Publishing eDNA Data in OBIS

From sequences to a global open biodiversity record

Emilie Boulanger, Elizabeth Lawrence, Stephen Formel, Saara Suominen

2026-10-27

Agenda

What is OBIS
What are relevant data standards for eDNA
How to format an eDNA dataset for OBIS and GBIF
How publish DNA-derived data to OBIS

If we have enough time

The OBIS eDNA QC tool
Mapping molecular data to Darwin Core

What is OBIS?

Ocean Biodiversity Information System

Global open-access data system for marine life
UNESCO Intergovernmental Oceanographic Commission
> 199 M occurrence records from >7,000 datasets
Data flows to GBIF — easy to publish once, reach both

Free to use. Free to contribute.

🌐 obis.org
📖 manual.obis.org

A Mature Global Community

OBIS is the world’s largest open-access repository
for marine biodiversity data.

36 nodes
across 99 countries
representing 1,000+ institutions
and 6,000+ scientists.

eDNA data in OBIS

OBIS currently holds 128 datasets with eDNA-derived occurrences, including 44,5 million records
About 2 million distinct sequences
That is 2% of all datasets, but 25% of all occurrence records in OBIS

What is special about DNA-derived data?

Enormous potential…

Expands access to biodiversity data at scale
Captures environmental, specimen, and bulk-sample DNA
Raw sequences already widely shared in NCBI

…but NCBI alone is not enough

Raw sequences cannot be searched by species in time and space
No link to spatial coordinates or sampling date
Cannot support distribution maps, trend analyses, or MPA assessments

How do we make sure we understand data from different sources?

eDNA data standards

Two major eDNA data standards exist

1. MIxS

Minimum Information about any (x) Sequence — for raw sequences

Used by
INSDC NCBI ENA DDBJ

2. Darwin Core (DwC)

Community vocabulary for biodiversity data — species, location, date, basis of record

Used by
OBIS GBIF ALA

Developing landscape

Rapidly changing field
For OBIS future directions include the DWC-DP and FAIReDNA terms

What is Darwin Core?

Stable, shared vocabulary for biodiversity data
- Standardized field names, identifiers, & definitions
Maintained by TDWG, used by OBIS, GBIF, and the wider biodiversity community
Not a database itself - a set of agreed-upon terms (e.g. scientificName, eventDate, decimalLatitude)

Think of it as everyone agreeing to call the same column the same thing - so your data and someone else’s can sit in the same table!

🤝

Core & Extension tables

Every Darwin Core Archive has one core table: either Event or Occurrence
Plus zero, one, or more extension tables (eMoF, DNA extension…)
Extensions link back to the core via an ID

What about eDNA data?

Darwin Core + DNA Derived Data Extension

Darwin Core: shared vocabulary for biodiversity data
DNA Extension: adds MIxS terms for sequences, primers, methods
Developed jointly by GBIF, OBIS, and the genomics community

meta.xml ← links all tables
eml.xml ← metadata (who, what, where, when, how)
occurrence.csv ← the occurrence records
dna_derived.csv ← the DNA extension

Five DNA data categories

Which one fits your data?

#	Category	Example
1	DNA-derived occurrences	Metabarcoding (ASVs/OTUs assigned to taxa)
2	Enriched occurrences	Voucher specimen + barcoded
3	Targeted species detection	qPCR / ddPCR assays
4	Name references	Sequence in GenBank only
5	Metadata only	Dataset without sequences

🔎 Use the GBIF decision tree to confirm your category

Key Metadata: eDNA Metabarcoding

From field collection to taxonomy — what to capture at each step

⛵ Field Sampling

Date, Coordinates, Environmental measurements

🧪 Biomarker / PCR

Primer sequence, primer reference, target gene, PCR conditions, length of product, concentration,

🧬 DNA Extraction

Concentration, Extraction method, Extracted amount

💻 Sequences & Taxonomy

Sequencing platform, Library layout, Public repositry ID (NCBI, ENA)
Taxonomy, annotation confidence and reference, Pipeline, Reference library

Category 1 — DNA-derived occurrences · basisOfRecord = MaterialSample

Key Metadata: Quantitative PCR (qPCR)

Targeted species detection — additional fields vs metabarcoding

⛵ Field Sampling

Date, Coordinates, Environmental measurements

🧪 PCR Protocol

PCR conditions

🧬 DNA Extraction

Concentration, Extraction method, Extracted amount

🎯 Target & Quantity

Target gene region, primers
Copy number, LOD, Cq, baseline

Category 3 — Targeted species detection · basisOfRecord = MaterialSample

How do we publish DNA-derived data ?

Your data needs to be in the right format + using the right vocabulary

The DNA publishing guide

Publishing DNA-derived data through biodiversity data platforms

From raw outputs → long format

DNA data is more complex than a lat/lon + species name

Your typical metabarcoding outputs:

File	Content
OTU/ASV table	Sequences × Samples (read counts)
Taxonomy table	Sequence [ID] → taxon assignment
Sample metadata	Location, date, method
FASTA file	Actual DNA sequences

The transformation:

One row = one unique sequence in one sample = one occurrence record

Example transformation

Table structure options

Option A — Occurrence Core

occurrence.csv 
  └── dna_derived.csv  (linked via occurrenceID)
  └── emof.csv         (linked via occurrenceID)

Option B — Event Core (recommended for eDNA)

event.csv
  └── occurrence.csv        (linked via eventID)
       └── dna_derived.csv  (linked via occurrenceID)
  └── emof.csv              (linked via eventID or occurrenceID)

Why Event Core? Sample-level metadata (location, date, method) is recorded once per sampling event rather than repeated in every row.

Key DwC fields to include: Event

Event core (mandatory fields)

eventID — unique, stable ID
eventDate — YYYY-MM-DD
decimalLatitude, decimalLongitude

Event table (strongly recommended fields)

minimumDepthInMeters, maximumDepthInMeters
sampleSizeValue (volume of sample)
sampleSizeUnit (units of volume sampled)
samplingProtocol - (link to your field sampling SOP)

→ the 📍where, 🕒when & 🧪how of collection

Key DwC fields to include: Occurrence

Occurrence (core) table (mandatory fields)

occurrenceID — unique, stable ID
scientificName — taxon name to lowest possible taxon rank
basisOfRecord = “MaterialSample”
occurrenceStatus = “present”

If Occurrence core, also: eventDate, decimalLatitude, decimalLongitude

Occurrence table (strongly recommended fields)

scientificNameID (WoRMS AphiaID)
organismQuantity (read count of sequence)
organismQuantityType = “DNA sequence reads”
sampleSizeValue (total read count in sample)
sampleSizeUnit = “DNA sequence reads”
samplingProtocol - (link to your SOP)
associatedSequences (link to e.g. GenBank or ENA accession)

→ what organism was detected 🐠🪸🪼

Key fields to include: DNA Extension

DNA Extension (example key fields)

DNA_sequence — ASV/OTU sequence
target_gene — e.g. “COI”, “18S rRNA”
pcr_primer_name_forward — and reverse
seq_meth — e.g. “Illumina MiSeq”
otu_class_appr — e.g. “DADA2 v1.18”
otu_db — reference database
sop — link to your protocol

→ 🧬the molecular context

All tables linked by eventID and occurrenceID

manual.obis.org/dna_data.html#quick-start-guide

eMoF extension table

Table to record all types of measurements (abiotic, biotic, environmental, sampling…)
Measurements recorded in long format
- measurementType, measurementValue, measurementUnit
Linking sampling info to eventIDs decreases duplication
Use controlled vocabulary whenever possible!

eventID	occurrenceID	measurementType	measurementValue	measurementUnit
YEARsite1samp1		temperature	25	C

measurementTypeID	measurementUnitID
http://vocab.nerc.ac.uk/collection/P01/current/TEMPPR01/	http://vocab.nerc.ac.uk/collection/P06/current/UPAA/

Resources for DNA terms

Resource	Link
DNA Extension term definitions	rs.gbif.org/extension/gbif/1.0/dna_derived_data_2024-07-11.xml
DwC Term Quick Reference Guide	dwc.tdwg.org/terms/
OBIS Manual (DNA chapter)	manual.obis.org/dna_data.html
GBIF DNA publishing guide	doi.org/10.35035/DOC-VF1A-NR22

Publishing to OBIS

Quality control

Before publishing — check for:

✅ Taxonomy matched to WoRMS (AphiaID required for marine taxa)
✅ Coordinates in decimal degrees, in the ocean
✅ Dates in ISO 8601 format (YYYY-MM-DD)
✅ Unique, stable occurrenceID and eventID
✅ Table linkages consistent (eventID, occurrenceID)

Tools:

Tool	What it checks
`obistools` (R package)	Taxonomy, geography, required fields
GBIF data validator	Darwin Core Archive structure
WoRMS Taxon Match Tool	Scientific names → AphiaIDs

Publishing workflow

Integrated Publishing Toolkits (IPT) are hosted by OBIS nodes — you do not need to run your own server. OBIS has nodes covering most world regions. Find yours at obis.org/nodes.

Special cases

Unknown sequences

Many sequences in any given study will remain uncharacterized
Populate the scientificName field with Biota incertae sedis
Or the lowest taxonomic information if available
- e.g. only assigned to Class level, scientificName = Teleostei, scientificNameID = urn:lsid:marinespecies.org:taxname:293496

For Biota incertea sedis, scientificNameID should be populated with urn:lsid:marinespecies.org:taxname:12.
Recommend that you populate verbatimIdentification with the name that was originally documented (e.g. phototrophic eukaryote).

Sequences without a WoRMS ID (AphiaID)

WoRMS is an extensive database of linnean names of marine species, confirmed by experts in each taxonomic group
Within eDNA datasets there are usually many taxonomic assignments (protists, prokaryotes) that cannot be found in the WoRMS database currently (i.e. no AphiaID available)
The name might be available and mapped to GBIF, making sharing datasets between GBIF and OBIS complicated
The submitter of the data may in these cases record the known species name, in scientificName, the ID of the taxon in another database in taxonConceptID and leave scientificNameID empty

Control samples

Control samples are important for quality control of resulting data
Currently, there is no feature for this implemented in the IPT
In the future, OBIS and GBIF are working on a solution to submit them as separate files within the same dataset
They will then not be mapped, to avoid that they end up in the GBIF or OBIS occurrence indexes, but will be available for anyone looking for that information

Metadata with no DwC terms

A lot of information, especially detailed parameters e.g. of bioinformatic workflow, do not have controlled vocabulary fields yet
The FAIRe project, “making eDNA data FAIR”, is in the process of developing new metadata fields to record all the relevant information of eDNA projects
The checklist is already available online: https://fair-edna.github.io/download.html
A lot of existing fields, a lot of new fields
Currently, the new fields are dropped from the IPT. But in the process of adding them to DwC and MIxS. In the meantime, they can be added in eMoF (extendedMeasurementOrFact)

A note on sensitive data

Common cases:

Endangered or commonly poached species locations
Species/locations with economic sensitivity

Options → you don’t have to choose between “share everything” or “share nothing”:

Generalize location - provide a region or polygon (footprintWKT) instead of an exact point
Delay publication - prepare to publish but set an embargo for later
Generalize taxonomic name - provide a higher taxon name

Note: Generalizations should be documented alongside your data! See OBIS Manual & GBIF Guide for more details

Resources

Tools to Help You

GBIF Metabarcoding Data Toolkit

Automates DwC mapping from bioinformatic outputs

mdt.gbif.org

robis (R package)

Query OBIS; retrieve DNA records with unnest_extension()

github.com/iobis/robis

obistools (R package)

Validation, QC, WoRMS matching, archive structure checks

github.com/iobis/obistools

OBIS R tutorial

Transform raw DNA data into a Darwin Core-compliant dataset

iobis.github.io/edna-training-beginner-track

Structure an eDNA Dataset in R

OBIS R tutorial: Transform raw DNA data into a Darwin Core-compliant dataset

time: ~90 min

🎯 By the end of this tutorial, you will be able to:

Read a raw ASV table, taxonomy file, and sample metadata sheet into R.
Combine these tables into a Darwin Core Occurrence table, mapping raw fields to Darwin Core terms.
Use the obistools package to match taxon names against WoRMS, and check coordinates, dates, and required fields.
Build the ExtendedMeasurementOrFact and DNADerivedData extension tables.
Write out a complete Darwin Core Archive.

What can FAIR data do?

Geographic outlier detection - OBIS eDNA taxonomy QC tool

dataset quality profile: alignment of species detections to known distribution and thermal ranges

What can FAIR data do?

Geographic outlier detection - OBIS eDNA taxonomy QC tool

Mapping molecular data to Darwin Core

Which information is entered where? A short exercise