DNA-derived Occurrence records should be tabular and shared as a text file. The preferred format is a CSV file but any other delimited text file is also acceptable (e.g. TSV). If your records are held in a spreadsheet we can accept XLS or XLSX files. We do not accept records held in any other formats (e.g. FASTA or FASTQ).
We do not accept unformatted records or raw sequencing output. The NBN Atlas follows the Darwin Core standard for sharing and storing biodiversity data, we also support a selection of terms from the DNA Derived Data Darwin Core Extension. All required fields in the NBN Atlas DNA-derived Occurrence Record Upload Template (attached to this article) must be populated. The template only includes our required and desirable terms. Any terms listed below and under the additional Darwin Core terms heading can be included as a field in your data. These terms have been tested on the NBN Atlas and confirmed to process correctly.
Any Darwin Core term can be included as a field within your data, but we cannot guarantee terms that are not listed here will process correctly. The Darwin Core Quick Reference Guide is an easy-to-read reference of the currently (as of 2023-09-18) recommended terms maintained as part of the Darwin Core standard. Terms must be formatted and spelled exactly as provided here.
Please send your occurrence records and completed metadata form to data@nbnatlas.org.
| Darwin Core Term | Definition and Examples |
occurrenceID Required | Definition: The unique and persistent row key or ID of the record that can follow any format. Examples: 2877 record_89 c8d77be |
datasetName Required | Definition: The title given to the data resource (this should match the name provided in the metadata form). |
license Required | Definition: A legally binding licence giving official permission to do something with the record. One of: CC0CC-BY CC-BY-NC OGL Additional Information: See the Data licence help guide. See the definition of Creative Commons licences. See the Open Government Licence. |
rightsHolder Required | Definition: A person or organisation owning or managing rights over the resource, usually the name of the Data Partner. |
taxonID Required | Definition: The Taxon Version Key (TVK) for the taxon supplied in the scientificName field. Examples: NBNSYS0000004130 NHMSYS0000516660 BMSSYS0000001357 Additional Information: TVKs can be obtained from the UKSI Sandbox. |
scientificName Required | Definition: The full scientific name. This should be the name of the lowest level taxonomic rank that can be determined. |
| taxonRank Required | Definition: The taxonomic rank of the taxon provided in the scientificName field. One of: species genus family Additional Information: The NBN Atlas will only accept DNA records for family, genus, species, or sub-species level classifications. |
identificationVerificationStatus Required | Definition: A categorical indicator of the extent to which the taxonomic identification has been verified to be correct. One of:
Additional Information: See the Verification Status Terms help guide for more information. |
eventDate Required | Definition: The date or range during which the occurrence was recorded. Dates or date ranges can be supplied in the following formats: a complete date YYYY-MM-DD (2008-09-04) DD/MM/YYYY (04/09/2008) partial dates a month and year in YYYY-MM (2008-09) format. a year in YYYY (2008) format. date ranges a complete date range in YYYY-MM-DD/ YYYY-MM-DD (2008-01-01/2009-02-25) format (preferred). a day range within the same month in YYYY-MM-DD/DD (2008-09-04/05) format. a month range within the same year in YYYY-MM/MM (2008-09/10) format. a year range in YYYY/YYYY (2008/2009) format. The year, month, and day can also be supplied in numeric format in fields labelled “year”, “month”, and “day”. These values do not need padding with zeros, e.g. “7” not “07”. |
recordedBy Required | Definition: Names of people, groups, or organisations responsible for recording the original Occurrence. Examples: John Rodwell Dennis, R. L. H. | Shreeve, T. G. Volunteer Not Provided |
gridReference Required if decimalLatitude and decimalLongitude are not supplied | Definition: Location of the record using the Ordnance Survey National Grid reference system. British (OSGB) and Irish (OSI) National Grid references are both accepted. Records from Northern Ireland should be supplied with an OSI grid reference or latitude/longitude coordinates. Channel Islands National Grid references are not accepted; CI records should be supplied with latitude/longitude coordinates. Examples: SU122421 SP5405 NT22 |
decimalLatitude Required if gridReference isn’t provided Must be used in conjunction with decimalLongitude | Definition: The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. Examples: 52.952516 |
decimalLatitude Required if gridReference isn’t provided Must be used in conjunction with decimalLongitude | Definition: The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. Examples: -1.144200 |
coordinateUncertaintyInMeters Required if decimalLatitude and decimalLongitude are supplied | Definition: The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Additional Information: See the Grid and coordinate based records on the NBN Atlas for more information. |
locality Desirable | Definition: The specific description of the place or place name where the record was made. |
basisOfRecord Required | Definition: The specific nature of the record. One of:
|
occurrenceStatus Required | Definition: the presence of individuals in the occurrence. The default for DNA data is present. Additional Information: The NBN Atlas will only accept presence records for DNA-derived occurrence records. |
| vitality Required | Definition: Whether the organism was alive or dead at the time of the occurrence. One of:
|
preparations Required | Definition: A list (concatenated and separated) of preparations and preservation methods. Additional Information: Please use DNA extract. |
| samplingProtocol Required | Definition: The name of, reference to, or description of the method or protocol used during the event. Examples: 5ml surface water sampling |
| organismQuantity Required | Definition: A number or enumeration value for the quantity of organisms. The type of value is described by the organismQuantityType term. Examples: 15346 |
| organismQuantityType Required | Definition: The type of quantification system used for the quantity of organisms. The value is quantified by the organismQuantity term. Examples: DNA sequence reads |
| associatedSequences Desirable | Definition: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the record. Examples: https://www.ncbi.nlm.nih.gov/nuccore/U34853.1 |
| DNA_sequence Required | Definition: The DNA sequence. Examples: GTGGGTTTGGAGCACCGCCAAGTCCTTAGAGTTT... Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| target_gene Required | Definition: Targeted gene or marker name for marker-based studies. Examples: CO1 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| pcr_primer_reference Required | Definition: Reference for the primers. Examples: https://doi.org/10.1186/1742-9994-10-34 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| env_medium Required for eDNA data | Definition: The environmental medium which surrounded your sample or specimen prior to sampling. Any of: liquid water [ENVO:00002006] fresh water [ENVO:00002011] brackish water [ENVO:00002019] seawater [ENVO:00002149] estuarine water [ENVO:01000301] contaminated water [ENVO:00002186] air [ENVO:00002005] organic material [ENVO:01000155] wood [ENVO:00002040] fecal material [ENVO:00002003] biofilm material [ENVO:01000156] planktonic material [ENVO:01000063] sediment [ENVO:00002007] clay [ENVO:01000015] silt [ENVO:01000016] sand [ENVO:01000017] gravel [ENVO:01000018] mud [ENVO:00002160] soil [ENVO:00001998] peat [ENVO:00002160] compost [ENVO:00005785] topsoil [ENVO:00005786] or any subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| env_broad_scale Required for eDNA data | Definition: The broad-scale environment the sample or specimen came from. One of: terrestrial biome [ENVO:00000446] freshwater biome [ENVO:00000873] estuarine biome [ENVO:01000020] marine biome [ENVO:00000447] or any subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| otu_db Desirable | Definition: The OTU database (i.e. sequences not generated as part of the current study) used to assigning taxonomy to OTUs or ASVs. Examples: NCBI Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| otu_seq_comp_appr Desirable | Definition: The OTU sequence comparison approach, such as tools and thresholds used to assign “species-level” names to OTUs or ASVs. Examples: blast version 2.12.0+ Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| otu_class_appr Desirable | Definition: The OTU classification approach / algorithm and clustering level (if relevant) when defining OTUs or ASVs. Examples: standard Linux tools Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| env_local_scale | Definition: The local environmental context the sample or specimen came from. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. any subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| target_subfragment | Definition: Name of subfragment of a gene or marker. Examples: V5 Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| pcr_primer_name_forward | Definition: Name of the forward PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. Examples: Riaz_12S_V5F Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| pcr_primer_forward | Definition: Forward PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. Examples: TAGAACAGGCTCCTCTAG Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| pcr_primer_name_reverse | Definition: Name of the reverse PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. Examples: Riaz_12S_V5R Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
| pcr_primer_reverse | Definition: Reverse PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. Examples: TTAGATACCCCACTATGC Additional Information: This term is part of the DNA Derived Data Darwin Core Extension. |
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