AndreaBozzo/ceres-open-data-index huggingface dataset:
Salish Sea Marine Survival (Steelhead) - Early Marine Survival of Puget Sound Steelhead

The primary objectives of this study are to estimate a predation rate by harbor seals on steelhead smolt in Puget Sound, and determine whether predation by harbor seals differs by region.  Nisqually River steelhead will be acoustic tagged, and 12 - 18 seals will be fitted with GPS/acoustic receiver instrument packs. Tag detection capabilities will be expanded by i) monitoring harbor seals in South and Central Puget Sound and Admiralty Inlet, ii) placing stationary receivers at seal haulouts and at random locations not frequented by harbor seals, iii) conducting mobile tracking to locate tags remaining in Puget Sound after the smolt outmigration period.  Seal time at depth and locations will be quantified in such a manner that estimates the amount of time seals spend at haulout locations to estimate the probability that a tag consumed by a harbor seal would be defecated near a haulout site.  Data on harbor seal abundance, behavior, steelhead tag locations, and smolt abundance will be combined to estimate the predation rate and total number of smolts consumed by harbor seals. 
In addition, recent fish health assays indicate high infection prevalence (87-100%) and intensity (800-2500 cysts/fish) of Nanophyetus salmonica in steelhead outmigrating from Central (Green) and South (Nisqually) Puget Sound Rivers. South and Central Puget Sound steelhead populations generally experience lower early marine survival rates than those from North Puget Sound rivers, where Nanophyetus infections in assayed steelhead were absent. High infection intensity among freshwater outmigrants could contribute to rapid mortality shortly after seawater entry. This study will use acoustic telemetry to evaluate differences in the early marine survival (near river mouth to Pacific Ocean) of specific pathogen-free (SPF) and Nanophyetus-infected Puget Sound steelhead smolts. This approach will help us understand effects of Nanophyetus infection at different stages of the steelhead smolt migration through Puget Sound.
Steelhead smolt locations.

Tags: animal and plant collection device, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, harbor seal, instrument not applicable, marine survival, migration, nanophyetus salmincola, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, predation, puget sound steelhead marine survival project, salish sea, steelhead
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Growth - Sustainable aquafeeds for marine finfish: Effects of vegetable oil replacement feeds containing novel microalgal and fungal oils on growth performance of juvenile sablefish

The concomitant replacement of fish meal and fish oil in carnivorous marine fish feeds by more sustainable terrestrial alternatives is problematic due to the limited capability of marine fish to synthesize physiological essential long chain n-3 and n-6 highly unsaturated fatty acids (HUFAs) from shorter chain fatty acid precursors present in some vegetable oils. This two-year study will employ sablefish (Anoplopoma fimbria) as a model marine finfish to systematically investigate the potential of fully replacing the added fish oil component of a typical low fishmeal feed suitable for marine aquaculture.

The focus of the proposed study will be on the effects of replacing fish oil in sablefish diets with sustainable lipid sources on diet utilization and growth. In particular, the overall goals of the proposed research are the following: 

1. Determine the ability of sablefish to synthesize essential HUFAs from shorter chain fatty acid precursors.

2. Explore the effects of supplementing alternative vegetable oil feeds with novel sources of essential fatty acids on growth and nutrient utilization.

3. Evaluate the feasibility of using these novel oils in practical feeds. Data obtained in these studies will further our understanding of sablefish nutrition and set the stage for future research on the effects of sustainable feed ingredients on product quality, fish health, and the reproductive potential of cultured broodstock programs. This research specifically addresses a priority of the 2008 National Marine Aquaculture Initiative, which is nutrition research involving alternative protein based diets and the influence of diet on product quality.
Fish weights and lengths.

Tags: alternative feed lipids, aquaculture, doc/noaa/nmfs/nwfsc, migrated from reut legacy data sets, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc- montlake laboratory, obsolete, sablefish, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Rockfish 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 rockfish in Puget Sound, primarily copper and quillback.

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
CHaMP metrics - Columbia Habitat Monitoring Program

The goal of CHaMP is to generate and implement a standard set of fish habitat monitoring (status and trend) methods in up to 26 watersheds across the Columbia River basin. The watersheds have been chosen to maximize the contrast in current habitat conditions and also represent a temporal gradient of expected change in condition through planned habitat actions. Surveys will be conducted in watersheds with perceived large juvenile life-stage survival gaps due to habitat impairments or that are home to existing high quality fish monitoring infrastructure. CHaMP implementation will occur on the spatial scale of the Technical Recovery Team (TRT) populations with the intention for inference on habitat quality and quantity at the fish population level. CHaMP is being built around a single habitat monitoring protocol with a program-wide approach to data collection and management.
CHaMP metric data set consists of the entire suite of measurements described in the 2012 CHaMP protocol. A three-person crew surveys the topography (both the in-channel bathymetry and out-of-channel topography including the near channel floodplain) at a site and collects auxiliary data at both the channel unit scale (fish cover estimates, large woody debris, ocular estimate of substrate, pebble counts of bed material in riffles, pool tail fines, and undercut banks) and the site level scale (macroinvertebrate drift, discharge, solar input, riparian structure, alkalinity, conductivity, photographs, and water and air temperature loggers). The crews post process the data collected at each of the sites, which entails a QC of the survey point data, importing the survey point data into ArcGIS and converting the points into a TIN, and converting the topographic TIN to a DEM.  Additional GIS products are also produced during the post-processing and include a water surface TIN, water surface DEM, and water depth raster.

Tags: animal and plant collection device - plankton collection device - plankton net, cb (conservation biology) division, columbia river basin, current meter - electromagnetic current meter, doc/noaa/nmfs/nwfsc, habitat, monitoring, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Mothership Cost Earnings Data - Economic Data Collection for Monitoring the Economic Effects of the West Coast Groundfish Trawl Rationalization Program

This project was initiated in response to regulation 50 CFR 660.114, which mandates that economic data be collected from every participant in the trawl rationalization program. The data are collected annually from catcher vessels, catcher processors, motherships, first receivers, and shorebased processors through paper-based forms. The four forms (specific to entity type) are mailed annually in May, and collect data about the fishing, buying, and processing information from the previous year. The entity must submit their data by September 1 in order to renew their limited entry trawl permits, reissue their quota share, vessel accounts, and receive their first receiver site licenses. The data, reports, tech memos, and academic papers are used by Northwest Region staff, Pacific Fishery Management Council (PFMC), and headquarters staff to inform management decisions, and to monitor the effects of the program.
Cost, earnings, and production data for motherships.

Tags: costs, doc/noaa/nmfs/nwfsc, employment, fishery-dependent, fram (fishery resource analysis and monitoring) division, national marine fisheries service, net revenue, noaa. u.s. department of commerce, northwest fisheries science center, pacific coast of the u.s., profit, revenue, surveys and questionnaires, tracked asset
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish Health data - Snake River sockeye salmon captive propagation

In the early 1990s, Redfish Lake sockeye salmon from the Sawtooth Basin in Idaho were on the brink of extinction, and they were listed as endangered under the US Endangered Species Act in 1991. To prevent extinction, a gene rescue captive broodstock program was established for the stock that consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery. 

Efforts through the decade of the 1990s consisted of developing techniques for successful culture of sockeye salmon to adulthood, establishing rearing and spawning protocols to ensure preservation of stock diversity, and habitat enhancement at the rearing lakes. In the early 2000s, the program began to include a demographic focus to boost the population through rearing and release of enough juveniles to produce some adult returns. For the last few years, NWFSC eyed egg production has resulted in over 150,000 smolts being released into the Stanley basin annually for recovery, with plans to increase NWFSC eyed egg production to support release of half a million smolts in the Stanley Basin by 2017.  In 2011, and for the fourth year in a row, record numbers of sockeye adults have returned to their native home in Idaho.
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, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, obsolete, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
CTD data - Pre-recruit surveys to aid stock assessment

Annual surveys of juvenile fish and ecosystem status have been conducted since 2011 surveying the entire coast of Oregon and southern Washington.  Trawl surveys are done at night in midwater along transects spaced every half degree of latitude and environmental, plankton, and benthic sampling occurred at specific locations and seabird, marine mammal and acoustic surveys are conducted underway between transects and stations.
Temperature, salinity, conductitity, chlorophyll, oxygen.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Refugio GNOME NRDA Shoreline Oiling May 29

On May 19, 2015, a pipeline owned ruptured in Santa Barbara County, California, near Refugio State Beach. An estimated 21,000 gallons of the oil flowed overland from the break site into the Pacific Ocean and spread across the marine environment. NOAA and our state and federal partners are investigating these impacts and will determine the amount of restoration needed to return the environment to the condition it was in before the spill and to compensate the public for environmental degradation from the time of the spill until recovery.

This layer represents a NOAA GNOME modeled hindcast of particles of oil reaching the affected area shoreline.

Tags: california, continent, doc/noaa/nos/orr, earth science, earth science services, environmental impacts, hazards management, hazards mitigation, human dimensions, national ocean service, noaa, north america, office of response and restoration, oil spills, refugio beach oil spill, u.s. department of commerce, united states of america
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Angus Sequence Data: Animal 519-2

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program does not have germplasm for this animal.</p><p dir="ltr">There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA06_i5-515_i7-102_S6_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA06_i5-515_i7-102_S6_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA06-i5-515-i7-102_S142_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA06-i5-515-i7-102_S142_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA06-i5-515-i7-102_S6_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA06-i5-515-i7-102_S6_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA06-i5-515-i7-102_S6_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA06-i5-515-i7-102_S6_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA06_i5-515_i7-102_S6_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA06_i5-515_i7-102_S6_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA06_i5-515_i7-102_S6_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA06_i5-515_i7-102_S6_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA06_i5-515_i7-102_S361_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA06_i5-515_i7-102_S361_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Hydrological and Water Chemistry Data: Faribault County, Minnesota, County Ditches 62 and 30, 2018—2023

<p dir="ltr">This dataset includes drainage discharge, water chemistry, and precipitation data and GIS shapefiles for research conducted on 249-ha County Ditch 62 (CD62) and adjacent 268-ha County Ditch 30 (CD30) watersheds in Faribault County, Minnesota, from 2018—23 and 2021—23, respectively. Three large bioreactor beds treat flow from the CD62 watershed. Water table depths in the outlet structures of the three bioreactors (BR1, BR2, and BR3) are included for 2021—23. Also, water table depths at three locations in the beds are included for 2022 and 2023. The beds were recharged with new woodchips during 2020; limited bioreactor data exist for 2018, and no bioreactor data exist for 2019—20. The purpose of the research was twofold: 1) to evaluate the performance of the bioreactors and the percentage of watershed discharge that was treated by them, and 2) to establish hydrologic and nutrient load pairing of side-by-side watersheds for a future study of management change on one of the watersheds.</p><p dir="ltr">A related dataset includes discharge and water chemistry data for CD62 and the bioreactors for the period September 2016 through July 2017:</p><ul><li>Feyereisen, Gary W.; Ghane, Ehsan; Schumacher, Todd; Dalzell, Brent J.; Williams, Mark R. (2024). Data from: Can woodchip bioreactors be used at a catchment scale? Nitrate Performance and sediment considerations. Ag Data Commons. Dataset. <a href="https://doi.org/10.15482/USDA.ADC/27932151.v1" target="_blank">https://doi.org/10.15482/USDA.ADC/27932151.v1</a></li></ul><p dir="ltr">Water chemistry analyses are yet being conducted on calendar year 2024 samples; data from these analyses and related hydrologic data are forthcoming.</p><p dir="ltr">Methods of sample and data collection are similar to those described in the above-referenced dataset and the related peer-reviewed publication:</p><ul><li>Feyereisen, G. W., Ghane, E., Schumacher, T. W., Dalzell, B. J., & Williams, M. R. (2023). Can Woodchip Bioreactors Be Used at a Catchment Scale? Nitrate Performance and Sediment Considerations. Journal of the ASABE, 66(2), 367-379. https://doi.org/10.13031/ja.15496</li></ul><p dir="ltr">A nitrate sensor (Hach Nitratax) was installed in CD62 in 2019. The monitoring station at CD30 was instrumented similarly to CD62: discharge (in a 15-inch drainage main) with area-velocity technology (Teledyne ISCO 2150), nitrate sensor (Hach Nitratax), and flow-weighted autosampling (Teledyne ISCO 6712).</p><p dir="ltr">The file “CD30-62 map w labels.png” shows the watershed boundaries and the location of the woodchip bioreactors (WBR) at the outlet of CD62.</p>

Tags: bioreactor, nitrate-removal, paired-watershed-study, subsurface-tile-drainage
Organization: Department of Agriculture
Angus Sequence Data: Animal 186-6

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program does not have germplasm for this animal.</p><p dir="ltr">There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA04_i5-515_i7-100_S4_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA04_i5-515_i7-100_S4_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA04-i5-515-i7-100_S140_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA04-i5-515-i7-100_S140_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA04-i5-515-i7-100_S4_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA04-i5-515-i7-100_S4_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA04-i5-515-i7-100_S4_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA04-i5-515-i7-100_S4_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA04_i5-515_i7-100_S4_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA04_i5-515_i7-100_S4_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA04_i5-515_i7-100_S4_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA04_i5-515_i7-100_S4_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA04_i5-515_i7-100_S359_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA04_i5-515_i7-100_S359_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
National Incident-Based Reporting System (NIBRS)

This collection provides data submitted to the FBI’s Uniform Crime Reporting (UCR) Program via the National Incident-Based Reporting System (NIBRS) for one or more months of the calendar year. It presents an overview of the offense categories that show the diversity and complexity of the data collected via NIBRS.  In addition, it includes detailed agency-level data by offense type.  

Tags: aggravated-assault, arrests, arson, assault, crime-statistics, crimes-against-persons, crimes-against-property, crimes-against-society, drug-abuse, embezzlement, fraud, gambling, incident-based, larceny, law-enforcement, murder, nibrs, offenses, rape, robbery, ucr-program, uniform-crime-reporting-program
Organization: Department of Justice
Growth Data - North Puget Sound Chinook salmon captive propagation

NOAA Fisheries is a cooperator with the Washington Department of Fish and Wildlife and the Lummi, Nooksack, and Stillaguamish Tribes in a 10-year program to rebuild the South Fork Nooksack River spring Chinook and Stillaguamish River fall Chinook stocks through a captive broodstock program.
The fork length to the nearest mm and weight to the nearest gram of fish is recorded on an approximately annual basis.

Tags: artificial propagation, chinook salmon, 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, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Killer whale prey - Diet and prey availability of SRKW top marine predators

SRKW have several data gaps regarding their ecology. Diet of killer whales is being determined by analyses of predation events and feces and from stomach content of harbor porpoises. The potential impact of Chinook predators is being evaluated through models.
Information on killer whale prey samples.

Tags: cb (conservation biology) division, chinook salmon, dna sequencer, doc/noaa/nmfs/nwfsc, killer whale, 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
National Use-of-Force Data Collection

This collection provides data on law enforcement uses of force that result in the death of a person, serious bodily injury of a person, or when law enforcement discharges a firearm at or in the direction of a person.  In addition, law enforcement agencies can indicate months where no incidents meeting the above criteria occurred.

Tags: law-enforcement, officer-involved-shootings, police, ucr-program, uniform-crime-reporting-program, use-of-force
Organization: Department of Justice