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Contact us (Online form)      BioData Home -      Retrieval -     Input -

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Support Home     BioData Lab Handbook      Using BioData Retrieval    Input, Data Review, and Field Support

Table of Contents for this page

Table of Contents

Overview

The goal of this page is to help you get started with retrieving data from BioData, the USGS aquatic bioassessment database. There are three retrieval steps to accomplish this task:

  1. Select Filter Criteria
  2. Select Data Sets
  3. Preview and Download your results

The USGS BioData Retrieval provides access to aquatic bioassessment data (biological community and physical habitat data) collected by USGS scientists from stream ecosystems across the nation.

STEP 1: Select Filter Criteria

Filter criteria are arranged in sections (for example, Geographic Location; Temporal; Biological Community/Data Type and Sample Type). The combination of filters from each section creates a "filter set" (combination of criteria) that refines the data set to meet your needs.

  1. Choose a filter or filters from one of more section, usually by selecting a radio button
  2. If presented with a list of options (e.g. Biological Community), move the option(s) you want from the "Available" to "Selected" pane, by: (a) Dragging and dropping, (b) Highlighting then clicking the "Add" button, or (c) double clicking the option.
    1. For each filter, specify your criteria:
  3. As you set your filter criteria, the Number of Samples Returnedat the top of the screen is updated automatically and is shown below the "Next" button.
  4. Repeat steps 1 and 2 until all options of interest are "Selected"
  5. Optionally you may save your filter set using "Save Filter Set" button in the top right-hand area of the selection pane; this saved filter set can be sent to colleagues or uploaded and re-used or refined as needed
  6. When your filters are set, click the "Next" button located at either the top or bottom left-hand region of the pane to go to the Select Data Set(s) page.

STEP 2: Select Data Set(s)

The data sets available from the BioData retrieval system are presented in two tables.

The upper table lists the data sets containing data that match the criteria you set. Check the boxes in the left-most column to select the data set(s) you would like to obtain, then select the "Next" button to go to the Preview and download page.

The lower table lists other potential data sets with no records matching the criteria you set. This list is provided so you may see an inventory of the data sets available in the system. If you desire, select the "Previous" button to edit your filter set.

Each table has six columns:

  • Check box
  • Category
  • Data Set Name
  • Description
  • Number of Matching Records
  • Data set column description link, denoted by a question mark icon

The upper table lists the data sets containing data that match the criteria you set...


The lower table lists other potential data sets with no records matching the criteria you set...

 

STEP 3: Preview and Download

Use this page to Preview and Download the data set(s) that you selected on the previous page:

  1. Preview each data set (one at a time) - if desired
  2. Select the file type
  3. Download data set(s) to a zip file, which includes:
    • all selected data sets
    • your filter criteria as an XML file that can be reused on the select filter criteria page
    • a KML file that can be used to display the selected sites on a map (e.g. Google Earth), and
    • a data dictionary

Preview each data set (one at a time) using the drop down list


Select format criteria for downloading data sets (excel, delimited text of XML)

Data Retrieval Details/Features

This section provides some details about the data retrieval system and data retrieval tips.

Data selection tips

  • Save your filter criteria (XML file) for additional data pulls or to share with colleages without sending large data files
  • Upload a site list
  • Taxon-specific filters allows you to look for specific fish, invertebrate, or algal taxa

Things to be aware of when downloading data sets from BioData

  • When combining data from different protocols be aware that similar named columns could represent very different data types or differently named columns could represent very similar data
  • When combining taxonomic data from different laboratories be sure and verify the laboratory procedures
  • Always know your metadata that comes with each data set you are working with

BioData Taxonomy

The system reports taxonomy in a standardized and harmonized taxonomic system using what we call the BioData Taxon Name and the Published Taxon Name - synonymy is resolved for you.

The system maintains and reports the taxonomic identities as reported by the field biologist (fish) or bench taxonomist (invertebrates, algae) - this is the Bench Taxon Name.

Taxonomic identity column definitions

Column

Definitions

BioDataTaxonName

Taxon according to BioData current taxonomic system

 

 

BenchTaxonName

The taxon name assigned by a taxonomist in the lab (at the "bench") or in the field. May be a conditional, provisional, or operational name. Serves as root name for crosswalks to other taxonomic systems

BenchTaxonNameReferenceCode

Code representing the Reference used to produce the name. BenchTaxonName + BenchTaxonNameReferenceCode = unique taxon concept

 

 

PublishedTaxonNameLevel

The taxonomic rank of the PublishedTaxonName (e.g. Phylum, Class, Order, Genus, etc.)

PublishedTaxonName

The nearest TaxonName that has been published following International Code of Zoological Nomenclature for inverts and fish or International Code of Botanical Nomenclature for algae; authority is not included. Provisional names cannot be used in this field.

PublishedTaxonNameAuthority

Taxonomic authority for PublishedTaxonName

ScientificName

Complete name of the Taxon, with Authority.


Example of how the Bench Taxon Reference Code can distinguish identities among identical Bench Taxon Names

Bench Taxon Name

Bench Taxon Name Reference

BioData Taxon Name

Hydropsyche

not specified

Ceratopsyche/Hydropsyche

Hydropsyche

Wiggins, 1996

Ceratopsyche/Hydropsyche

Hydropsyche

Morse and Holzenthal, 2008

Hydropsyche

Ceratopsyche

Morse and Holzenthal, 2008

Ceratopsyche


Examples of differences between BioDataTaxonName and PublishedTaxonName . Typically this is because of standardized conditional or provisional taxonomic designations such as hybrid, groups, complexes, etc.are not covered by either the Zoological or Botanical codes

BioData Taxon Name

Bench Taxon Name

PublishedTaxonName

Lepomis machrochirus x Lepomis cyanellus

Lepomis machrochirus x Lepomis cyanellus

Lepomis

Hydropsyche depravata group

Hydropsyche depravata group

Hydropsyche


Examples of when BioDataTaxonName and BenchTaxonName differ because of changes in taxonomy or our understanding of what a taxon represents over time

Bench Taxon Name

BioData Taxon Name

PublishedTaxonName

Nixe criddlei

Ecdyonurus criddlei

Ecdyonurus criddlei

Caudatella californica

Caudatella heterocaudata californica

Caudatella heterocaudata californica

Seratella molita

Ephemerellidae

Ephemerellidae

 

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