4 Formatting data tables

4.1 Darwin Core Term Checklist for OBIS

There are many Darwin Core terms listed in the TDWG quick reference guide. However, not all these terms are necessary for publishing data to OBIS.

For your convenience, we have created a checklist of all the Darwin Core terms relevant for OBIS data providers. You can reference this list to quickly see which terms are required by OBIS, which data table (Event, Occurrence, eMoF, DNA) they can be found in, and which Darwin Core class each term belongs to. These terms correlate with the IPT vocabulary mapping you will do when it comes time to publish your dataset. You may notice some terms are accepted in multiple data tables (e.g., Event and Occurrence) - this is because it depends on your dataset structure. If you have an Event Core, you will include some terms that would not be included if you had Occurrence Core. For guidance on specific class terms (e.g., location, taxonomy, etc.), see the Darwin Core section of the manual.

Note that when you publish your dataset on the IPT, if you use a term not listed below it will be an unmapped field and will not be published alongside your data. You may still wish to include such fields in your dataset if you are publishing to other repositories, just know that they will not be included in your OBIS dataset. You may include this information either by putting it in the dynamicProperties field in JSON format, or putting the information into the eMoF. Alternatively, you may have fields that you do not wish to be published and that do not correspond to one of these terms (e.g. personal notes). This is okay - if they are not mapped to one of the terms, that column in your dataset will not be published.

Term OBIS Required Term’s DarwinCore Class Event Table Occurrence Table eMoF Table DNA Table
eventDate required event x x
eventID required event x x x
decimalLatitude required location x x
decimalLongitude required location x x
occurrenceID required occurrence x x x
occurrenceStatus required occurrence x
basisOfRecord required record x x
scientificName required taxon x
scientificNameID strongly recommended taxon x
DNA_sequence strongly recommended dna x
env_broad_scale strongly recommended dna x
env_local scale recommended dna x
env_medium strongly recommended dna x
lib_layout recommended dna x
nucl_acid_amp recommended dna x
nucl_acid_ext recommended dna x
otu_class_appr recommended dna x
otu_db recommended dna x
otu_seq_comp_appr recommended dna x
pcr_primer_forward strongly recommended dna x
pcr_primer_name_forward strongly recommended dna x
pcr_primer_name_reverse strongly recommended dna x
pcr_primer_reference strongly recommended dna x
pcr_primer_reverse strongly recommended dna x
samp_name recommended dna x
samp_vol_we_dna_ext recommended dna x
seq_meth recommended dna x
sop recommended dna x
target_gene strongly recommended dna x
target_subfragment strongly recommended dna x
day recommended event x x
endDayOfYear recommended event x x
eventRemarks optional event x x
eventTime recommended event x x
fieldNotes optional event x
fieldNumber optional event x
habitat recommended event x x
month strongly recommended event x x
parentEventID required (if exists) event x
sampleSizeUnit strongly recommended event x x
sampleSizeValue strongly recommended event x x
samplingEffort strongly recommended event x x
samplingProtocol strongly recommended event x x
startDayOfYear recommended event x
verbatimEventDate recommended event x
year strongly recommended event x x
bed optional geologicalContext x x
earliestAgeOrLowestStage optional geologicalContext x x
earliestEonOrLowestEonothem optional geologicalContext x x
earliestEpochOrLowestSeries optional geologicalContext x x
earliestEraOrLowestErathem optional geologicalContext x x
earliestPeriodOrLowestSystem optional geologicalContext x x
formation optional geologicalContext x x
group optional geologicalContext x x
highestBiostratigraphicZone optional geologicalContext x x
latestAgeOrHighestStage optional geologicalContext x x
latestEonOrHighestEonothem optional geologicalContext x x
latestEpochOrHighestSeries optional geologicalContext x x
latestEraOrHighestErathem optional geologicalContext x x
latestPeriodOrHighestSystem optional geologicalContext x x
lithostratigraphicTerms optional geologicalContext x x
lowestBiostratigraphicZone optional geologicalContext x x
member optional geologicalContext x x
dateIdentified optional identification x
identificationID optional identification x
identificationQualifier recommended identification x
identificationReferences optional (required for imaging data) identification x
identificationRemarks recommended identification x
identificationVerificationStatus optional (required for imaging data) identification x
identifiedBy optional (required for imaging data) identification x
identifiedByID optional identification x
typeStatus optional identification x
continent strongly recommended location x x
coordinatePrecision strongly recommended location x x
coordinateUncertaintyInMeters strongly recommended location x x
country recommended location x x
countryCode optional location x x
county optional location x x
footprintSpatialFit optional location x x
footprintSRS optional location x x
footprintWKT recommended location x x
geodeticDatum recommended location x x
georeferencedBy optional location x x
georeferencedDate optional location x x
georeferenceProtocol optional location x x
georeferenceSources optional location x x
higherGeography optional location x x
higherGeographyID optional location x x
island optional location x x
islandGroup optional location x x
locality recommended location x x
locationAccordingTo recommended location x x
locationID strongly recommended location x x
locationRemarks recommended location x x
maximumDepthInMeters strongly recommended location x x
maximumDistanceAboveSurfaceInMeters optional location x x
maximumElevationInMeters optional location x x
minimumDepthInMeters strongly recommended location x x
minimumDistanceAboveSurfaceInMeters optional location x x
minimumElevationInMeters optional location x x
municipality optional location x x
pointRadiusSpatialFit optional location x x
stateProvince optional location x x
verbatimCoordinates optional location x x
verbatimCoordinateSystem optional location x x
verbatimDepth optional location x x
verbatimElevation optional location x x
verbatimLatitude optional location x x
verbatimLocality optional location x x
verbatimLongitude optional location x x
verbatimSRS optional location x x
waterBody recommended location x x
materialSampleID recommended materialSample x
measurementAccuracy recommended measurementOrFact x
measurementDeterminedBy optional measurementOrFact x
measurementDeterminedDate optional measurementOrFact x
measurementID recommended measurementOrFact x
measurementMethod recommended measurementOrFact x
measurementRemarks recommended measurementOrFact x
measurementType strongly recommended measurementOrFact x
measurementTypeID strongly recommended measurementOrFact x
measurementUnit strongly recommended measurementOrFact x
measurementUnitID strongly recommended measurementOrFact x
measurementValue strongly recommended measurementOrFact x
measurementValueID strongly recommended measurementOrFact x
associatedMedia recommended occurrence x
associatedReferences optional occurrence x
associatedSequences recommended occurrence x
associatedTaxa optional occurrence x
behavior recommended occurrence x x
catalogNumber recommended occurrence x
disposition optional occurrence x
establishmentMeans optional occurrence x
georeferenceVerificationStatus recommended occurrence x
individualCount strongly recommended occurrence x x
lifeStage recommended occurrence x x
occurrenceRemarks recommended occurrence x
organismQuantity strongly recommended occurrence x x
organismQuantityType strongly recommended occurrence x x
otherCatalogNumbers optional occurrence x
preparations optional occurrence x
recordedBy recommended occurrence x
recordedByID recommended occurrence x
recordNumber recommended occurrence x
reproductiveCondition recommended occurrence x
sex recommended occurrence x x
associatedOccurrences optional organsim x
associatedOrganisms optional organsim x
organismID recommended organsim x
organismName recommended organsim x
organismRemarks recommended organsim x
organismScope optional organsim x
previousIdentifications recommended organsim x
accessRights recommended record x x
bibliographicCitation recommended record x x
collectionCode optional record x x
collectionID optional record x x
dataGeneralizations optional record x x
datasetID recommended record x x
datasetName recommended record x x
dynamicProperties recommended record x x
informationWithheld optional record x x
institutionCode optional record x x
institutionID optional record x x
language recommended record x x
license recommended record x x
modified recommended record x x
ownerInstitutionCode optional record x x
references recommended record x x
rightsHolder recommended record x x
type strongly recommended record x x x
acceptedNameUsage recommended taxon x
acceptedNameUsageID recommended taxon x
higherClassification recommended taxon x
infraspecificEpithet recommended taxon x
nameAccordingToID recommended taxon x
namePublishedInID optional taxon x
namePublishedInYear optional taxon x
nomenclaturalCode optional taxon x
nomenclaturalStatus optional taxon x
originalNameUsage recommended taxon x
originalNameUsageID recommended taxon x
parentNameUsage recommended taxon x
parentNameUsageID recommended taxon x
phylum recommended taxon x
scientificNameAuthorship recommended taxon x
specificEpithet recommended taxon x
subgenus recommended taxon x
taxonConceptID optional taxon x
taxonID optional taxon x
taxonomicStatus optional taxon x
taxonRank strongly recommended taxon x
taxonRemarks recommended taxon x
verbatimTaxonRank recommended taxon x
vernacularName recommended taxon x
type or eventType strongly recommended event x
class recommended taxon x
family recommended taxon x
genus strongly recommended taxon x
kingdom strongly recommended taxon x
order strongly recommended taxon x