REST API for Identification Engine

The BOLD ID Engine Web Service provides the ability to query the COI ID Engine via URL.

An XML file of the top public matches (up to 100) can be retrieved by querying a COI sequence.

General Parameters Description

sequence

Specifies the query sequence (sequences are not case sensitive).

Example:

  • sequence=AACTTTATATTTTATTTTTGGTATTTGAGCCGGAATAGTAGGAAC......
db

Specifies the identification database to query (db names are case sensitive).

Options:

  • db=COX1 Every COI barcode record on BOLD with a minimum sequence length of 500bp (warning: unvalidated library and includes records without species level identification). This includes many species represented by only one or two specimens as well as all species with interim taxonomy. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon.
  • db=COX1_SPECIES Every COI barcode record with a species level identification and a minimum sequence length of 500bp. This includes many species represented by only one or two specimens as well as all species with interim taxonomy.
  • db=COX1_SPECIES_PUBLIC All published COI records from BOLD and GenBank with a minimum sequence length of 500bp. This library is a collection of records from the published projects section of BOLD.
  • db=COX1_L640bp Subset of the Species library with a minimum sequence length of 640bp and containing both public and private records. This library is intended for short sequence identification as it provides maximum overlap with short reads from the barcode region of COI.

XML includes Process ID, Identification, similarity (out of a total of 1), specimen public page, collection county, gps for each match

Example: To retrieve the top matches from the Public Database for a sequence:
	http://boldsystems.org/index.php/Ids_xml?db=COX1_SPECIES_PUBLIC&sequence=NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTTTAGATTTTATTTTTGGAGCTTGGTCTGGCATAGTAGGCACCGCCCTAAGACTTATTATTCGGGCTGAATTAGGACAACCTGGTAGACTTATTGGTGATGATCAAATTTACAACGTGGTCGTAACAGCTCATGCTTTTGTGATAATTTTTTTTATAGTTATGCCCATTATAATTGGTGGATTTGGAAATTGACTTGTTCCCTTAATATTAGGTGCTCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGACTTCTTCCACCTTCTTTAACTCTTCTCCTATCCAGAGGAATAGTTGAAAGAGGTGTTGGCACAGGATGAACTGTTTATCCTCCTTTAGCTGCTGGAATCGCCCATGCAGGCGCTTCTGTGGACTTAGGAATTTTTTCTCTTCATATAGCGGGAGCTTCTTCTATTTTAGGGGCGGTAAATTTTATTACTACTTCTATTAATATGCGTGCCAATGGTATAACTTTAGATCGAATACCTTTATTTGTCTGATCCGTTTTTATTACTGCTATTCTTTTACTACTCTCTCTTCCCGTTTTAGCAGGGGCAATCACAATACTTCTCACTGACCGTAACTTAAATACTTCTTTCTTTGACCCCGCTGGAGGAGGAGATCCATTCTTTATCAACATAAATGCC

Example response: 

								
									
										JSDPX043-08
										COI-5P
										BOLD: Public Records
										BOLD Systems, 2013
										Hymenopenaeus debilis
										0.8314
										
											
												http://www.boldsystems.org/index.php/Public_RecordView?processid=JSDPX043-08
											
											
												Portugal
												
													36.46
													-8.02