AndreaBozzo/ceres-open-data-index huggingface dataset:
Electro-olfactograms - Neurobehavioral impacts of copper on juvenile salmon

Research support for various organizations in NOAA (Northwest Regional Office (NWR), HQ Office of Protected Resources, National Ocean Service (NOS) Coastal Services Center) for copper related to the harmful impacts of urban stormwater runoff, pesticide use, antifoulant use, and mining (e.g., proposed hardrock mining in Alaska). This has been a core focus of Ecotoxicology research for years, and may redirect to address key and high-profile data gaps specific to salmon habitat threats in Alaska.
Electrophysiological recordings from the olfactory system of salmonids.

Tags: doc/noaa/nmfs/nwfsc, ecotoxicology, instrument not applicable, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, nwfsc montlake, nwfsc mukilteo, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey (trawl sample)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey trawl samples. The Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey started in 1977 and is a collaborative effort between the Northwest Fisheries Science Center and Fisheries and Oceans Canada Pacific Region. This survey produces the Pacific hake biomass estimate that is essential to the management of the west coast fishery. Data collected are used to generate biological information and inform stock assessments made by the Hake Treaty Joint Technical Committee, a body formed by the U.S.-Canada International Hake/Whiting Treaty. The survey is typically conducted on a biennial basis. Because this is an international survey, two research vessels cover the entire U.S. and Canadian West Coasts. The survey design includes 10-nm spaced transects that run approximately perpendicular to the coast for the area that extends from Point Conception, California in the south to the West Coast of Vancouver Island in the north, and 20-nm transects north of WCVI to Dixon Entrance, Alaska. Transects are conducted using a NOAA Fishery Survey Vessel equipped with scientific echosounders and fishing nets to validate fish aggregations identified in the acoustic data. Midwater trawls are also equipped with a stereo camera to assist in determining the species composition of collected organisms.

Tags: alaska, california, canada, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, pacific hake, story map: noaa fisheries west coast offshore scientific surveys, united states, washington, whiting
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Lingcod data - Movement and habitat use patterns of top predators and keystone species in the benthic food web

We have been using and continue to use acoustic telemetry methods to monitor the movement behavior and define habitat use of groundfish species in and out of Puget Sound waters. Detections of individual fishes has been collected at small and large scales over short and long term periods. We have data on sixgill and sevengill sharks, spiny dogfish, lingcod, copper, quillback, yellowtail and black rockfish, and spotted ratfish. These data are being used to describe the spatio-temporal patterns of behaviors expressed by top predators and other important members of the groundfish community in Puget Sound and along the West Coast. We intend for this information to inform the strength of inter- and intra-specific interactions quantified by ecosystem-scale models as well as the development of models used to determine the efficacy of spatial management strategies such as Marine Protected Areas. This has been a research topic since 2003, and will continue with work on listed species such as yelloweye and canary rockfish.
Acoustic telemetry data for lingcod.

Tags: acoustic tags, animal and plant collection device, animal movement, british columbia, cb legacy data sets, demersal fish, doc/noaa/nmfs/nwfsc, home range, instrument not applicable, lingcod, marine reserves, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound, strait of georgia and howe sound, strait of juan de fuca, west coast of united states
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Habitat Use Database - Groundfish Essential Fish Habitat (EFH) Habitat Use Database (HUD)

The Habitat Use Database (HUD) was specifically designed to address the need for habitat-use analyses in support of groundfish EFH, HAPCs, and fishing and nonfishing impacts components of the 2005 EFH EIS. 
HUD functionality and accessibility, and the ecological information upon which the HUD is based, will be  improved in order for this database to fully support fisheries and ecosystem science and management. Upgrades to and applications of the HUD will be facilitated through a series of prioritized phases:

â¢ Fully integrate the data entry, quality control, and reporting capabilities from the original HUD Access database with a web-based and programmatic interface. Improve software for HUD to accommodate the most current habitat maps and habitat classification codes. This will be achieved by NMFS in consultation with HUD architects at Oregon State University.

â¢ Review and update the biological and ecological information in the HUD. 

â¢ Develop and apply improved models that will be used to create updated habitat suitability maps for all west coast groundfish species using the updated HUD and Pacific coast seafloor habitat maps.

â¢ Integrate habitat suitability models with the online groundfish EFH data catalog
(http://efh-catalog.coas.oregonstate.edu/overview/).
2005 habitat-use analysis supporting groundfish EFH.

Tags: database, doc/noaa/nmfs/nwfsc, essential fish habitat, fram (fishery resource analysis and monitoring) division, habitat assessment, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, southwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish Health Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon.
All fresh mortalities larger than 100 mm are sent to Fish Health for pathology.  Autopsy data is maintained on their database.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, manchester research station, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Habitat Analysis - Trinity River Restoration Potential

The goal of the Trinity River project is to identify the potential positive effects of large-scale restoration actions in a 63 kilometer reach of the Trinity River below Lewiston Dam, in the hope of guiding on the ground restoration actions. River restoration plans often propose numerous rehabilitation actions to address key habitat impairments for salmonids. However, restoration plans rarely propose alternative sets of actions or attempt to quantify the potential benefits to targeted biota. In this paper, we use geomorphic and biological analyses to estimate restoration potential for each of 37 reaches in a 64-km section of Trinity River, California, from the North Fork Trinity River to Lewiston Dam (the focus of habitat rehabilitation efforts under the Trinity River Restoration Program). We first predicted the channel pattern that might develop based in each reach on slope-discharge criteria, and then used these potential patterns along with floodplain width to estimate the maximum sinuosity that restoration actions could likely achieve, as well as a maximum side-channel length that might be created in each reach. For each scenario, we then used existing stream habitat and juvenile salmonid data from previous studies in the Trinity River and other watersheds to determine current and restored carrying capacity. Potential increases in Chinook and steelhead carrying capacity range from 39% for a relatively realistic estimate of increasing habitat quality (more low velocity areas with cover) to 67% for a more optimistic scenario that increases both sinuosity and habitat quality. Only the most optimistic scenario that increases habitat quality, increases sinuosity, and constructs tens of kilometers of side channels more than doubles potential juvenile salmonid production (140% increase). These quantitative predictions provide a frame of reference for evaluating alternative restoration options, and for setting measureable restoration goals.
Database of habitat capacity estimates.

Tags: chinook salmon, doc/noaa/nmfs/nwfsc, fe legacy data sets, habitat characteristics, landscape ecology, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, population surveys, restoration, steelhead, trinity river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Predicted riparian vegetation - 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 predicted reference conditions throughout the basin based on key reach-scale variables, which we empirically derived from a limited number of reference sites. We developed a GIS data set that depicts pre-settlement riparian vegetation in the Columbia River Basin to guide stream restoration for endangered salmon. However, the modeled riparian species composition was quite inaccurate, so we are not distributing these model results. 

Methods: 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 include randomly sampled basin-wide data (drainage area 200,000 km2), as well as intensively reconstructed watershed-level data (3,000 km2). Second, based on the reconstructed riparian vegetation points, which are arrayed along a 1-mile (1600 m) grid, we are developing statistical models to estimate potential historic riparian vegetation types (conifer, hardwood, willow-shrub, grass, sage) as well as the probability of occurrence of individual species at stream reach level (~ 200 m) in the basin. We examined environmental variables, such as mean annual precipitation, average minimum and maximum temperature, channel gradient, channel bankful width, floodplain width, and fine sediment supply potential, against five vegetation types and found that precipitation and temperature discriminate vegetation groups. We also developed vegetation response curves against each variable, using kernel density estimates to describe the probability of each vegetation type occurring across the range of each environmental variable.
GIS hydrography layer with riparian 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
Contaminants, lipids, fatty acids, and stable isotopes in tissues of various marine mammals - Biomonitoring of marine mammals as part of the Marine Mammal Health and Stranding Response Program (MMHSRP)

In 1992, the Marine Mammal Protection Act established the Marine Mammal Health and Stranding Response Program (Title IV) which operates in support of the Recovered Protected Species goal of NMFSâs Strategic Plan. The Northwest Fisheries Science Center (NWFSC) is the NMFS lead for the biomonitoring components and quality assurance of chemical analyses for the MMHSRP. Information generated by this activity addresses deficiencies in data quality and quantity on the levels of toxic chemical contaminants in marine mammals and their prey, refines methods and approaches for understanding linkages between exposure and specific biological effects and measures, and improves the dissemination of the information to constituents and resource managers. Furthermore, these data will provide a measure of the quality of marine mammal habitats.

Various analytical methods developed at the NWFSC will be used for the following marine mammal projects: integrated assessment studies of contaminants and other chemical tracers to assess feeding ecology or population health; monitoring of contaminants from stranded animals in support of studies and from species for which few data exist; continued investigations of potential relationships between contaminant exposure and population effects; participation in Interlaboratory Comparison Exercises conducted by National Institute of Standards and Technology and other similar entities comparing analytical results for chemical tracers; and development of quality control materials and quality assurance criteria for new analytical methods as they are developed as part of our Quality Assurance Program. The results of the chemical tracer analyses will be summarized in a report that will be sent to the Office of Protected Resources by the 4th quarter of FY18.
Concentrations of POPs, polycyclic aromatic hydrocarbons and their metabolites, total lipid and lipid profiles, fatty acids, and stable isotopes in samples derived from marine mammal biopsies and necropsies.

Tags: doc/noaa/nmfs/nwfsc, fatty acids, feeding ecology, instrument not applicable, marine mammals, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, persistent organic pollutants, stable isotopes, toxic effects
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
OBSOLETE: Coral genetic - Taxonomic and genetic identification of deep-sea corals in bycatch and field surveys -linked to groundfish survey dataset

Data for this project will reside in the West Coast Groundfish Bottom Trawl Survey Data Base. This proposal relates to a continuation and augmentation of our efforts in creating a DNA sequence repository and voucher collection of coral and sponge species found off the U.S. West Coast, and initial steps toward population-level analysis in deep-sea octocorals and sponges using microsatellite loci. We propose to continue taking genetic samples from specimens collected during the 2012 West Coast Groundfish Bottom Trawl Survey, and continue DNA sequencing of those specimens. We will then link the DNA data to our verified specimens to create a West Coast repository that will serve not only as an essential resource for coral researchers and other stakeholders, but also as a foundation for future research efforts at the NWFSC, aimed at understanding the biogeography and ecology of coral species in these deep-sea communities. 

Our primary goals with this funding opportunity are to hire an NRC postdoctoral fellow to work full-time on this project, and to continue to support at-sea specimen collection.

Coral DNA represented by Data Set "Deep Sea Coral voucher sequence dataset".

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Puget Sound steelhead life cycle model analyses - Population Viability Analysis

This research was initiated by the Puget Sound Steelhead Technical Recovery Team to develop viability criteria for threatened Puget Sound steelhead and to support recovery planning of this species. It involves conventional population viability analysis (PVA) combined with decision support systems such as Bayesian Networks. These systems are parameterized with information on abundance, productivity, spatial structure, and diversity obtained from various sources, including PVAs of individual populations from time-series data of abundance, productivity, age structure, iteroparity, influence of resident fish on anadromous abundance, and influence of human activities such as hatchery production, harvest, and habitat alteration. The work will also focus on assessing status of these listed species every five years as part of NOAA Fisheries' coastwide status review updates for listed salmonids.
These data will be outputs from life cycle models developed by the Puget Sound steehead recovery team to evaluate.

Tags: cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, population status assessment, population viability analysis
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Juvenile Salmonid Parasite Data

Data on Parasite communities in juvenile Chinook salmon, Coho salmon, and steelhead.

Tags: animal and plant collection device, climate change, columbia river, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, instrument not applicable, marine ecosystems, national marine fisheries service, noaa. u.s. department of commerce, northern california current, northwest fisheries science center, oceanography, salmon, survival modeling
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
California coast sablefish - Reproductive Life History Analysis of Sablefish Populations off the Washington and California Coasts

Sablefish (Anoplopoma fimbria) have a wide distribution along the Pacific coast, extending from Baja California to Alaska, the Bering Sea and through to the eastern coast of Japan.  A unique feature of these fish is the wide variation in temperature and depth that sablefish experience throughout their life cycle, extending from depths 200m as adults to the surface as larvae and juveniles. While the landed weight of sablefish in the commercial fishery is relatively small, the exceptionally high value of this species ranks it 3rd in economic value to walleye pollock and Pacific cod. As such, sablefish are highly managed throughout the Pacific, and understanding the biology of this species is essential for proper management. The aim of this project is to characterize the reproductive life history of two populations of sablefish in coastal Washington and California. 

Fish will be collected from the same geographical location on a monthly basis for one year. The reproductive status will be determined from gonadal histology and plasma sex steroid levels, and age will be determined from otoliths. It is expected that data on size, age, rate of gonadal development, seasonal timing of spawning, fecundity, frequency of reproduction, and potential shifts in distribution of sexes will be obtained. This study applies directly to the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act, because the data will be used to improve stock assessments and estimates of spawning biomass in this commercially important species. This project is a cooperation with the commercial fishing industry and scientists at the Northwest Fisheries Science Center (NWFSC) and Southwest Fisheries Science Center (SWFSC).
Size, sex, gonad stage, fecundity.

Tags: bodega bay, ca, doc/noaa/nmfs/nwfsc, instrument not applicable, migrated from resource enhancement and utilization technologies division, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, reproductive biology, sablefish, santa cruz, seattle, wa, washington, westport
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
BPA genetic monitoring - BPA Genetic Monitoring of Snake River Chinook Salmon and Steelhead

This is a long-term (30-year) NWFSC Genetics and Evolution Program study to monitor the genetic characteristics and population dynamics of hatchery- and natural-origin Chinook salmon and steelhead in the Snake River Basin, which are both species listed as threatened under the US Endangered Species Act. Genetic tools are used to determine if naturally spawning hatchery fish are influencing the adaptive potential and viability of wild fish in the basin. This work involves long-term annual field work to collect DNA from threatened Chinook salmon and steelhead at numerous locations throughout the Snake and Salmon River Basin and analyze the genetic signatures from the collections in the context of a long-term historical baseline of hatchery production and natural variation in wild salmonid production there.
Initiated in 1989, this study monitors genetic changes associated with hatchery propagation in multiple Snake River sub-basins for Chinook salmon and steelhead.  We also derive estimates of reproductive success for individual families and groups of fish.  The information obtained from this study directly addresses a critical knowledge gap identified by comanagers, which is: under what conditions does hatchery supplementation provide a sustained contribution to natural production?  Co-managers are ODFW, CTUIR, NPT, WDFW, IDFG, and SBT.  This type of monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations.

Tags: artificial propagation, cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, hatchery, manchester research station, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, salmon, snake river, snake river basin, unknown physical collection device
Organization: National Oceanic and Atmospheric Administration, Department of Commerce