5.3 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
eventID (required for Occurrence extension, not required for Occurrence Core)
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 also be included in the extendedMeasurementOrFact table. Measurements can remain in the Occurrence table as long as they can be mapped to the appropriate DwC term (e.g. DwC:Occurrence:sex). Nnot every data aggregator outside of OBIS indexes the eMoF table, so otherwise this information may be lost.

5.3.0.1 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.

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)
Copy these columns to a new sheet named Occurrence (note it is good practice to never make changes to your original datasheet)
Create and add occurrenceIDs for each unique occurrence record
Add and fill basisOfRecord and occurrenceStatus fields
Ensure your column names map to Darwin Core terms
- scientificName + scientificNameID

Watch our video tutorial for a demonstration of this procedure:

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