AndreaBozzo/ceres-open-data-index huggingface dataset:
Environmental DNA (eDNA) Metabarcoding Pilot Study on National Wildlife Refuges - Tabular Data

This reference contains tabular datasets resulting from the eDNA pilot study on National Wildlife Refuges. 

1. ZIP file contains all datasets as received from the authors: a folder for each participating refuge containing two Excel workbooks, one for the MiFish marker results and one for the COI marker results. Each workbook has several sheets including one for the raw compiled data, one for each site, and filtered combined data. 

2. CSV of filtered data for all participating refuges combined.  This dataset was compiled by extracting the filtered datasheet for each refuge from the excel workbook and combining them into a CSV using an r script. 

3. CSV of the total OTU, OTU species, unique families, and number of fish, mammal, amphibian, mollusk, and bird species for each participating refuge. This csv was compiled by Rachel Maxey (I&M Data Manager) by extracting the data from the refuge workbooks and combining manually into a CSV. 

4. CSV of the full Site data download from Survey 123. 

5. Data dictionaries and metadata for site information and eDNA results tables.

Tags: aquatic-habitat, biodiversity, edna, environmental-dna, metabarcoding, species-richness
Organization: Department of the Interior
Survey data for Wetland Habitat Assessment Protocol Framework

Pre-processed survey data from the Wetland Habitat Assessment Protocol survey. These files result from following WHAP SOP 3A and 3B, which includes data quality control and cleanup, GIS data intersects, and flattening related tables to produce these files. We used the WHAP data pre-processing scripts for this process (see ServCat reference 157116).

Tags: barnyard-grass, barnyardgrass, cockspur, crypsis, crypsis-schoenoides, data, echinochloa-crus-galli, general-biology-communities-and-ecosystems-wetland, japanese-millet, large-barnyard-grass, moist-soil, persicaria, persicaria-maculosa, prickle-grass, pricklegrass, seed-estimation, smartweed, spotted-ladysthumb, swamp-prickle-grass, swamp-pricklegrass, swamp-timothy, watergrass, wetland, whap
Organization: Department of the Interior
Survey sample design data for Kanuti NWR's Scoter/Scaup aerial breeding pair survey

This record contains geospatial datasets related to the sample design for Kanuti National Wildlife Refuge's aerial breeding pair survey of scaup and scoters. This includes a GPX file for use in a GPS unit by the survey pilot. This includes the 40 endpoints for the 20 transect lines of Kanuti's scaup/scoter survey.  The file also includes route info (1 "polyline") that connects the transect endpoints such that the transect lines are visible to the pilot.

This reference also contains a zipped folder with multiple shapefiles related to the survey transects and study area. Within the zipped folder, KanutiScaupScoterArea.shp contains a polygon representing the sampling area for the survey. KanutiOriginal_10_Scoter_lines.shp contains polyline features for the original 10 transects where the survey is conducted. KanutiAlternate_10_Scoter_lines.shp contains polyline features for 10 alternative transects for the survey that were implemented beginning in 2017.

Additionally, this reference contains a link to the ArcGIS Online feature service containing authoritative inventory and monitoring site locations. The feature layers can be filtered to where PRIMR_ID='FF07RKAN00-037' to subset the data to features relevant to this specific survey.

Information on how to carry out the survey may be found in the cross-referenced protocol narrative (ServCat reference 178482).

Tags: aerial-survey, aythya-affinis, aythya-marila, common-loon, ff07rkan00-037, gavia-immer, gavia-pacifica, gavia-stellata, general-biology-species-birds, general-management-monitoring, gis, gps, great-northern-diver, great-northern-loon, greater-scaup, initial-survey-instructions, kanuti-national-wildlife-refuge, lesser-scaup, melanitta-deglandi, melanitta-perspicillata, pacific-diver, pacific-loon, protocol, red-throated-diver, red-throated-loon, scaup, scoters, shapefiles, surf-scoter, white-winged-scoter
Organization: Department of the Interior
R1: Oregon Coast: 2009 Aerial Photography of Nesting Seabird Colony Islands for Monitoring Purposes - Selected (Colony) Images Used For Counting, Geospatial Representation

Photography from helicopter taken for the purposes of resource monitoring, specifically seabird colony status and distribution. Oregon Coast aerial and boat based photography taken in June, 2009 on 35mm slide film.  Primarily captured from a helicopter roughly 800-900' in altitude, Right Front Photographer - Shawn Stephenson, USFWS, Right Rear Photographer - David Ledig, USFWS 

These slides have been scanned at 1200 - 5000 DPI and have about 1-foot pixel resolution. Please note that these photos have not been georeferenced. The photos have not been orthorectified and therefore there will be photo anomalies and mis-matches between adjoining photos. Caution should be exercised if attempting to use this imagery to conduct measurements.

This geospatial representation includes the best quality images for each nesting seabird colony. The metadata includes grades for image quality.

Tags: aerial-photograph, digital-scan, ff01rorg00-002, ff01rtar00-002, general-management-inventory, general-management-monitoring, primr, seabird-colony, slide-film
Organization: Department of the Interior
Sewall Vegetation Classification and Imagery for Block Island, Canaan Valley, Cherry Valley, Conscience Point, Elizabeth A. Morton, Erie, Featherstone, Great Swamp, James River, John H. Chafee, Mason Neck, Ninigret, Nomans Land Island, Occoquan Bay, Presquile, Patuxent Research Refuge, Rappahannock River Valley, Sachuest Point, Seatuck, Target Rock, Trustom Pond, Wallkill, Wertheim National Wildlife Refuges

James W. Sewall Company used its standard photointerpretation and ortho-mapping workflow on 112K acres across  the North Atlantic - Appalachian region. Refuges include: Block Island, Canaan Valley, Cherry Valley, Conscience Point, Elizabeth A. Morton, Erie, Featherstone, Great Swamp, James River, John H. Chafee, Mason Neck, Ninigret, Nomans Land Island, Occoquan Bay, Presquile, Patuxent Research Refuge, Rappahannock River Valley, Sachuest Point, Seatuck, Target Rock, Trustom Pond, Wallkill, Wertheim National Wildlife Refuges. Aerial photography using color infrared (CIR) film was acquired during the spring and early summer at a scale of 1"=1000' (1:12,000). Sewall's photointerpreter conducted fieldwork to establish what would be classified. These shapefile contains the interpreted attributes.

Tags: aerial-imagery, forest, forest-typing, general-biology-communities-and-ecosystems-forest, general-management-habitat-management-habitat-models, general-management-habitat-management-strategic-habitat-conservation-shc, general-management-natural-resources-management-forest-management, general-management-natural-resources-management-wildlife-management, imagery, land-cover, land-use, landuse, refuges, sewall, vegetation, vegetation-cover
Organization: Department of the Interior
Continuous Forest Inventory Plots at Sam D. Hamilton Noxubee National Wildlife Refuge

This data set consists of continuous forest inventory plots (Point Shapefile 212 plots) systematically located across Noxubee NWR.   Data contains only the plot number and the geographic location (Latitude and Longitude) of the plot center.

Tags: basal-area, cfi, general-biology-communities-and-ecosystems-woodland, general-management-inventory, general-management-monitoring, general-management-natural-resources-management-forest-management, growth, monitoring, mortality, plot, prism, regeneration
Organization: Department of the Interior
FWS American Woodcock Singing Ground Survey Zones Map

The American woodcock (Scolopax minor) is a popular game bird throughout eastern North America. The management objective of the U. S. Fish and Wildlife Service (FWS) is to increase populations of woodcock to levels consistent with the demands of consumptive and non-consumptive users (U. S. Fish and Wildlife Service 1990). Reliable annual population estimates, harvest estimates and information on recruitment and distribution are essential for comprehensive woodcock management. Unfortunately, this information is difficult and often impractical to obtain. The American Woodcock Singing-ground Survey was developed to meet part of these information needs by monitoring changes in annual abundance indices.

This map depicts latitude line boundaries that assist Woodcock Singing Ground Survey (SGS) participants in determining which survey window their route falls within. The survey window determines when the route can be run on an annual basis.

More information on the Woodcock SGS can be found at these links:
https://naturecounts.ca/nc/amwo/resources.jsp
https://www.fws.gov/project/american-woodcock-singing-ground-survey

Tags: american-woodcock, scolopax-minor
Organization: Department of the Interior
Surficial Substrates in the Cuyahoga River, Ohio, 2021

Substrates in the Cuyahoga River, OH were mapped to assess the availability of  Lake Sturgeon (Acipenser fulvescens) spawning habitat and age-0 Lake Sturgeon habitat. Mapping was conducted with a recreational grade side-scan sonar unit from the river mouth at Lake Erie (river kilometer (rkm) 0) to near the confluence of the Little Cuyahoga River (rkm 71). Side-scan sonar images were georectified in a post-processing software and substrate patches were manually digitized and classified in a geographic information system (GIS). Ground-truthing data were collected following side-scan sonar surveys to determine the accuracy of patch classifications. Substrate composition at ground-truthing locations was determined through visual assessments when feasible and assessed with tactile feel when water depth or clarity prevented visual assessment. Substrate patch types classified from side-scan sonar imagery are provided as polygon shapefiles and ground-truthing observations are provided as point shapefiles.

Tags: biota, cuyahoga-river, general-geology-and-soils-geomorphology-stream-river-processes, general-management-habitat-management-habitat-models, habitat-suitability-indices, inland-waters, lake-erie, lake-sturgeon, ohio, substrate
Organization: Department of the Interior
Mid-Columbia River NWRC and Central Washington NWRC: Invasive Plant Inventory and Early Detection Prioritization Tool (IPIEDT) - Area and Species Tables, 2019

The IPIEDT is an Access Database file. The user responds to questions in a “yes/no/unknown” format or chooses from a list of states or conditions that best describe the situation. Each descriptive response corresponds to a numerical value which is then used to calculate species and area scores and generate ranked lists. A higher species or area score correlates to a higher priority for inventory.

The workshop's resulting data tables are archived so that the results of the workshop are preserved if the master database receives changes based on new threats or areas. Each Invasive Plant Species and Area Prioritization Workshop will have an IPIEDT Access database and 2-3 stand-alone CSV outputs. Each table is offered as an open source CSV and the Access Database tool zipped and is also available for download.

Tags: biota, database, general-biology-invasive-species-invasive-exotic-plants, habitat-management, invasive-species, ipiedpt, ipiedt, ipip, nonindigenous-species, planning, prioritization, weeds, workshop
Organization: Department of the Interior
Malheur National Wildlife Refuge: Invasive Plant Inventory and Early Detection Prioritization Tool (IPIEDT) - Area, Species, Area-Species Link Tables, 2021

The IPIEDT is an Access Database file. The user responds to questions in a “yes/no/unknown” format or chooses from a list of states or conditions that best describe the situation. Each descriptive response corresponds to a numerical value which is then used to calculate species and area scores and generate ranked lists. A higher species or area score correlates to a higher priority for inventory.

The workshop's resulting data tables are archived so that the results of the workshop are preserved if the master database receives changes based on new threats or areas. Each Invasive Plant Species and Area Prioritization Workshop will have an IPIEDT Access database and 2-3 stand-alone CSV outputs. Each table is offered as an open source CSV and the Access Database tool zipped and is also available for download.

Tags: biota, database, general-biology-invasive-species-invasive-exotic-plants, habitat-management, invasive-species, ipiedpt, ipiedt, ipip, nonindigenous-species, planning, prioritization, weeds, workshop
Organization: Department of the Interior
Geospatial Data: Vegetation Conditions (FNAI) and At-risk Plants on St. Vincent National Wildlife Refuge 2019

Geospatial Data regarding vegetation conditions on St. Vincent NWR during 2019.  Data consists of rare plant detections, individual vegetation plot assessments, and current land cover based on the Florida Natural Area Inventory.  All data are presented as lat/long NAD 83.

Tags: assessment, at-risk, classification, condition, corkwood, cover-types, cucumberleaf-sunflower, drummonds-yellow-eyed-grass, florida-beargrass, fnai, general-biology-at-risk-biota-te-species, general-biology-invasive-species-invasive-exotic-plants, general-biology-species-plants, general-fire-fire-management-prescribed-burning, general-management-inventory, godfreys-blazing-star, gulf-coast-lupine, gulfcoast-lupine, helianthus-debilis-ssp-cucumerifolius, inventory, large-leaved-jointweed, largeleaf-jointweed, leitneria-floridana, liatris-provincialis, linum-westii, lupinus-westianus, natural-communities, nolina-atopocarpa, plants, polygonella-macrophylla, rare-species, st-vincent, wests-flax, within-prescription, xyris-drummondii
Organization: Department of the Interior
Capture and Morphometric Data from Ocelots around Laguna Atascosa National Wildlife Refuge from 2011-2021. Version 1.1. U.S. Fish and Wildlife Service, Los Fresnos, Texas, USA.  https://doi.org/10.7944/m32b-ps86

The U.S. Fish and Wildlife Service (USFWS) captured endangered ocelots to monitor the local population on Laguna Atascosa National Wildlife Refuge in Texas. This dataset includes data from 69 captures and measurements of 24 male or female ocelots by U. S. Fish and Wildlife Service staff from 2011-2021. Ocelots were captured in box-traps, and if appropriate for tracking their movements, were sedated, anesthetized, fit with a VHF or GPS collar, and released on USFWS lands following protocols in Sternberg and Swarts (2021; https://doi.org/10.7944/pbwy-se62 and https://doi.org/10.7944/wx3d-jd10). 

This data package includes TXT files as uploaded to the Global Biodiversity Information Facility (GBIF) website as well as associated files. Including all these files and uploading them to GBIF helps meet improved data curation standards including making the data more findable and interoperable to a broad suite of public users. Review the associated metadata file to assist you in understanding and using these data.

This dataset's DOI is https://doi.org/10.7944/m32b-ps86.

Tags: capture-felidae-leopardus-pardalis-mammal-measurement-morphometrics-observation-ocelot-occurren, general-biology-species-mammals, leopardus-pardalis, ocelot
Organization: Department of the Interior
Series of aerial images over Monte Vista National Wildlife Refuge, acquired July 13th, 1965

This data set includes 31 georeferenced versions of black and white aerial photographs from July 13th, 1965, taken over Monte Vista National Wildlife Refuge. A georeferenced mosaic of the photographs is included in the data set. Like other historic photos, this image allows for interpretation of habitat types on the refuge in 1965. Change over time estimates can be made from this image using current imagery for comparison. This image, along with others, are being used by refuge staff to assist in understanding and visualizing the historical content of the lands within the refuge and how they have changed. The original black and white aerial photograph was acquired in digital form from USGS EarthExplorer. Individual frames were referenced to the 2009 NAIP color imagery with ArcMap 10.0. The resolution of the image is 0.8 meters. This image should be used for resource-level interpretation only.

Tags: aerial-photo, biota, colorado, ecosystems, hydrologic-basins, refuge-boundaries
Organization: Department of the Interior
Steady-State One-Dimensional Flow Model for the Cuyahoga River, Ohio, 2022

The availability of suitable Lake Sturgeon (Acipenser fulvescens) spawning habitat and age-0 Lake Sturgeon habitat in the Cuyahoga River, OH. A one-dimensional model was developed with the Hydrologic Engineering Center’s River Analysis System (HEC-RAS) 6.3.1 software to simulate flows at three discharges, representing the 25th, 50th, and 75th percentile of spring discharge (April-June) over an 11 to 34 year period, depending on availability of data at USGS gaging stations. 

The upstream extent of the model domain was just downriver of the confluence of the Little Cuyahoga River at river kilometer (rkm) 70.919. The upper extent was chosen to avoid unaccounted flow inputs between the upstream extent of the model and the upstream most gaging station, U.S. Geological Survey (USGS) gage 04206000 in Old Portage, OH. The lower domain of the model was in the mouth of the Cuyahoga River at Lake Erie (rkm 0), approximately 7.5 kilometers from the National Oceanic and Atmospheric Administration (NOAA) tidal gage 9063063. The model domain included four USGS gaging stations: 04206000, 04206425 (Jaite, OH), 04208000 (Independence, OH), and 04208504 (Newburgh Heights, OH), which were used to determine the percentiles of spring discharge and to calibrate the model to the three discharges considered. 

Known water surface elevations (KWSE) were utilized for the upstream and downstream reach boundary conditions for the steady-state flow analysis. For the downstream KWSE, daily mean water surface elevations were calculated from the NOAA gage (9063063) in Cleveland Harbor for each profile with profiles corresponding to dates when bathymetric surveys occurred, the three flow percentiles (i.e., 25th, 50th, 75th), and mean flow. Upstream KWSE was calculated by adding the gage height to the gage elevation (i.e., bed elevation) from the most upstream USGS stream gage (04206000).

Tags: acipenser-fulvescens, cuyahoga-river, general-biology-communities-and-ecosystems-riverine, general-biology-species-fishes, general-management-habitat-management-habitat-models, general-management-natural-resources-management-fisheries-management, general-water-hydrology-surface-water, habitat-suitability-indices, lake-erie, lake-sturgeon, mathematical-modeling, ohio, streamflow, surface-water-non-marine
Organization: Department of the Interior
Field Data: Spatial distribution of estuarine diamond-backed terrapins (Malaclemys terrapin) and risk analysis from commercial blue crab (Callinectes sapidus) trapping at the Savannah Coastal Refuges Complex, USA

This data set consists of field data collected as part of the study to examine estimation of diamond-backed terrapins and commercial blue crap trapping.  Data consists of metadata, CSV, and spatial information (raster and vector) provided as a geodatabase.

Tags: blue-crab, bluepoint, by-catch, callinectes-sapidus, crab, crab-trap, detection, diamond-backed-terrapin, diamondback-terrapin, general-biology-at-risk-biota-te-species, general-biology-communities-and-ecosystems-salt-marsh, general-biology-species-amphibians-and-reptiles, general-biology-species-invertebrates, general-management-monitoring, headcount-bias-observer-variables, malaclemys-terrapin, mortality, occupancy-modeling-risk, pots, transects, usgs
Organization: Department of the Interior
LiDAR Derived Bare Earth Digital Elevation Model, 2016: Minidoka National Wildlife Refuge

This lidar data set includes unclassified swath LAS 1.4 files, classified LAS 1.4 files, breaklines, digital elevation models (DEMs), first return digital surface models (DSMs), and intensity imagery. Geographic Extent: Fourteen partial counties in Utah, covering approximately 7,005 total square kilometers; partial coverage of three counties covering approximately 182 square kilometers in the Minidoka QL1 AOI. This area is part of the Bear Lake / Cache Valley QL1 AOI. Dataset Description: The Utah 2016 Lidar project called for the planning, acquisition, processing, and derivative products of lidar data to be collected at a nominal pulse spacing (NPS) of 0.35 meters. Project specifications are based on the U.S. Geological Survey National Geospatial Program Base Lidar Specification, Version 1.2. The data was developed based on a horizontal projection/datum of NAD83 (2011), UTM Zone 12, meters and vertical datum of NAVD88 (GEOID12B), meters. Lidar data was delivered as flightline-extent unclassified LAS swaths, as processed Classified LAS 1.4 files formatted to 215 individual 1,000 meter x 1,000 meter tiles; as tiled intensity imagery, as tiled bare earth DEMs, and as tiled first return DSMs all tiled a 2,000 meter x 2,000 meter schema (82 tiles). Continuous breaklines were produced in Esri shapefile format. Ground Conditions: Lidar was partially collected in fall of 2016, while no snow was on the ground and rivers were at or below normal levels. In order to post process the lidar data to meet task order specifications and meet ASPRS vertical accuracy guidelines, Quantum Spatial, Inc. established a total of 28 ground control points that were used to calibrate the lidar to known ground locations established throughout the project area. An additional 5 independent accuracy checkpoints, 5 in Bare Earth and Urban landcovers (5 NVA points), 6 in the Shrubs and Tall Grass category (6 VVA points), were used to assess the vertical accuracy of the data. These checkpoints were not used to calibrate or post process the data.

Tags: bare-earth, dem, digital-terrain-model, elevation-data, idaho, lidar, light-detection-and-ranging, topography
Organization: Department of the Interior
R1: Aquatic Monitoring for Climate Change - Fish Assemblage and Habitat - Tabular and Relational Datasets

This reference contains relational and tabular datasets for Aquatic Monitoring for Climate Change - Fish Assemblage and Habitat survey (PRIMR IDs: FF01RKTN00-035, FF01RLPO00-089, FF01RMLH00-125, FF01RWLP00-108, FF01RWMF00-084).
These datasets represent ongoing long-term aquatic health and climate change monitoring at Refuges, and incorporates all continuous measures from the pilot project. 

Service programs (Refuges, Fish and Aquatic Conservation, and Water Resources) are collaborating to implement a long-term aquatic monitoring program for evaluating effects of climate change at National Wildlife Refuges (NWRs) in the Columbia-Pacific Northwest Region (IR9). The goal is to evaluate evidence of climate change on physical and habitat variables, and potentissociations al associations with changes in fish assemblages in wadeable streams. The program relies on two site specific protocols (SSPs), one addressing habitat and fish surveys (this SSP) and another addressing temperature and stream flow. For habitat and fish, objectives are to: establish a survey reach within a stream at each of five NWRs across the range of ecoregions in IR9; describe habitat in each survey reach once every five years or less; describe fish assemblages in each survey reach once every five years or less; analyze for temporal changes in habitat and fish assemblages, and assess potential temporal associations between habitat and fish assemblages. Data collected at survey reach are based on a subset of protocols developed by the U.S. Environmental Protection Agency for the Environmental Monitoring and Evaluation Program (EMAP; Peck et al. 2006).

Tags: aquatic-vertebrates, ff01rktn00-035, ff01rlpo00-089, ff01rmlh00-125, ff01rwlp00-108, ff01rwmf00-084, fish-assemblage, general-air-and-climate-weather-and-climate-climate-change, general-biology-species-fishes, general-management-inventory, general-management-monitoring, physical-habitat, primr-survey
Organization: Department of the Interior