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BOLD DNA sequence

Linking BOLD DNA sequences to specimens published in GBIF

Linking DNA sequence barcode data from BOLD to specimens in GBIF has a high priority in the GBIF work-plan. The GBIF Science Committee represented by SC chair Rod Page, published in December 2016 a snapshot of the iBOL dataset doi:10.15468/inygc6 including a total of 2,789,906 occurrences. However, the link to the museum specimens themselves has not been maintained. Example: gbifKey:1415958347 and the corresponding BOLD data record with processid:LON2542-15.

The most reliable specimen identifier in GBIF is the dwc:occurrenceID. There is also the traditional and (more) human readable dwc:catalogNumber identifying a museum specimen. The BOLD Process ID is the most important identifier for material samples corresponding to the museum specimens. BOLD also provide a "Museum ID" and a "Sample ID" however, nether match exactly the occurrenceID or the catalogNumber in GBIF.

GBIF BOLD
occurrenceKey = 1426521030 Process ID = NOBAS010-14
occurrenceID = urn:catalog:O:F:75130 Museum ID = O-F-75130
catalogNumber = 75130 Sample ID = O-F-75130
eventID/fieldNumber = [blank] Field ID = MY1-0568

Mapping from BOLD API to GBIF IPT

Feedback on the proposed mapping using the issues tracker is most welcome! What would be the appropriate measurementType and measurementMethod?

MeasurementOrFact :: http://rs.gbif.org/extension/dwc/measurements_or_facts.xml

  • measurementID = boldAPI:processid
  • measurementType = "BOLD-sequence" [alt. = BOLD-sequence + (markercode)]
  • measurementValue = boldAPI:nucleotides
  • measurementAccuracy = NULL
  • measurementUnit = NULL
  • measurementDeterminedDate = boldAPI:run_dates
  • measurementDeterminedBy = boldAPI:sequencing_centers
  • measurementMethod = boldAPI:markercode [alt. = boldAPI:seq_primers]
  • measurementRemarks = http://www.boldsystems.org/index.php/API_Public/sequence?ids= + processid

Simple Multimedia :: http://rs.gbif.org/extension/gbif/1.0/multimedia.xml

  • type = "StillImage"
  • format = "image/jpeg"
  • identifier = boldAPI:image_urls
  • references
  • title = occurrenceID [alt. = processID]
  • description = boldAPI:captions
  • created = boldAPI:copyright_years
  • creator = boldAPI:photographers
  • contributor
  • publisher = boldAPI:copyright_institutions (??)
  • audience = "experts"
  • source = "BOLD"
  • license = boldAPI:copyright_licenses
  • rightsHolder = boldAPI:copyright_institutions
  • datasetID