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BOLD

A DNA barcode reference library
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Actions4

  • Combined (Specimen + Sequence) Actions
  • Sequence Actions
  • Speciman Actions
  • Stat Actions

Overview

This node integrates with the BOLD (Barcode of Life Data) system, a DNA barcode reference library. It allows users to retrieve combined data about specimens and sequences from the BOLD public API. This is useful for researchers, biologists, or bioinformaticians who want to query barcode index numbers, taxonomic information, geographic data, and other metadata related to DNA barcoding projects.

Typical use cases include:

  • Fetching specimen and sequence data filtered by specific Barcode Index Numbers (BINs).
  • Retrieving records associated with particular datasets, institutions, or researchers.
  • Querying data based on geographic regions or taxonomic groups.

For example, a user might request all combined specimen and sequence records for taxa "Aves" and "Reptilia" collected in "Canada" or "Alaska".

Properties

Name Meaning
Additional Fields A collection of optional filters to refine the GET request. Includes:
- BINs Pipe-separated list of Barcode Index Numbers (e.g., `BOLD:AAA5125
- Container Pipe-separated list of dataset or project identifiers (e.g., `SSBAA
- Geography Pipe-separated list of geographical names such as countries or provinces/states (e.g., `Canada
- IDs Pipe-separated list of process or sample identifiers (e.g., `ACRJP618-11
- Institutions Pipe-separated list of institution names (e.g., `Biodiversity Institute of Ontario
- Researchers Pipe-separated list of researcher names (e.g., `Thibaud Decaens
- Taxon Taxon name or pipe-separated list of taxa (e.g., `Aves

Output

The node outputs an array of JSON objects representing the retrieved records from the BOLD API.

  • For the "combined" resource with the "get" operation, the output JSON contains the field bold_records.records, which is extracted and returned as the main data array.
  • Each record includes detailed information about specimens and sequences matching the specified filters.
  • The node does not output binary data.

Dependencies

  • The node makes HTTP GET requests to the BOLD public API endpoints:
    • Combined data: http://www.boldsystems.org/index.php/API_Public/combined
  • No authentication or API keys are required.
  • Requires internet access from the n8n environment to reach the BOLD API.

Troubleshooting

  • Empty results: If no records are returned, verify that the filter values (e.g., BINs, Taxon, Geography) are correctly formatted and exist in the BOLD database.
  • Network errors: Ensure the n8n instance has internet connectivity and can reach boldsystems.org.
  • Invalid parameters: The API expects pipe-separated strings for multiple values; incorrect formatting may lead to no results or errors.
  • API changes: Since this relies on a public API, any changes or downtime on the BOLD side may affect functionality.

Links and References

Discussion