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that when you publish your dataset on the IPT, if you use a term not listed below it will be an unmapped field and will not be published alongside your data.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 This is okay - if they are not mapped to one of the terms, that column in your dataset will not be published.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