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USGS2018

Department of the Interior metadata implementation guide—Framework for developing the metadata component for data resource management

The Department of the Interior (DOI) is a Federal agency with over 90,000 employees across 10 bureaus and 8 agency offices. Its primary mission is to protect and manage the Nation’s natural resources and cultural heritage; provide scientific and other information about those resources; and honor its trust responsibilities or special commitments to American Indians, Alaska Natives, and affiliated island communities. Data and information are critical in day-to-day operational decision making and scientific research. DOI is committed to creating, documenting, managing, and sharing high-quality data and metadata in and across its various programs that support its mission. Documenting data through metadata is essential in realizing the value of data as an enterprise asset. The completeness, consistency, and timeliness of metadata affect users’ ability to search for and discover the most relevant data for the intended purpose; and facilitates the interoperability and usability of these data among DOI bureaus and offices. Fully documented metadata describe data usability, quality, accuracy, provenance, and meaning. Across DOI, there are different maturity levels and phases of information and metadata management implementations. The Department has organized a committee consisting of bureau-level points-of-contacts to collaborate on the development of more consistent, standardized, and more effective metadata management practices and guidance to support this shared mission and the information needs of the Department. DOI’s metadata implementation plans establish key roles and responsibilities associated with metadata management processes, procedures, and a series of actions defined in three major metadata implementation phases including: (1) Getting started—Planning Phase, (2) Implementing and Maintaining Operational Metadata Management Phase, and (3) the Next Steps towards Improving Metadata Management Phase. DOI’s phased approach for metadata management addresses some of the major data and metadata management challenges that exist across the diverse missions of the bureaus and offices. All employees who create, modify, or use data are involved with data and metadata management. Identifying, establishing, and formalizing the roles and responsibilities associated with metadata management are key to institutionalizing a framework of best practices, methodologies, processes, and common approaches throughout all levels of the organization; these are the foundation for effective data resource management. For executives and managers, metadata management strengthens their overarching views of data assets, holdings, and data interoperability; and clarifies how metadata management can help accelerate the compliance of multiple policy mandates. For employees, data stewards, and data professionals, formalized metadata management will help with the consistency of definitions, and approaches addressing data discoverability, data quality, and data lineage. In addition to data professionals and others associated with information technology; data stewards and program subject matter experts take on important metadata management roles and responsibilities as data flow through their respective business and science-related workflows. The responsibilities of establishing, practicing, and governing the actions associated with their specific metadata management roles are critical to successful metadata implementation.

Techniques and Methods↗
USGS2026

RoadxStr user’s guide—For collection of road-stream crossing assessment field observations

Intersections of drainage networks and road networks represent a critical nexus between natural waterways and human infrastructure. Managing these systems involves decisions related to management of infrastructure, hydrologic and geomorphic processes, and ecological connectivity. Interactions among these systems influence multiple values, including the intactness of transportation networks, public safety, water quality, and ecosystem function that collectively amount to billions of dollars. Despite the importance of road-stream crossings, there are countless gaps in knowing where and what they are. These gaps limit the degree to which managers can inventory and assess stream and road networks to inform decisions. To address this first-level need, we developed RoadxStr (road-stream crossings): a survey tool that effectively characterizes road-stream crossings across the full stream and drainage network. This document describes the RoadxStr Field Form, available within a mobile application, which is designed for rapid and standardized data collection involving assessment of a road-stream crossing, including the road, crossing structure(s), and the nearby hydrologic channel. This document provides instructions on how to (1) access and download the RoadxStr Field Form within the mobile application service and (2) use and complete a RoadxStr Field Form survey.

Techniques and Methods↗
USGS2024

Case definitions for wildlife diseases

Welcome to the first manual of “Case Definitions for Wildlife Diseases,” a “living” electronic publication. The plan is to add and update this manual’s case definitions periodically as warranted; thus, this manual will never be completed, and readers should download the latest versions of specific chapters (that is, definitions) when available. Constructive suggestions from readers are welcome and will help guide adjustments as this project progresses. The purpose of this manual is to provide case definitions for selected diseases of importance to wildlife in Canada and the United States. Case definitions provide standard sets of criteria for classifying the degree of certainty of a particular diagnosis and help improve surveillance data quality and comparability. Better data and standardization allow for improved data sharing, which increases geographic and species surveillance coverage and permits more robust analyses. The definitions included in this manual have been developed by veterinary pathologists, epidemiologists, and wildlife biologists primarily from the U.S. Geological Survey National Wildlife Health Center (NWHC) and Canadian Wildlife Health Cooperative (CWHC). Pathologists from each organization reviewed and finalized the definitions. Each case definition has been peer reviewed by two scientific experts before publication. This manual begins with the case definition template. This generic template includes four sections: “Individual, Place, and Time Criteria for Diagnosis and Testing,” “Field Criteria for Diagnosis,” “Laboratory Criteria for Diagnosis,” and “Epidemiological Linkage Criteria for Diagnosis” and can be used to guide development of new case definitions. Information in each section is then combined to provide an overall case classification. Disease diagnoses are classified as “Confirmed,” “Presumptive,” or “Suspected;” and evidence of a pathogen or toxin is classified as “Exposed” or “Present/Detected.” Each subsequent chapter is then a case definition for a specific disease of wildlife, and infectious and non-infectious diseases are included.

Techniques and Methods↗
USGS2024

[Disease/condition] case definition [template] for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition template can be used for any disease/pathogen for any species. An editable version of this template is available for download at https://doi.org/10.3133/tm19A1 .

Techniques and Methods↗
USGS2024

West Nile virus (avian) case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to West Nile virus and applies to all avian species.

Techniques and Methods↗
USGS2024

Avian botulism case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to avian botulism and applies to all avian species.

Techniques and Methods↗
USGS2024

Ophidiomycosis (snake fungal disease) case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to Ophidiomycosis (snake fungal disease) and applies to all snakes.

Techniques and Methods↗
USGS2026

Aspergillosis (Avian) case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining: (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to aspergillosis and applies to all avian species.

Techniques and Methods↗
USGS2024

Electrocution (avian) case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to electrocution and applies to all avian species.

Techniques and Methods↗
USGS2024

Stony coral tissue loss disease (SCTLD) case definition for wildlife

Diagnostic laboratories receive carcasses and samples for diagnostic evaluation and pathogen/toxin detection. Case definitions bring clarity and consistency to the evaluation process. Their use within and between organizations allows more uniform reporting of diseases and etiologic agents. The intent of a case definition is to provide scientifically based criteria for determining (a) if an individual carcass has a specific disease and degree of confidence in that diagnosis and (b) if there is evidence of a pathogen or toxin in a carcass or sample (for example, swab, tissue sample, skin scraping, blood/serum sample, environmental sample, or other). This case definition is specific to Stony Coral Tissue Loss Disease (SCTLC) and applies to several species of scleractinian corals across seven families: Faviidae, Meandrinidae, Merulinidae, Montastraeidae, Astrocoeniidae, Scleractinia, and Siderastreidae. Other species presumed to be susceptible are in Families Agaridiidae, Faviidae, and Pocilloporidae.

Florida↗
USGS2011

Groundwater technical procedures of the U.S. Geological Survey

A series of groundwater technical procedures documents (GWPDs) has been released by the U.S. Geological Survey, Water-Resources Discipline, for general use by the public. These technical procedures were written in response to the need for standardized technical procedures of many aspects of groundwater science, including site and measuring-point establishment, measurement of water levels, and measurement of well discharge. The techniques are described in the GWPDs in concise language and are accompanied by necessary figures and tables derived from cited manuals, reports, and other documents. Because a goal of this series of procedures is to remain current with the state of the science, and because procedures change over time, this report is released in an online format only. As new procedures are developed and released, they will be linked to this document.

Techniques and Methods↗
USGS2023

Field techniques for fluorescence measurements targeting dissolved organic matter, hydrocarbons, and wastewater in environmental waters: Principles and guidelines for instrument selection, operation and maintenance, quality assurance, and data reporting

The use of field deployable fluorescence sensors by the U.S. Geological Survey has become increasingly common for a wide variety of surface water and groundwater investigations. This report addresses field deployable fluorometers that measure the fluorescence response of various substances in water exposed to incident light generated by the sensor. An introduction to the basic principles of field measurements of fluorescence is provided, as well as technical background information on sensors that target dissolved organic matter, wastewater, and hydrocarbons, including sensor selection, operating principles, key features, and design elements. General deployment, operation and maintenance protocols, quality-assurance techniques, and suggestions for data reporting are presented to facilitate and standardize the collection and accurate communication of data collected by the U.S. Geological Survey across studies, sites, and sensor types. Sensor performance issues and common interferences are also described. An appendix is included to describe sensor calibration criteria and procedures, reporting units, and specific approaches to correct for interferences for fluorescence of dissolved organic matter sensors.

Techniques and Methods↗
USGS2013

Optical techniques for the determination of nitrate in environmental waters: Guidelines for instrument selection, operation, deployment, maintenance, quality assurance, and data reporting

The recent commercial availability of in situ optical sensors, together with new techniques for data collection and analysis, provides the opportunity to monitor a wide range of water-quality constituents on time scales in which environmental conditions actually change. Of particular interest is the application of ultraviolet (UV) photometers for in situ determination of nitrate concentrations in rivers and streams. The variety of UV nitrate sensors currently available differ in several important ways related to instrument design that affect the accuracy of their nitrate concentration measurements in different types of natural waters. This report provides information about selection and use of UV nitrate sensors by the U.S. Geological Survey to facilitate the collection of high-quality data across studies, sites, and instrument types. For those in need of technical background and information about sensor selection, this report addresses the operating principles, key features and sensor design, sensor characterization techniques and typical interferences, and approaches for sensor deployment. For those needing information about maintaining sensor performance in the field, key sections in this report address maintenance and calibration protocols, quality-assurance techniques, and data formats and reporting. Although the focus of this report is UV nitrate sensors, many of the principles can be applied to other in situ optical sensors for water-quality studies.

Techniques and Methods↗
USGS2022

Quality assurance report for Loch Vale Watershed, 2010–19

The Loch Vale Watershed Research and Monitoring Program collects long-term datasets of ecological and biogeochemical parameters in Rocky Mountain National Park to support both (1) management of this protected area and (2) research into watershed-scale ecosystem processes as those processes respond to atmospheric deposition and climate variability. The program collects data on precipitation depth and atmospheric deposition chemistry—as well as surface water biogeochemistry—within the watershed and in other areas of the park. These data are used by resource managers, scientists, policy makers, and students, so it is important that all collected data meet high quality standards. This report presents an evaluation of data quality for precipitation, atmospheric ammonia, and surface water quality samples collected from 2010 to 2019. This report also presents changes made to the monitoring and laboratory equipment used during the study period and describes new data streams added to the project, including atmospheric ammonia, surface water chlorophyll-a, and dissolved oxygen in two lakes: The Loch and Sky Pond. Quality-assurance procedures looked at the accuracy and precision of measurements made over the study period and found that precipitation and surface water chemistry data were 99 percent accurate and precise. Records that failed to meet quality standards were removed from published databases. From 2010 to 2014, a colocated precipitation gauge and deposition collector were installed on site as quality checks. From 2014 to 2018, power loss at the site resulted in significant loss of precipitation data records during the snow seasons. Those problems were addressed by installing new solar-power equipment in 2019. Measurements of deposition chemistry, atmospheric ammonia deposition, and surface water biogeochemistry were all sufficiently complete and consistent to support project data needs.

Colorado↗
USGS2015

General classification handbook for floodplain vegetation in large river systems

This handbook describes the General Wetland Vegetation Classification System developed as part of the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration (UMRR) Program, Long Term Resource Monitoring (LTRM) element. The UMRR is a cooperative effort between the U.S. Army Corps of Engineers, U.S. Geological Survey, U.S. Fish and Wildlife Service, and the states of Illinois, Iowa, Minnesota, Missouri, and Wisconsin. The classification system consists of 31 general map classes and has been used to create systemic vegetation data layers throughout the diverse Upper Mississippi River System (UMRS), which includes the commercially navigable reaches of the Mississippi River from Minneapolis, Minnesota, in the north to Cairo, Illinois, in the south, the Illinois River, and navigable portions of the Kaskaskia, Black, St. Croix, and Minnesota Rivers. In addition, this handbook describes the evolution of the General Wetland Vegetation Classification System, discusses the process of creating a vegetation data layer, and describes each of the 31 map classes in detail. The handbook also acts as a pictorial guide to each of the map classes as they may appear in the field, as well as on color-infrared imagery. This version is an update to the original handbook published in 2004.

Techniques and Methods↗
USGS2010

A Natural History Summary and Survey Protocol for the Southwestern Willow Flycatcher

The Southwestern Willow Flycatcher (Empidonax traillii extimus) has been the subject of substantial research, monitoring, and management activity since it was listed as an endangered species in 1995. When proposed for listing in 1993, relatively little was known about the flycatcher's natural history, and there were only 30 known breeding sites supporting an estimated 111 territories rangewide (Sogge and others, 2003a). Since that time, thousands of presence/absences surveys have been conducted throughout the historical range of the flycatcher, and many studies of its natural history and ecology have been completed. As a result, the ecology of the flycatcher is much better understood than it was just over a decade ago. In addition, we have learned that the current status of the flycatcher is better than originally thought: as of 2007, the population was estimated at approximately 1,300 territories distributed among approximately 280 breeding sites (Durst and others, 2008a). Concern about the Southwestern Willow Flycatcher on a rangewide scale was brought to focus by Unitt (1987), who described declines in flycatcher abundance and distribution throughout the Southwest. E. t. extimus populations declined during the 20th century, primarily because of habitat loss and modification from activities, such as dam construction and operation, groundwater pumping, water diversions, and flood control. In 1991, the U.S. Fish and Wildlife Service (USFWS) designated the Southwestern Willow Flycatcher as a candidate category 1 species (U.S. Fish and Wildlife Service, 1991). In July 1993, the USFWS proposed to list E. t. extimus as an endangered species and to designate critical habitat under the Act (U.S. Fish and Wildlife Service, 1993). A final rule listing E. t. extimus as endangered was published in February 1995 (U.S. Fish and Wildlife Service, 1995); critical habitat was designated in 1997 (U.S. Fish and Wildlife Service, 1997). The USFWS Service released a Recovery Plan for the Southwestern Willow Flycatcher in 2002 (U.S. Fish and Wildlife Service, 2002), and re-designated critical habitat in 2005 (U.S. Fish and Wildlife Service, 2005).

Techniques and Methods↗
USGS2011

Monitoring habitat restoration projects: U.S. Fish and Wildlife Service Pacific Region Partners for Fish and Wildlife Program and Coastal Program Protocol

The U.S. Fish and Wildlife Service's (FWS) Pacific Region (Region 1) includes more than 158 million acres (almost 247,000 square miles) of land base in Idaho, Oregon, Washington, Hawai`i, the Commonwealth of the Northern Mariana Islands, American Samoa, Guam, the Republic of Palau, the Federated States of Micronesia, and the Republic of the Marshall Islands. Region 1 is ecologically diverse with landscapes that range from coral reefs, broadleaf tropical forests, and tropical savannahs in the Pacific Islands, to glacial streams and lakes, lush old-growth rainforests, inland fjords, and coastal shoreline in the Pacific Northwest, to the forested mountains, shrub-steppe desert, and native grasslands in the Inland Northwest. Similarly, the people of the different landscapes perceive, value, and manage their natural resources in ways unique to their respective regions and cultures. The Partners for Fish and Wildlife Program (Partners Program) and Coastal Program work with a variety of partners in Region 1 including individual landowners, watershed councils, land trusts, Soil and Water Conservation Districts, non-governmental organizations, Tribal governments, Native Hawaiian organizations, and local, State, and Federal agencies. The Partners Program is the FWS's vanguard for working with private landowners to voluntarily restore and conserve fish and wildlife habitat. Using non-regulatory incentives, the Partners Program engages willing partners to conserve and protect valuable fish and wildlife habitat on their property and in their communities. This is accomplished by providing the funding support and technical and planning tools needed to make on-the-ground conservation affordable, feasible, and effective. The primary goals of the Pacific Region Partners Program are to: Promote citizen and community-based stewardship efforts for fish and wildlife conservation Contribute to the recovery of at-risk species, Protect the environmental integrity of the National Wildlife Refuges, Contribute to the implementation of the State Comprehensive Wildlife Conservation Strategies, and Help achieve the objectives of the National Fish Habitat Partnerships and regionally based bird conservation plans (for example, North American Waterfowl Management Plan, U.S. Pacific Island Shorebird Conservation Plans, Intermountain West Regional Shorebird Plan, etc.). The Partners Program accomplishes these priorities by: Developing and maintaining strong partnerships, and delivering on-the-ground habitat restoration projects designed to reestablish habitat function and restore natural processes; Addressing key habitat limiting factors for declining species; Providing corridors for wildlife and decrease impediments to native fish and wildlife migration; and Enhancing native plant communities by reducing invasive species and improving native species composition. The Coastal Program is a voluntary fish and wildlife conservation program that focuses on watershed-scale, long-term collaborative resource planning and on-the-ground restoration projects in high-priority coastal areas. The Coastal Program conducts planning and restoration work on private, State, and Federal lands, and partnerships with other agencies-Native American Tribes, citizens, and organizations are emphasized. Coastal Program goals include restoring and protecting coastal habitat, providing technical and cost-sharing assistance where appropriate, supporting community-based restoration, collecting and developing information on the status of and threats to fish and wildlife, and using outreach to promote stewardship of coastal resources. The diversity of habitats and partners in Region 1 present many opportunities for conducting restoration projects. Faced with this abundance of opportunity, the Partners Program and Coastal Program must ensure that limited staffing and project dollars are allocated to benefit the highest priority resources and achieve the highest quality results for Federal trust species. In 2007, the Partners Program and Coastal Program developed a Strategic Plan to guide program operations and more efficiently conserve habitat by focusing partnership building and habitat improvement actions within 35 Partners Program Focus Areas and 9 Coastal Program Focus Areas (U.S. Fish and Wildlife Service, 2010). The Strategic Plan also contains four other goals: broaden and strengthen partnerships; improve information sharing and communications; enhance workforce; and increase accountability to ensure that program resources are used efficiently and effectively. This protocol will help achieve all goals of the Strategic Plan.

Techniques and Methods↗
USGS2018

Monitoring riparian-vegetation composition and cover along the Colorado River downstream of Glen Canyon Dam, Arizona

Vegetation in the riparian zone (the area immediately adjacent to streams, such as stream banks) along the Colorado River downstream of Glen Canyon Dam, Arizona, supports many ecosystem and societal functions. In both Glen Canyon and Grand Canyon, this ecosystem has changed over time in response to flow alterations, invasive species, and recreational use. Riparian-vegetation cover and composition are likely to continue to change as these pressures persist and new ones emerge. Because this system is a valuable resource that is known to change in response to flow regime and other disturbances, a long-term monitoring protocol has been designed with three primary objectives: Annually measure and summarize the status (composition and cover) of native and non-native vascular-plant species within the riparian zone of the Colorado River between Glen Canyon Dam and Lake Mead. At 5-year intervals, assess change in vegetation composition and cover in the riparian zone, as related to geomorphic setting and dam operations, particularly flow regime. Collect data in a manner that can be used by multiple stakeholders, particularly the basinwide monitoring program overseen by the National Park Service’s Northern Colorado Plateau Network Inventory and Monitoring program. A protocol for the long-term monitoring of riparian vegetation is described in detail and standard operating procedures are included herein for all tasks. Visual estimates of foliar and ground covers are collected in conjunction with environmental measurements to assess correlations of foliar cover with abiotic and flow variables. Sample quadrats are stratified by frequency of inundation, geomorphic feature, and by river segment to account for differences in vegetation type. Photographs of sites are also taken to illustrate qualitative characteristics of the site at the time of sampling. Procedures for field preparation, generating random samples, data collection, data management, collecting and managing unknown species collections, and reporting are also described. Although this protocol is intended to be consistent over the long-term, procedures for minor and major revisions to the protocol are also outlined.

Arizona↗