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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Overview of the BioData Taxonomic System

Current Versions of the BioData Taxonomy

Community

CSV

Tab-delimited (TSV)

Excel 97/03

Excel 07

XML

Fish

CSV

TSV

Excel 97/03

Excel 07

XML

Invertebrate

CSV

TSV

Excel 97/03

Excel 07

XML

Algae

Please see the Complete BioData Taxonomy

Complete BioData Taxonomy (includes current, deprecated, and retired taxa)

Previous Versions of the BioData Taxonomy ( Fish | Invertebrate | Algae )

Naming Conventions for Conditional and Provisional Taxa

Citations used in the BioData Taxonomy

This download includes all Bench Taxon Name Reference Codes with their complete citations

Community

CSV

Tab-delimited (TSV)

Excel 97/03

Excel 07

XML

FishCSVTSVExcel 97/03Excel 07XML

Invertebrates

CSV

TSV

Excel 97/03

Excel 07

XML

AlgaeCSVTSVExcel 97/03Excel 07XML

Background

There are three important attributes (columns) that establish a taxon's identity (the "Taxon Concept") and whether the taxon is acceptable to the system for a data upload.

  1. BenchTaxonName
  2. BenchTaxonNameReferenceCode
  3. TaxonConceptState

BioData uses the combination of BenchTaxonName and the "according to" BenchTaxonNameReferenceCode to establish the identity of a taxon. Each combination of name and reference code defines a distinct Taxon Concept. A concept that does not have a reference code is a "nominal" concept. BioData accepts many of these types of concepts, but the long-term value of data can be significantly enhanced by proper usage of a referenced concept.

Taxon Concepts can have one of three states (TaxonConceptState)

  1. Current - meaning the concept is considered up-to-date and will be accepted in data
  2. Deprecated - meaning the concept will be accepted in data but may be rejected in the near future
  3. Retired - meaning the concept has been retired from use and will be rejected if used for incoming data

For more information please see the BioData Taxonomic System page.

Download format definitions

  • CSV = Comma-separated values or comma delimited
  • Tab-delimited (TSV) = Tab-separated values or tab delimited
  • Excel 97/03 = Format used in Microsoft Excel 97- Excel 2003 workbooks, extension is .xls
  • Excel 07 = Format used in Microsoft Excel 2007 - present workbooks, extension is .xlsx

  • XML = Extensible Markup Language
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