Introduction

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services.

BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 800 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 450 samples from 93 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis.

BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN’s). A simple web-data input interface and self-guided, public data-retrieval web site provides access to bioassessment data. BioData currently accepts data collected using two national protocols: (1) NAWQA and (2) U.S. Environmental Protection Agency (USEPA) National Rivers and Streams Assessment (NRSA). Additional collection protocols are planned for future versions.

Highlights

Use the BioData Management System to:

• Capture, review, edit, finalize, approve, and archive bioassessment data collected for local, regional, and national aquatic bioassessment, monitoring, and research purposes.
• Store data collected using two nationally accepted protocols with the capability to add support for additional protocols in the future.

Use the BioData Retrieval System to:

• Retrieve bioassessment data through a single public web site (https://aquatic.biodata.usgs.gov).
• Retrieve data using a unified and consistent taxonomic identification system that accounts for changes in taxonomic nomenclature.

BioData Management System

The BioData management system provides field biologists with data input, review, approval, and management capabilities through a password-protected web application (fig. 2). Data review, revision, and automated data-validation tools make quality-assurance practices more efficient and routine. BioData management system also supports communication and data exchange between field biologists and partner laboratories. Once approved, data are made available from the data-retrieval web site.

Selected Data Input Features

• Manage and organize samples by project.
• Manage data entry and editing rights for each project.
• Enter data using self-guided data-entry forms with built-in help and data validation.
• Auto-save – data are securely and instantly saved for retrieval.
• Review and validate data to find and fix problems quickly and easily.
• Manage laboratory orders and notification of laboratories through email when a project places or modifies an order.
• Review individual taxa records–select and mark identifications for further review and verification.
• Print shipping lists, bottle labels, and USGS National Water-Quality Laboratory (NWQL) Analytical Services Request forms.
• Access to online documentation for laboratories that includes taxonomic reference lists and requirements for data upload.
• Validate data from laboratories automatically – view and download laboratory data-validation reports.

Figure 2. BioData input screens showing how to (A, B) manage samples, enter, review, revise, and approve data from field and laboratory records; (C) create laboratory order forms; and (D) download reports.

BioData Retrieval System

The BioData Retrieval System, https://aquatic.biodata.usgs.gov, is a one-stop location for USGS bioassessment data from across the United States (fig. 3). Scientists, resources managers, and the public can use this centralized, web-accessible database to view, browse, access, and download bioassessment data.

Selected Retrieval Features

• Easy step-wise data selection features using a variety of criteria.
• View the number of samples before download.
• Save data-selection criteria for future use, email the file to collaborators.
• Preview datasets before they are retrieved.
• Choose file formats for data retrieval – Excel, tab-delimited, comma delimited, XML. More formats may be added in the future.
• A standardized, unified taxonomic system is used for fish, invertebrates and algae ─ synonomy is resolved. Fish data sets include ITIS TSN’s. ITIS TSN’s are planned for invertebrates and algae over time commensurate with advances in ITIS.

Figure 3. BioData retrieval web site screens showing how to (E) select retrieval criteria; (F, G) view and save customized retrieval formats; and (H, I) preview and retrieve bioassessment data.

Get started using BioData

Users and uses of BioData:

• USGS can enter, store, and retrieve project bioassessment data
• Government agencies can retrieve the data for national, regional, statewide, and local research and assessment
• Academic professionals and students can retrieve the data for course work and academic research
• Research scientists can retrieve the data to test scientific hypothesis and report findings
• Resource managers can retrieve the data for assessments to evaluate criteria and goals
• Fishermen and outdoor enthusiasts can learn about invertebrate, fish, and algae data for their favorite recreational and fishing locations
• The general public can learn about aquatic organisms for a water body of interest

What BioData delivers to users:

• Tens of thousands of bioassessment sample data that include fish, invertebrates, algae, and supporting habitat data
• Bioassessment data from thousands of sites (fig. 4)
• Taxomonic lists of aquatic organisms found at select sites nationwide
• Step-by-step instruction on data input and retrieval

More information can be found on the BioData web site at https://aquatic.biodata.usgs.gov to:

• Obtain a login and become a BioData USGS technical user
• Retrieve data in three easy steps: (1) select filter criteria, (2) choose data sets, (3) preview and select download format
• Become a BioData laboratory

For More Information

Donna Myers, Chief, Office of Water Quality, dnmeyers@usgs.gov, (703) 648-5012
Pete Ruhl, BioData Project Manager, Office of Water Quality, pmruhl@usgs.gov, (703) 648-6841

BioData Users Group (USGS BUG)

Mitchell Harris, Illinois WSC, maharris@usgs.gov, (217) 328-9716
Jana Stewart, Wisconsin WSC, jsstewar@usgs.gov, (608) 821-3855
Scott Grotheer, National Water Quality Laboratory, Denver, sagrothe@usgs.gov, (303)236-3486
Dorene MacCoy, Idaho WSC, demaccoy@usgs.gov, (208) 387-1354
Sarah Spaulding, Fort Collins Science Center, sspaulding@usgs.gov, (303) 492-5158
Tracey Cadkin, Center for Integrated Data Analysis, tcadkin@usgs.gov, (608) 821-3877

Revised January 12, 2012

First posted November 14, 2011