Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact myusgs@usgs.gov. Thank you for your prompt attention to this matter.
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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.

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.

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

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 that this is appropriate.
  • Understand the data sets you are working with. The Project Abstract is a description of the data collected by a project; the sample type characterizes how samples are collected in the field and; the laboratory procedures outlines how samples were processed in the lab.

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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