AndreaBozzo/ceres-open-data-index huggingface dataset:
Ocean CTD Chlorophyll Nutrient Data - Juvenile Salmon & Ocean Ecosystem Survey

FY20 will mark the 23nd year of sampling, making the Juvenile Salmon and Ocean Ecosystem Survey (JSOES) the longest running salmon survey on the west coast. JSOES has clearly demonstrated correlations between ocean conditions and the distribution, abundance, and survival of juvenile Columbia River (CR) salmon in the Northern California Current (NCC) nearshore ecosystem. For example, our ocean indicators provide managers from the federal and state governments, tribes, and other agencies/groups the ability to forecast adult returns one to two years in advance for coho and spring/summer Chinook salmon. We continue to show the importance of evaluating ocean conditions to support management decisions and to provide context for efforts by the Northwest Power and Conservation Council (NWPCC) and BPA to restore and enhance salmon production. 

The primary goal of our work is to develop a mechanistic understanding of how trophic dynamics and conditions in the ocean and CR plume affect survival of juvenile salmonids. This knowledge will allow us to improve forecasts in a quantitative rather than qualitative manner, and decouple the effects of mitigation efforts in the freshwater environment from the effects of a changing ocean environment. These improved forecasts will lead to well-informed recommendations for an ecosystem approach to management strategies based on the full suite of river, plume, and ocean environments.
Conductivity, temperature, depth (CTD) casts and Chlorophyll and Nutrients.

Tags: animal and plant collection device, climate change, columbia river, ctd, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, marine ecosystems, marine survival, national marine fisheries service, newport, noaa. u.s. department of commerce, northern california current, northwest fisheries science center, oceanography, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Northern California Current Ecosystem Survey (station)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Northern California Current Ecosystem Survey stations. The Northern California Current Ecosystem Surveys started in 1996 and is led by NMFS Northwest Fisheries Science Center. These surveys expand the biophysical sampling conducted along the Newport Line out to the edge of the U.S. Exclusive Economic Zone. These surveys help us understand lower trophic level responses to environmental variability across the Pacific Northwest and California Current ecosystem. We also incorporate information on the abundance and distribution of mid-trophic level nekton, marine mammals, and birds. These samples inform broad-scale analyses of hydrography, phytoplankton, zooplankton, larval and juvenile fish, and ocean acidification and hypoxia. This survey is also part of a larger collaboration with Oregon State University researchers studying the marine biodiversity and size structure across broad spatial scales in the northern California Current. The Northern California Current Ecosystem Survey samples seasonally from northern Washington to the Oregon/California border, and offshore to 200 nautical miles off Newport, Oregon and 150 nautical miles off Crescent City, California on the NOAA Ship Bell M. Shimada. Seasonal sampling efforts include CTD, acoustic transects, zooplankton, ichthyoplankton, and macro-plankton sampling via bongo and Methot nets, as well as midwater and beam trawls.

Tags: doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Hyporheic Microbes Database - Microbes in the hyporheic zone

The hyporheic zone (i.e., where surface & groundwater converge) is a geomorphic feature that contributes to the overall health of streams & rivers.  Much of the function of the hyporheic zone depends on microbes, that modify & recycle nutrients & other biological molecules.  How the hyporheic zone is altered in stream restorations is understudied.  This project attempts to document changes microbial activity & community structure in restored reaches of an urban stream, Thornton Creek in Seattle, including attempts to "seed" or accelerate population of newly installed hyporheic elements by transplanting hyporheic material from a pristine system, the Cedar River watershed.  Assessment of the microbial component is being performed in concert with assessments of macroinvertebrate communities & water quality measures.

Filemaker Pro database of results from field & lab effort.

Tags: doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species

Using morphometric characteristics of modern salmonid (Oncorhynchus spp.) vertebrae, we have developed classification models to identify salmonid vertebrae to the species level with relatively low error rates. This is a study to validate the performance of our classification models on ancient salmonid specimens using analysis of ancient DNA. We have putatively identified a sample of ancient (ca. 1000 to 2900 ybp) vertebrae (from the Wenatchee River basin) to species with our models. Using molecular markers to identify the ancient vertebrae to species, we will be able to evaluate the performance of our models that use vertebral morphology for species identification. If identification methods that are based on vertebral morphology perform successfully, we will have a rapid, low cost, nondestructive method to identify ancient salmonid vertebrae. If applied to midden sites throughout the Columbia River basin, and potentially to other river systems draining into the Pacific Ocean, we will improve our understanding of historical anadromous salmonid occupancy and have a more complete picture of historical population and ESU structure. Additionally, the results of this work have the potential to make a significant contribution to inland and coastal anthropological/archaeological investigations. Collaborators include: Virginia Butler (Portland State University, Dept. of Anthropology), Harriet Huber (AFSC), and Dongya Yang (Simon Fraser University, Ancient DNA Laboratory).
Ancient vertebrae measurements.

Tags: ancient dna, cb (conservation biology) division, classification, doc/noaa/nmfs/nwfsc, morphometrics, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, quantitative pcr machine, vertebrae identification, wenatchee river basin
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Salish Sea Genetics - Salish Sea genetic inventory

The Salish Sea comprises most of the Puget Sound water area. Marine species are generally assemblages of discrete populations occupying various ecological niches. Genetic changes to  populations can occur as a result of genetic drift, introgression between populations, local adaptation, etc. This project provides genetic baseline data to monitor genetic change in plants, animals, and algae.
Genetic data.

Tags: animal and plant collection device, 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, salish sea
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Composition of fish and feeds - Developing diets and feeding strategies for improved growth and performance of juvenile and adult sablefish

Feed costs and time to harvest are key factors affecting the economic viability of domestic sablefish (Anoplopoma fimbria) aquaculture. Use of fast growing all-female monosex stocks dramatically reduces time to harvest, but our research to date indicates that the commercial salmon feeds typically used by industry are not optimally formulated for sablefish and there is still a high degree of potential for improved growth and feed conversion. The effects of dietary balance of protein, fat, and carbohydrate on productive performance, growth and feed conversion at any post-juvenile stage of development are unknown, and there are no commercial diets specifically formulated for sablefish aquaculture in the marketplace. Dietary nutrient imbalances combined with inappropriate feeding schedules and strategies contribute to poor nutrient utilization and are unlikely to fully support the growth potential of this species, impeding continued efforts to improve performance during grow-out to harvest. Thus, research activity focuses on establishing performance optimized diets and feeding strategies that support maximum growth, efficient feed conversion and other economically important traits such as fillet yield.
Information on proximate composition of fish and tissues and aqua feeds and of feed constituents and selected fish tissues.

Tags: 11-ketotestosterone, aquaculture, aquafeeds, doc/noaa/nmfs/nwfsc, drying oven, efs (environmental and fisheries sciences) division, genetics, growth, igf1, lipid extractor, marine fishes, metabolism, muffle furnace, national marine fisheries service, nitrogen determinator, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, sablefish
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Ocean Salmon Distributions

This project extends and advances existing ocean distribution and size models for Chinook Salmon, a major prey of Southern Resident Killer Whales (SRKW) and target of important fisheries, to provide ocean distribution estimates for multiple run-types (fall, summer, and spring Chinook) arising from rivers from California to Alaska by season and under variable oceanic conditions. It leverages very large tag-recapture databases that have been developed for Chinook Salmon over the past 50 years â hundreds of millions of fish tagged and millions recovered â and links these recoveries to a range of fisheries in which Chinook are targeted or captured as bycatch. It integrates data coast-wide, from Alaska to California, and over more than 30 years (1978-2015), to provide a first synthetic, quantitative description of Chinook distribution that can be used to understand the total Chinook prey field available to SRKW, fishers, and other predators in different seasons and under alternate ocean states. In addition, this projects examines long-term trends in Chinook salmon size and their biological implications. Chinook populations have shown pronounced trends toward smaller and younger fish returning to spawn, and these trends have accelerated in the last 15 years. This erosion of the age-size structure and life-history 
diversity may negatively affect population productivity via reductions in reproductive potential, and may compromise the long-term viability of populations and jeopardize the sustainability of Chinook salmon fisheries. Consequently, long-term shifts in life-history characteristics, which are likely caused by changing ecological conditions in the ocean, might need to be accounted for when estimating reference points for fishery management. This work supports ongoing efforts to recover SRKW populations, informs the SRKW critical habitat designation process and recovery plans, feeds into the PFMC SRKW ad hoc work group, and is directly in line with the NMFS Ecosystem-Based Fisheries Management Road Map and Policy as well as the National Climate Science Strategy.

Tags: cb (conservation biology) division, chinook, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, ocean distribution, salmon, southern resident killer whales, srkw
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
CCIEA data and model output - California Current Integrated Ecosystem Assessment

The California Current Integrated Ecosystem Assessment (CCIEA) is a joint project between staff at the NWFSC, SWFSC, NMML, ONMS, and WCRO to provide managers and policy makers with integrated science products in support of ecosystem-based management of marine resources. Key products include: conceptual models; ecosystem indicator suites, status and trend reports, and related analyses; risk assessments; and analyses of management scenarios in ecosystem models. Major clients include the Pacific Fishery Management Council, the West Coast Region, National Marine Sanctuaries along the West Coast, and the West Coast states.
Data and model output gathered and generated by the California Current Integrated Ecosystem Assessment team.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Zooplankton Data - Juvenile Salmon & Ocean Ecosystem Survey

FY20 will mark the 23nd year of sampling, making the Juvenile Salmon and Ocean Ecosystem Survey (JSOES) the longest running salmon survey on the west coast. JSOES has clearly demonstrated correlations between ocean conditions and the distribution, abundance, and survival of juvenile Columbia River (CR) salmon in the Northern California Current (NCC) nearshore ecosystem. For example, our ocean indicators provide managers from the federal and state governments, tribes, and other agencies/groups the ability to forecast adult returns one to two years in advance for coho and spring/summer Chinook salmon. We continue to show the importance of evaluating ocean conditions to support management decisions and to provide context for efforts by the Northwest Power and Conservation Council (NWPCC) and BPA to restore and enhance salmon production. 

The primary goal of our work is to develop a mechanistic understanding of how trophic dynamics and conditions in the ocean and CR plume affect survival of juvenile salmonids. This knowledge will allow us to improve forecasts in a quantitative rather than qualitative manner, and decouple the effects of mitigation efforts in the freshwater environment from the effects of a changing ocean environment. These improved forecasts will lead to well-informed recommendations for an ecosystem approach to management strategies based on the full suite of river, plume, and ocean environments.
Oblique Bongo Tows for juvenile salmonid prey field index.

Tags: animal and plant collection device, climate change, columbia river, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, marine ecosystems, marine survival, national marine fisheries service, newport, noaa. u.s. department of commerce, northern california current, northwest fisheries science center, oceanography, salmon, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Killer whale industry - Baseline Data Collection of Southern Resident Killer Whale (SRKW) Industry Members

SRKW were listed as endangered in 2005. This study collected baseline data about the industry to be able to determine social impacts to the industry as a result of the SRKW listing. Primary data was collected, analyzed, and reported. Northwest Regional Office and Protected Species Office staff used some study results in an Environmental Assessment completed in 2011. This information will also be used to compare future data collections to measure social changes as a result of new vessel regulations.
Primary qualitative/quantitative dataset.

Tags: bellingham, cb legacy data sets, doc/noaa/nmfs/nwfsc, everett, instrument not applicable, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc, obsolete, orcas island, port townsend, san juan island, seattle, social impact, srkw, wa
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Predicted channel types - Potential for Habitat Improvement in the Columbia River Basin

Basin-wide analysis of potential to improve tributary habitats in the Columbia River basin through restoration of habitat-forming processes.

Identification of geomorphological target conditions for river restoration is typically based on locally measured reference conditions, yet few reference sites remain in much of the 630,000 km2 Columbia River Basin, USA. Therefore, we predict reference conditions throughout the basin based on key reach-scale variables, which we empirically derived from a limited number of reference sites. Our typology predicts channel type based primarily on channel slope in confined reaches (floodplain width less than 4 times the bankful channel width) and on slope, drainage area, precipitation, and relative transport capacity in unconfined reaches (floodplain width greater than 4 times channel width). Channel types are cascade, step-pool, plane-bed, and pool-riffle in confined reaches, and braided, island-braided, meandering, and straight in unconfined reaches. Accuracy of channel type prediction in confined reaches is generally high compared to prediction accuracy in unconfined reaches. Lower accuracy in the unconfined reaches is largely due to vertical accuracy of the 10- m digital elevation model (DEM), which is insufficient to accurately estimate channel slope in low relief areas. However, lack of sediment supply information also limits our ability to predict floodplain channel type accurately. Therefore, we evaluate the effect of incorporating an estimate of relative transport capacity to help separate single thread channels (straight and meandering) from multi-thread channels (braided and island-braided) and increase prediction accuracy. Finally, we use existing ecoregion maps to show how channel type distributions vary among geologic regions, and suggest analysis options for mapping reference condition across large river basins. 

We also attempted to develop a GIS data set that depicts pre-settlement riparian vegetation in the Columbia River Basin to guide stream restoration for endangered salmon. To do this, we first created a data layer of historic riparian vegetation information from survey notes that were taken mid 19th to early 20th century during the Public Land Survey System (PLSS) conducted by General Land Office (GLO). Our reconstructed riparian vegetation data included randomly sampled basin-wide data (drainage area 200,000 km2), as well as intensively reconstructed watershed-level data (3,000 km2). Our modeled output was too inaccurate to be useful.
GIS hydrography layer with multiple stream attributes.

Tags: columbia river, columbia river basin, doc/noaa/nmfs/nwfsc, fe legacy data sets, habitat, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, restoration
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Water chemistry - Investigation of Methods to Improve Homing by Hatchery Salmon

Investigate olfactory imprinting techniques that will improve homing by hatchery salmon to their hatchery of origin, and thereby reduce potential risks from these fish to wild fish populations.  Improvement of homing by hatchery salmon will have broad application in the Pacific Northwest and will allow managers to maximize the fishery benefit of returning hatchery fish to sport and commercial fisheries.

Water chemistry.

Tags: doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Mukilteo water sensor time series - Field work coupling measurements of carbon chemistry and distribution of free-living organisms

To estimate the carbon chemistry conditions experienced by free-living organisms, we will conduct coupled biological/carbon chemistry sampling for key zooplankton species and settlement plate experiments. As funding allows, we will also increase the capability of the NWFSC to conduct these types of studies in the future.
Time series of water sensor measurements collected from the NWFSC Mukilteo pier and facility intake. Measurements include pCO2, pH, temp, salinity, DO. Set to start online winter 2012-13.

Tags: carbon dioxide emissions, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, mukilteo, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, ocean acidification, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
California Current Cetacean and Ecosystem Assessment Survey (extent)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ California Current Cetacean and Ecosystem Assessment Survey. The California Current Cetacean and Ecosystem Assessment Survey started in 1991 and is led by NMFS Southwest Fisheries Science Center. This survey includes ship-, aerial-, and land-based surveys of marine mammals throughout the California Current Large Marine Ecosystem. Survey data have been used to estimate cetacean population size and trends, delineate cetacean population stock structure, describe cetacean and seabird distributions and hotspots, develop species distribution models, and inform marine mammal stock assessment reports pursuant to statutory requirements under the Marine Mammal Protection Act (MMPA). Research vessels conduct line-transect surveys, typically every three years, in summer and fall and span waters out 300 nautical miles offshore, from the US-Canada to US-Mexico border. NOAA research vessels (David Starr Jordan, McArthur, McArthur II, Reuben Lasker, Bell M. Shimada) collect visual sightings data for cetaceans and seabirds, passive acoustic (e.g., towed or drifting array) data for cetaceans, tissue biopsy sampling used for genetics analysis, and oceanographic sampling.

Tags: california, california current, cetaceans, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce