/bold_sequence

Linking BOLD sequences to specimens in GBIF

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