. + http://purl.obolibrary.org/obo/GAZ_00051075 + PWS + Prince William Sound + Prince William Sound is a region of rain, icefields, and glaciers. Only two (Whittier and Valdez) of Prince William Sound’s largest human communities are connected via road. The terminus of the Alaska oil pipeline ends in this region and results in a fairly high footprint of human activity in a relatively small region. Pink salmon, chum salmon, and sockeye salmon fisheries are current mainstays of local communities with hatchery enhancement of these species (particularly pink salmon) a fundamental dynamic in the region. + +The bounding coordinates of this SASAP region are: +North: 61.5189 degrees +South: 59.357 degrees +East: -145.1013 degrees +West: -149.1761 degrees + 2021-03-24T21:28:55Z + + + + + + A department within the government of Alaska with a mission to protect and improve the state's sport fishery resources. + Alaska Department of Fish and Game, Division of Sport Fish + The Division of Sport Fisheries provides the following core services: (a) fisheries management, (b) fisheries research, (c) fisheries enhancement, (d) protection and restoration of fish habitats for the ebefit of fish and sport anglers, (e) communication and outreach, and (f) providing leadership and administrative support for the Division's core functions. + 2021-03-25T18:04:16Z + + + + + + + + A department within the government of Washington which is dedicated to preserving, protecting, and perpetuating the state's fish, wildlife, and ecosystems while providing sustainable fish and wildlife recreational and commercial opportunities. + WDFW + https://ror.org/03dnb3013 + Washington Department of Fish and Wildlife + 2021-03-25T18:05:41Z + + + + + + + Salmon size working group + 2021-03-25T18:47:18Z + + + + + + + + + http://en.wikipedia.org/wiki/Cook_Inlet +https://www.wikidata.org/wiki/Q5166925 + A large estuary stretching 180 miles from the Gulf of Alaska to Anchorage in south-central Alaska. It separates the Kenai Peninsula from mainland Alaska and branches into the Knik Arm and Turnagain Arm at its northern end, almost surrounding Anchorage. The watershed covers about 100,000 km2 of southern Alaska, east of the Aleutian Range and south of the Alaska Range, receiving water from its tributaries the Knik River, the Little Susitna River, and the Susitna and Matanuska rivers. The watershed includes the drainage areas of Mount McKinley. Within the watershed there are several national parks and four historically active volcanoes. + + + + + + https://orcid.org/0000-0001-6102-1110 + Marissa L. Baskett + 2021-04-20T15:53:13Z + + + + + + + + Milo Adkison + 2021-04-20T15:44:32Z + + + + + + + + + + Graduate degree program + 2021-04-21T18:09:16Z + + + + + + Julie Raymond-Yakoubian + 2021-04-19T23:57:10Z + + + + + + + + + Charity + 2021-04-21T17:14:16Z + + + + + + Federal/non-federal partnerships and programs + 2021-04-20T23:24:11Z + + + + + + Old Harbor Native Corporation (OHNC) was established in 1971 under the terms of the Alaska Native Claims Settlement Act (ANCSA). + +OHNC’s mission is to preserve and protect the culture, values and traditions of its community, shareholders and descendants; and to work together to create economic and educational opportunities while promoting self-determination and pride. + Old Harbor Native Corporation + OHNC's website is accessible at: https://www.oldharbornativecorp.com/ + 2021-04-20T21:29:40Z + + + + + diff --git a/src/main/resources/ontologies/SENSO.owl b/src/main/resources/ontologies/SENSO.owl new file mode 100644 index 00000000..66444b11 --- /dev/null +++ b/src/main/resources/ontologies/SENSO.owl @@ -0,0 +1,126 @@ + + + definition source + 2020-11-04T19:47:37Z + + + + + + + + + + + + 2021-09-28 + + + + Sensitive Data Ontology (SENSO) + Version 0.1.0 + + Ontology to support sensitive data annotation of datasets housed at the Arctic Data Center (https://arcticdata.io) + + + + + + + + + + + + + Non-sensitive data + None of the data includes sensitive or protected information. + 2021-09-28 + + Non-sensitive data + + + + + Data Sensitivity Category + 2021-09-28 + + Data sensitivity categories assign a level of sensitivity for datasets and provide guidelines for acceptable distribution and use. + + + + + + + + + + + + + + + + + + + + + + + + + definition + 2021-09-28T19:46:54Z + + + + + data sensitivity + + 2021-09-30 + the sensitivity of the given data + + + + + + + + Sensitive data + The data contains human subjects data or other sensitive data. Release of the data could cause harm or violate statutes, and must remain confidential following restrictions from an Institutional Review Board (IRB) or similar body. + 2021-09-28 + + Some or all data is sensitive and should not be distributed + + + + + De-identified data + Sensitive data has been de-identified, anonymized, aggregated, or summarized to remove sensitivities and enable safe data distribution. Examples include ensuring that human subjects data, protected species data, archaeological site locations and personally identifiable information have been properly anonymized, aggregated and summarized. + 2021-09-28 + + Some or all data is sensitive but has been made safe for open distribution + + + + + + + + + + diff --git a/src/test/java/org/dataone/cn/indexer/annotation/OntologyModelServiceTest.java b/src/test/java/org/dataone/cn/indexer/annotation/OntologyModelServiceTest.java index 61f19064..5922403a 100644 --- a/src/test/java/org/dataone/cn/indexer/annotation/OntologyModelServiceTest.java +++ b/src/test/java/org/dataone/cn/indexer/annotation/OntologyModelServiceTest.java @@ -67,6 +67,8 @@ public void testECSOMeasurementTypeExpansion() { values.add("http://purl.dataone.org/odo/ECSO_00000514"); values.add("http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType"); values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://www.w3.org/2002/07/owl#Class"); assertEquals(values, concepts.get("annotation_value_uri")); } catch (Exception e) { @@ -93,4 +95,266 @@ public void testPropertyExpansion() { fail(e.getMessage()); } } + + @Test + public void testMOSAiCExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("https://purl.dataone.org/odo/MOSAIC_00000865"); + + Set values = new HashSet(); + values.add("https://purl.dataone.org/odo/MOSAIC_00000865"); + values.add("https://purl.dataone.org/odo/MOSAIC_00000036"); + values.add("https://purl.dataone.org/odo/MOSAIC_00012000"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://www.w3.org/2002/07/owl#Class"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testMOSAiCSameAsExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("https://purl.dataone.org/odo/MOSAIC_00000225"); + + Set values = new HashSet(); + values.add("https://purl.dataone.org/odo/MOSAIC_00000022"); // Project + values.add("https://purl.dataone.org/odo/MOSAIC_00000225"); // MOSAiC + values.add("https://purl.dataone.org/odo/MOSAIC_00000226"); // Multidisciplinary drifting Observatory for the Study of Arctic Climate (sameAs) + values.add("https://purl.dataone.org/odo/MOSAIC_00000023"); // MOSAiC20192020 (sameAs) + values.add("http://www.w3.org/2002/07/owl#NamedIndividual"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testARCRCExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("http://purl.dataone.org/odo/ARCRC_00000051"); + + Set values = new HashSet(); + /** + * Add values for ARCRC:SnowDepth and its supertypes: + * + * SnowDepth -> Snow Key Variable Arctic Key Variable -> Arctic Report Card Component + */ + values.add("http://purl.dataone.org/odo/ARCRC_00000051"); // ARCRC:SnowDepth + values.add("http://purl.dataone.org/odo/ARCRC_00000502"); // ARCRC:SnowKeyVariable + values.add("http://purl.dataone.org/odo/ARCRC_00000040"); // ARCRC:KeyVariable + values.add("http://purl.dataone.org/odo/ARCRC_00000500"); // ARCRC:ArcticReportCardComponent + + + /** + * Add values for ARCRC:SnowDepth's equivalentClass of ECSO:SnowDepth and its supertypes: + * + * SnowDepth -> Water Depth -> Depth -> linearMeasurementType -> Measurement Type + */ + values.add("http://purl.dataone.org/odo/ECSO_00001205"); // ECSO:SnowDepth + values.add("http://purl.dataone.org/odo/ECSO_00000553"); // ECSO:linearMeasurementType + values.add("http://purl.dataone.org/odo/ECSO_00001203"); // ECSO:WaterDepth + values.add("http://purl.dataone.org/odo/ECSO_00001250"); // ECSO:Depth + values.add("http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType"); + + // Values for high level stuff + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("http://www.w3.org/2002/07/owl#NamedIndividual"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testNamedIndividualExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("http://purl.dataone.org/odo/ARCRC_00000507"); + + Set values = new HashSet(); + values.add("http://purl.dataone.org/odo/ARCRC_00000507"); // ARCRC:Greenland itself + values.add("http://www.w3.org/2002/07/owl#NamedIndividual"); // the type of ARCRC:Greenland + values.add("http://purl.dataone.org/odo/ARCRC_00000505"); // ARCRC:GeographicNamedPlace (type of ARCRC:Greenland) + values.add("http://purl.dataone.org/odo/ARCRC_00000506"); // ARCRC:Place (supertype of GeographicNamedPlace) + values.add("http://purl.dataone.org/odo/ARCRC_00000500"); // ARCRC:ArcticReportCardComponent + values.add("http://purl.obolibrary.org/obo/GAZ_00001507"); // sameAs + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testEquivalentPropertyExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("https://purl.dataone.org/odo/MOSAIC_00002250"); + + Set values = new HashSet(); + values.add("http://www.w3.org/ns/ssn/deployedSystem"); + values.add("https://purl.dataone.org/odo/MOSAIC_00002250"); + + assertEquals(values, concepts.get("annotation_property_uri")); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testADCADExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("https://purl.dataone.org/odo/ADCAD_00034"); + + + // Assert on Solr fields returend + Set fields = new HashSet(); + fields.add("annotation_property_uri"); + fields.add("annotation_value_uri"); + assertEquals(concepts.keySet(), fields); + + // Assert on Solr field values returned + Set values = new HashSet(); + values.add("https://purl.dataone.org/odo/ADCAD_00034"); + values.add("https://purl.dataone.org/odo/ADCAD_00067"); + values.add("https://purl.dataone.org/odo/ADCAD_00033"); + values.add("https://purl.dataone.org/odo/ADCAD_00000"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://localhost/plosthes.2017-1#2863"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("https://www.wikidata.org/wiki/Q2329"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testSALMONExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("https://purl.dataone.org/odo/MOSAIC_00000041"); + + + // Assert on Solr fields returend + Set fields = new HashSet(); + fields.add("annotation_property_uri"); + fields.add("annotation_value_uri"); + assertEquals(concepts.keySet(), fields); + + // Assert on Solr field values returned + Set values = new HashSet(); + values.add("https://purl.dataone.org/odo/MOSAIC_00000041"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("https://purl.dataone.org/odo/MOSAIC_00012000"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testSALMONAlignmentExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("http://purl.dataone.org/odo/salmon_000529"); + + // Assert on Solr fields returend + Set fields = new HashSet(); + fields.add("annotation_property_uri"); + fields.add("annotation_value_uri"); + assertEquals(concepts.keySet(), fields); + + // Assert on Solr field values returned + Set values = new HashSet(); + values.add("http://purl.dataone.org/odo/SALMON_00000672"); + values.add("http://purl.dataone.org/odo/SALMON_00000572"); + values.add("http://purl.dataone.org/odo/SALMON_00000528"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("http://purl.dataone.org/odo/salmon_000529"); + values.add("http://purl.dataone.org/odo/SALMON_00000529"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testSASAPExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("http://purl.dataone.org/odo/SASAP_00000393"); + + + // Assert on Solr fields returend + Set fields = new HashSet(); + fields.add("annotation_property_uri"); + fields.add("annotation_value_uri"); + assertEquals(concepts.keySet(), fields); + + // Assert on Solr field values returned + Set values = new HashSet(); + values.add("http://purl.dataone.org/odo/SASAP_00000098"); + values.add("http://purl.dataone.org/odo/SASAP_00000174"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://purl.dataone.org/odo/SASAP_00000393"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } + + @Test + public void testSENSOExpansion() { + try { + Map> concepts = OntologyModelService.getInstance().expandConcepts("http://purl.dataone.org/odo/SENSO_00000002"); + + + // Assert on Solr fields returend + Set fields = new HashSet(); + fields.add("annotation_property_uri"); + fields.add("annotation_value_uri"); + assertEquals(concepts.keySet(), fields); + + // Assert on Solr field values returned + Set values = new HashSet(); + values.add("http://purl.dataone.org/odo/SENSO_00000002"); + values.add("http://www.w3.org/2000/01/rdf-schema#Class"); + values.add("http://purl.dataone.org/odo/SENSO_00000001"); + values.add("http://www.w3.org/2002/07/owl#Class"); + values.add("http://www.w3.org/2000/01/rdf-schema#Resource"); + + assertEquals(values, concepts.get("annotation_value_uri")); + } catch (Exception e) { + e.printStackTrace(); + fail(e.getMessage()); + } + } }