AndreaBozzo/ceres-open-data-index huggingface dataset:
West Coast DA Event data - West Coast Toxic Pseudo-nitzschia bloom

Beginning in the spring of 2015 the US West Coast began to experience the most wide-spread toxic Pseudo-nitzschia bloom to date, after approximately eight years without a toxic bloom event.  Some species of Pseudo-nitzschia produce the neurotoxin domoic acid, which can have deleterious effects on marine wildlife (e.g. mammals and seabirds) as well as human consumers of food items (e.g. shellfish, crabs, sardines, anchovies) that are contaminated with the toxin. This multi-agency project aims to survey the bloom region, which stretches from southern California into the Gulf of Alaska, on the greatest spatial and temporal extent possible.  Goals of the survey are to identify the extent of the bloom, the concentration of domoic acid in the bloom, the Pseudo-nitzschia species responsible for the toxicity, and the relationship of the bloom event to prevailing oceanographic and atmospheric conditions.  The survey will allow for the creation of maps showing the spatial extent and concentrations of domoic acid, Pseudo-nitzschia, and oceanographic parameters such as temperature and salinity.   The data collected from the survey will inform inferences as to the cause(s) of the toxic event.  The effort will employ targeted research cruises, cruises of opportunity, and shore based sampling.  Samples will be analyzed for marine toxins, harmful algal species, and other environmental and oceanographic parameters using state-of-the-art methodologies.
Dataset contains domoic acid measurements, Pseudo-nitzschia species identifications and enumerations, and other physical oceanographic, biological and chemical oceanographic data.

Tags: and depth, animal and plant collection device, animal and plant collection device - plankton collection device - plankton net, biotoxins, ctd, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, in-situ instrument - in-situ instrument (not specified), marine toxin, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, pseudo-nitzschia, sake survey, sonde and probe - conductivity, temperature, underway data collection instrument, underway data collection instrument - thermosalinograph, water sampler bottle - niskin bottle, water sampler bottle - surface sample bottle
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Stream flow and temperature maps - Effect of Climate Change on Salmon Population Vulnerability

1. Steelhead (Oncorhynchus mykiss) and other Pacific salmon are threatened by unsustainable
levels of harvest, genetic introgression from hatchery stocks and degradation or loss of freshwater
habitat. Projected climate change is expected to further stress salmon through increases
in stream temperatures and altered stream flows.
2. We demonstrate a spatially explicit method for assessing salmon vulnerability to projected
climatic changes (scenario for the years 20302059), applied here to steelhead salmon across
the entire Pacific Northwest (PNW). We considered steelhead exposure to increased temperatures
and more extreme high and low flows during four of their primary freshwater life stages:
adult migration, spawning, incubation and rearing. Steelhead sensitivity to climate change
was estimated on the basis of their regulatory status and the condition of their habitat. We
assessed combinations of exposure and sensitivity to suggest actions that may be most effective
for reducing steelhead vulnerability to climate change.
3. Our relative ranking of locations suggested that steelhead exposure to increases in temperature
will be most widespread in the southern Pacific Northwest, whereas exposure to substantial
flow changes will be most widespread in the interior and northern Pacific Northwest.
There were few locations where we projected that steelhead had both relatively low exposure
and sensitivity to climate change.
4. Synthesis and applications. There are few areas where habitat protection alone is likely to
be sufficient to conserve steelhead under the scenario of climate change considered here.
Instead, our results suggest the need for coordinated, landscape-scale actions that both
increase salmon resilience and ameliorate climate change impacts, such as restoring connectivity
of floodplains and high-elevation habitats.

Stream flow and temperature gridded data for PNW.

Tags: climate change, climate/ocean exchanges, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, habitat, habitat characteristics, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pacific nw, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Townet database - Evaluating the ecological health of Puget Sound's pelagic foodweb

To evaluate effects of human influence on the health of Puget Sound's pelagic ecosystems, we propose a sampling program across multiple oceanographic basins measuring key attributes of the pelagic foodweb. We will quantify seasonal abundance and composition of pelagic biota from lower trophic levels (e.g., bacteria and phytoplankton) to middle trophic levels (e.g., zooplankton, small pelagic fishes, and jellyfish), as well as assess the individual condition of forage fish and juvenile salmon. 

The goals of this program:

1) Determine how foodweb endpoints vary across natural and anthropogenic gradients.

2) Determine how these characteristics vary across Puget Sound.

3) Evaluate a number of biological metrics for monitoring ecosystem health.

These outputs will improve our basic understanding of pelagic ecology in Puget Sound, better define what comprises a healthy pelagic ecosystem in Puget Sound, determine foodweb-relevant indicators that are sensitive to human influence, and help prioritize regional protection and restoration efforts. Work is conducted by NOAA personnel and contractors in collaboration with tribal partners (Squaxin, Port Gamble/S'Klallam), undergraduate research interns, and citizen volunteers.
Filemaker Pro database containing fish data collection.

Tags: admiralty inlet, animal and plant collection device, bacterial communities, balance, chlorophyll a, doc/noaa/nmfs/nwfsc, ecosystem, fe (fish ecology) division, food web, heterotrophic production, hood canal, length board, low dissolved oxygen, marine microbes, microbial abundance, national marine fisheries service, nearshore pelagic, noaa. u.s. department of commerce, north central ps basin, northwest fisheries science center, nutrients, puget sound, rosario basin, salmon, south central ps basin, south ps basin, whidbey basin north, whidbey basin south
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Ocean acidification genetics - Genetics and genomics of response to ocean acidification

We are applying a variety of genetic tools to assess the response of our ocean resources to ocean acidification, including gene expression techniques, identification of candidate genes, and application of genomics. The focus of this research is to determine whether or to what extent the responses of key marine organisms to ocean acidification are evolutionary or phenotypically plastic. At present, this research focuses on invertebrates such as arthropods (e.g., Dungeness crab) and molluscs (e.g., clams, oysters, mussels), but will eventually also include vertebrates (e.g., marine and anadromous fishes).
Genetics and traits.

Tags: cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, genetics, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, ocean acidification
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Analyses of water and tissue samples - Evaluating the impacts of pesticides on ESA-listed salmon and their habitats

Long-running science support for the agency (Office of Protected Resources, others) related to the use of modern pesticides throughout the United States as a limiting factor for endangered species conservation and recovery. This work is currently supporting several national ESA Biological Opinions, and is under review by the National Academy of Sciences. The NAS panel recommendations are expected in the summer of 2013, and these will guide additional research in FY14 and beyond.
Analyses of water and tissue samples for pesticides.

Tags: 92606, doc/noaa/nmfs/nwfsc, ecotoxicology, endangered species act, mass spectrophotometer, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, nwfsc mukilteo, salmon, stormwater
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Collaborative Pre-Recruit Survey (station)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Pre-Recruit Survey stations. The Collaborative Pre-Recruit Survey started in 2011 and is led by NMFS Northwest Fisheries Science Center. This survey includes researchers from NOAAâs Northwest Fisheries Science Center, Oregon State University, University of Oregon, and the University of California, Santa Cruz. This consistent survey has generated significant information on within- and between-year variability in the California Current Marine Ecosystem and has yielded valuable insights into the food web off our coast. Parameters and ecological processes quantified during this effort are used in forecasts involving species, assemblages, and ecosystems and also to parameterize ecosystem models used to evaluate cumulative risks and managerial strategies. Annual surveys are conducted within the coastal ecosystem off Oregon and Washington. At all stations a Cobb Trawl at 30 m is towed. Data on hydrology, plankton, small fish, and predators are collected along transects over the continental shelf from Oregon and Washington. Specimens are collected for diet analysis, growth, containment load, and other studies related to the ecology and production of commercially important taxa and their relationships within the food web.

Tags: acoustic automated analysis, bell m. shimada, climate indicators, doc/noaa/nmfs/nwfsc, ecosystem indicator, fish eggs and larvae, food web, juvenile fishes, krill, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oceanography, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Methow River Steelhead - Methow River Steelhead hatchery reform research

Steelhead in Pacific Northwest hatcheries are typically reared for release as 1-year-old smolts, rather than the 2Â¬and 3-year-old smolt life history patterns found in nature. High growth rates associated with accelerated hatchery rearing to a 1-year-old smolt life history may contribute to maladaptive behavioral traits and reduced post-release survival, and may constitute a primary mechanism leading to reduced fitness in hatchery fish. This project provides for implementation and evaluation of major hatchery reforms identified for the US Fish and Wildlife Serviceâs Winthrop National Fish Hatchery (WNFH).  The project combines hatchery-scale and laboratory scale research to investigate the effects of two growth regimes on i) post-release survival and behavior, ii) on maturation and residualism, iii) age-at-maturity, iv) epigenetic changes, and v) reproductive success of returning adults.
PIT tag data for age-1 and age-2 steelhead smolts released from Winthrop National Fish Hatchery for release years 2010-2015.

Tags: behavioral syndromes, doc/noaa/nmfs/nwfsc, domestication selection, hatchery, hatchery reform, in-situ instrument - in-situ instrument (not specified), manchester research station, maturation, methow river, migrated from resource enhancement and utilization technologies division, montlake laboratory, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, smoltification, steelhead, survival
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Un-ionized Ammonia (UIA) - Live Hauling of Fish

In certain markets, live fish can be sold for substantially higher prices than fresh dressed fish. A significant live-haul industry has developed in the U.S. and fish are commonly hauled 1,500-2,000 miles (25-30 hours) to market. The most common species hauled are tilapia, channel catfish, and rainbow trout; a smaller amount of marine rockfish, hybrid striped bass, and carp are also hauled. The most significant advancement in hauling technology in the last 20 years has been the use of bottled oxygen gas or liquid oxygen to maintain adequate dissolved oxygen levels. These types of systems can maintain significantly higher DO levels than systems using air. Some common stressors include harvest and loading procedures (pumping or out of water transfer), shaking as the transport vehicle is moving, low frequency sound from the vehicle and water treatment systems, crowding, and poor water quality (high ammonia and carbon dioxide levels, low dissolved oxygen), high light levels, or extreme water temperature. The physical shape and construction of the hauling unit may have an important impact on localized low DOs, physical damage to the fish, and survivability. Very little information has been published on the chemical and physical conditions in transport systems during long-distance transport and this limited data may not be representative of current commercial systems. 

This research will be conducted with NWFSC staff in cooperation with private fish farmers in the Pacific Northwest. Specific sub-objectives will include the following:

(1) Documentation of water quality during transport and impact on mortality and product quality

(2) Design of efficient aeration systems for oxygen transfer and carbon dioxide stripping

(3) Determination of the impact of transport tank design and aerator type on the thermal balance during hauling.

The impact of this project will be increased survival and product quality of transported fish as a result of adopting the recommended protocols and utilization of the models. Project outputs will include peer-reviewed publications, popular publications, and conference presentations.
Un-ionized ammonia will be based on TAN, temperature, salinity, and pH. UIA will be computed from Tables 9 or 10 in http://fisheries.org/hatchery.

Tags: aquaculture, doc/noaa/nmfs/nwfsc, gas transfer, hagerman valley, heat transfer, idaho, migrated from resource enhancement and utilization technologies division, montlake, national marine fisheries service, nitrogen determinator, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, water quality
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
LCREP catch records - Lower Columbia River Ecosystem Monitoring Project

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU).

3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals.

5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists.

6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU.

7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis.

Fish catch composition, fish length and weight for Lower Columbia sites.

Tags: chemical contaminants, chinook salmon, chinook salmon growth rates, chum salmon, coho salmon, doc/noaa/nmfs/nwfsc, fish community composition, fish diet, lower columbia river, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, population surveys, salmon lipid content, salmon prey availability
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Bioenergetics model output - Trophic impacts of bald eagles in the Puget Sound food web

This project is developing models to examine the ecological roles of bald eagles in the Puget Sound region. It is primarily being done by NMFS FTEs, in collaboration with scientists from the State of Washington and University of Washington. Trophic ecology of bald eagles will be described using ecosystem-scale food web models and bioenergetics models. Working models and scientific manuscripts will be the main products. The target audience is the Puget Sound Partnership, resource management agencies, and stakeholders in the Puget Sound area. This is an on-going, stand-alone project without a firm deadline.
Spreadsheet.

Tags: bald eagle, bioenergetics modeling, cb (conservation biology) division, climate change, doc/noaa/nmfs/nwfsc, ecosystem modeling, food web, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Species Composition - Bycatch Reduction Engineering Research

Through key regional collaborations with the Pacific States Marine Fisheries Commission, Oregon Department of Fish and Wildlife, Alaska Fisheries Science Center, and the fishing industry, the Marine Habitat Ecology Team at the  NWFSC has been able to pursue a wide-ranging array of conservation engineering projects relevant to reducing bycatch in the west coast groundfish and ocean shrimp trawl fisheries. Examples of types of research projects pursued during any given year include: 1) Reducing Chinook salmon, eulachon, rockfish, and Pacific halibut bycatch in midwater and bottom trawl fisheries using Bycatch Reduction Devices (BRDs), 2) Examining selectivity characteristics of codends that differ in mesh size and configuration in bottom trawl fisheries, and 3) Testing other novel bycatch engineering modifications to mobile and fixed gears. Much of our current work has been in response to the fishing industries concerns over catches of overfished and rebuilding rockfishes and Pacific halibut allocated in the Pacific coast Groundfish Trawl Rationalization Catch Share Program. The trawl rationalization program, starting in January 2011, established formal Annual Catch Limits (ACLs) and individual catch share quotas. In addition to ACLs, fishing opportunities may also be limited by hard caps or IBQs for non-groundfish species (e.g., Chinook salmon, and Pacific halibut). Bycatch of overfished and prohibited species in the west coast groundfish trawl fishery has the potential to constrain the fishery such that a substantial portion of available harvest may be left in the ocean.
Species composition (lengths, weights, counts) for regular and bycatch reduction device-impacted trawls.

Tags: doc/noaa/nmfs/nwfsc, fram (fishery resource analysis and monitoring) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Oceanographic data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and Canada. Scientists from the Northwest Fisheries Science Center (NWFSC) and Department of Fisheries and Oceans-Canada are responsible for conducting the survey. The survey consists of a series of transects that are oriented generally east-west, and are spaced at a nominal 10-nautical mile interval. Sea depth at the nearshore end of individual transects is typically 50 m; offshore extents are typically at a depth of 1,500 m. Geographical coverage extends from near Morro Bay, CA north to Dixon Entrance. Acoustic data are collected during daylight hours with a Simrad EK60 scientific echo sounder coupled with the ER60 software system. Trawl samples from pelagic and bottom trawls are used to classify the observed backscatter layers to species and size composition and to collect specimens of Pacific hake and other organisms. Analysis of acoustic data involves identification and delineation of backscatter layers that are attributed to Pacific hake. The biomass estimate and length-at-age composition of Pacific hake generated from this survey are used in analysis and management of the stock. This survey is conducted on a biennial basis. There is a firm deadline for producing the biomass estimate in the middle of the December following the survey.
Oceanographic data collected from CTDs, XBTs, SBEs, and the ADCP.

Tags: acoustic survey, acoustics, and depth, bathythermograph, bell m. shimada, ctd, current meter - acoustic current meter - acoustic doppler current meter, doc/noaa/nmfs/nwfsc, echo integration-trawl survey, fram (fishery resource analysis and monitoring) division, hake, iats, merluccius productus, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, pacific hake, pacific whiting, sonde and probe - conductivity, temperature, u.s. and canadian waters off the pacific coast, underway data collection instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce