Skip to content

Latest commit

 

History

History
59 lines (48 loc) · 3.21 KB

format_occurrence.md

File metadata and controls

59 lines (48 loc) · 3.21 KB
Raw

How to format Occurrence tables

If your dataset structure is based on Occurrence core, or has an Occurrence extension (remember that all OBIS data have at least one occurrence record associated, regardless of what organization structure you have chosen), there are several terms that are required in your dataset by OBIS. These required data fields include the following eight terms:

  • occurrenceID
  • occurrenceStatus
  • basisOfRecord
  • scientificName
  • scientificNameID (strongly recommended)
  • eventDate (not required for Occurrence extension, required for Occurrence Core)
  • decimalLatitude (not required for Occurrence extension)
  • decimalLongitude (not required for Occurrence extension)

While these are the bare minimum, you should strongly consider adding other terms if you have the corresponding information/data in your dataset or documentation. Other terms you should consider adding are identified by their associated Darwin Core class below. See the term checklist for a more complete list of potential terms for Occurrence table.

  • Class Occurrence| DwC: associatedMedia
  • Class Occurrence| DwC: associatedReferences
  • Class Occurrence| DwC: associatedSequences
  • Class Occurrence| DwC: associatedTaxa
  • Class Occurrence| DwC: preparations
  • Class Occurrence| DwC: recordedBy
  • Class Occurrence| DwC: materialSample
  • Class Occurrence| DwC: materialSampleID
  • Class Record | DwC: bibliographicCitation
  • Class Record | DwC: catalogNumber
  • Class Record | DwC: collectionCode
  • Class Record | DwC: collectionID
  • Class Record | DwC: dataGeneralizations
  • Class Record | DwC: datasetName
  • Class Record | DwC: institutionCode
  • Class Record | DwC: modified
  • Class Taxon | DwC: kingdom
  • Class Taxon | DwC: scientificNameAuthorship
  • Class Taxon | DwC: taxonRank
  • Class Taxon | DwC: taxonRemarks

Note that any terms related to measurements, either biotic (e.g., sex, lifestage, biomass) or abiotic will be included in extendedMeasurementOrFact table not the Occurrence table.

Stepwise Guidance to Format an Occurrence Table (with spreadsheets)

Before proceeding with formatting the Occurrence table, be sure you have completed taxon matching to obtain WoRMS LSIDs for the scientificNameID field.

  1. Identify columns in your raw data that match with Occurrence fields
    • Include columns with measurements for now, but they will be moved to an eMoF table(s)
  2. Copy these columns to a new sheet named Occurrence (note it is good practice to never make changes to your original datasheet)
  3. Create and add occurrenceIDs for each unique occurrence record
  4. Add and fill basisOfRecord and occurrenceStatus fields
  5. Ensure your column names map to Darwin Core terms
    • scientificName + scientificNameID

Watch our video tutorial for a demonstration of this procedure:

<iframe width="560" height="315" src="https://www.youtube.com/embed/G_AmAmS7ILc" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

After formatting your Occurrence Core or Extension table, you can format your extendedMeasurementOrFact table.