OBIS & Darwin Core: What They Are and Why They Matter

Meet OBIS, the global network behind it, and see why publishing your eDNA data through it matters.

Learning objectives

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

Explain what OBIS is and how it relates to GBIF and UNESCO’s Intergovernmental Oceanographic Commission (IOC).
Describe why publishing eDNA data through a standardized system like OBIS matters, beyond simply depositing sequences in NCBI.
Give examples of how eDNA data already published in OBIS is being reused.
Query OBIS for existing DNA-derived occurrence records using the robis package.

Prerequisites for this episode

Completed Episode 1: Introduction to eDNA & Biodiversity Data

What is OBIS?

OBIS — the Ocean Biodiversity Information System — is a global, open-access data system for marine life.

Endorsed by UNESCO’s Intergovernmental Oceanographic Commission (IOC).
Holds more than 199 million occurrence records from over 7,000 datasets.
Data published in OBIS also flows to GBIF — publish once, reach both networks.
Free to use, free to contribute to.

🌐 obis.org · 📖 manual.obis.org

OBIS is not just a repository. It actively feeds into global biodiversity assessments, climate analyses, and conservation planning — for example the IPBES Global Assessment, UN World Ocean Assessments, and the CBD’s Kunming-Montreal Global Biodiversity Framework.

A mature, global community

OBIS is the world’s largest open-access repository for marine biodiversity data, built by a genuinely global network:

36 nodes across 99 countries
Representing 1,000+ institutions
And 6,000+ scientists

OBIS sits within UNESCO’s IOC (IODE, established 1961), and works alongside partners including GBIF, TDWG, EMODnet, GOOS, and DataONE. Find your regional OBIS node at obis.org/nodes — most contributors publish through their node’s Integrated Publishing Toolkit (IPT) rather than running their own infrastructure.

Why publish eDNA data through OBIS?

eDNA captures biodiversity signals that other survey methods often miss:

Cryptic and rare marine taxa
Non-invasive, scalable sampling
Community-level biodiversity signals

But raw sequences alone aren’t enough. Sequences deposited only in NCBI/GenBank cannot be searched by species, in time, or in space — there’s no link to coordinates or sampling dates, so they can’t support distribution maps, trend analyses, or Marine Protected Area assessments.

Publishing through OBIS (and GBIF) turns a sequence into reusable biodiversity data:

Benefit	Why it matters
Open DOI	Citable in publications
Long-term archive	FAIR data
Global reach	OBIS + GBIF
Sequence search	Reuse & reanalysis

Your sequences become findable — OBIS’s sequence search tools let others search for similar sequences across all published datasets, but only because the data is submitted in a standardized form. That standardization is the subject of the next episode.

eDNA is already in OBIS — and being used

OBIS currently holds around 128 datasets containing eDNA-derived occurrences, totaling roughly 44.5 million records and about 2 million distinct sequences. That’s only ~2% of all datasets in OBIS, but they contribute 25% of all occurrence records — eDNA datasets tend to be large.

Real eDNA datasets already published include eDNA surveys from Monterey Bay, 16S rRNA metabarcoding of pico- to mesoplankton, and fish eDNA surveys across multiple ocean basins. This data is being used for species distribution modeling, biodiversity assessments, MPA baseline studies, and global meta-analyses.

You can query these records directly from R using the robis package, filtering for the DNA extension:

library(robis)

# occurrence records that include the DNA Derived Data extension
occurrence(
  hasextensions = "DNADerivedData",
  taxonid = 127160  # e.g. Actinopteri
)

🧪 Exercise 2.1: Explore DNA-derived occurrences in OBIS

Using robis::occurrence(), retrieve DNA-derived occurrence records for a marine group you’re interested in (look up its WoRMS AphiaID first, or search by scientificname instead of taxonid). How many records do you get back, and which datasets do they come from?

Solution

library(robis)

recs <- occurrence(
  scientificname = "Actinopteri",
  hasextensions = "DNADerivedData"
)

nrow(recs)
unique(recs$datasetName)

Try changing scientificname to a taxon of your own interest — the AphiaID or scientific name both work with occurrence().

Resources and community

Resource	Link
OBIS Manual (DNA chapter)	manual.obis.org/dna_data.html
GBIF DNA publishing guide	doi.org/10.35035/DOC-VF1A-NR22
OBIS helpdesk	helpdesk@obis.org

The OBIS community is genuinely welcoming to beginners, and the helpdesk responds quickly if you get stuck formatting your own dataset.

Instructor notes

Estimated time: 60 minutes

Pacing notes:

Spend more time on “why publish through OBIS” than on OBIS trivia — the NCBI-is-not-enough argument (no space/time link) is the point learners most need to internalize before the standards episode.
If running Exercise 2.1 live, warn learners that robis::occurrence() requires an internet connection and can be slow for very common taxa; suggest picking a narrower group.

Common errors:

Confusing an AphiaID with a GBIF taxon key — robis wants the AphiaID (or a plain scientific name).
Expecting occurrence() results to already contain sequence data — the DNA sequences themselves live in the DNADerivedData extension, fetched separately with occurrence(..., extensions = "DNADerivedData") if needed.

Discussion prompts:

What biodiversity questions could not be answered if eDNA data stayed only in NCBI/GenBank?
Why might publishing through a regional OBIS node be easier than running your own IPT?

Key points

OBIS is a global, UNESCO IOC-endorsed system for marine biodiversity data that also feeds data to GBIF; you publish once and reach both.
Raw sequences in NCBI alone can’t answer where or when a species was detected — publishing through OBIS links sequences to space, time, and method.
eDNA datasets are a small fraction of OBIS’s holdings by dataset count, but a large fraction of its records, and are already used in real biodiversity assessments.
robis::occurrence(hasextensions = "DNADerivedData") lets you query existing DNA-derived occurrence records directly from R.

--- title: "OBIS & Darwin Core: What They Are and Why They Matter" description: "Meet OBIS, the global network behind it, and see why publishing your eDNA data through it matters." time: "~60 min" --- ```{r} #| label: setup #| include: false #| eval: false library(robis) ``` ::: {.callout-note icon=false} ## {{< fa bullseye >}} Learning objectives By the end of this episode, you will be able to: - Explain what OBIS is and how it relates to GBIF and UNESCO's Intergovernmental Oceanographic Commission (IOC). - Describe why publishing eDNA data through a standardized system like OBIS matters, beyond simply depositing sequences in NCBI. - Give examples of how eDNA data already published in OBIS is being reused. - Query OBIS for existing DNA-derived occurrence records using the `robis` package. ::: ::: {.callout-important icon=false collapse=true} ## Prerequisites for this episode - Completed [Episode 1: Introduction to eDNA & Biodiversity Data](01-introduction.qmd) ::: --- ## What is OBIS? **OBIS — the Ocean Biodiversity Information System** — is a global, open-access data system for marine life. - Endorsed by UNESCO's Intergovernmental Oceanographic Commission (IOC). - Holds more than 199 million occurrence records from over 7,000 datasets. - Data published in OBIS also flows to [GBIF](https://gbif.org) — publish once, reach both networks. - Free to use, free to contribute to. 🌐 [obis.org](https://obis.org) · 📖 [manual.obis.org](https://manual.obis.org) OBIS is not just a repository. It actively feeds into global biodiversity assessments, climate analyses, and conservation planning — for example the IPBES Global Assessment, UN World Ocean Assessments, and the CBD's Kunming-Montreal Global Biodiversity Framework. ### A mature, global community OBIS is the world's largest open-access repository for marine biodiversity data, built by a genuinely global network: - **36 nodes** across **99 countries** - Representing **1,000+ institutions** - And **6,000+ scientists** OBIS sits within UNESCO's IOC (IODE, established 1961), and works alongside partners including GBIF, TDWG, EMODnet, GOOS, and DataONE. Find your regional OBIS node at [obis.org/nodes](https://obis.org/nodes) — most contributors publish through their node's Integrated Publishing Toolkit (IPT) rather than running their own infrastructure. --- ## Why publish eDNA data through OBIS? eDNA captures biodiversity signals that other survey methods often miss: - Cryptic and rare marine taxa - Non-invasive, scalable sampling - Community-level biodiversity signals But raw sequences alone aren't enough. **Sequences deposited only in NCBI/GenBank cannot be searched by species, in time, or in space** — there's no link to coordinates or sampling dates, so they can't support distribution maps, trend analyses, or Marine Protected Area assessments. Publishing through OBIS (and GBIF) turns a sequence into reusable biodiversity data: | Benefit | Why it matters | |---|---| | Open DOI | Citable in publications | | Long-term archive | FAIR data | | Global reach | OBIS + GBIF | | Sequence search | Reuse & reanalysis | **Your sequences become findable** — OBIS's sequence search tools let others search for similar sequences across all published datasets, but only because the data is submitted in a standardized form. That standardization is the subject of the next episode. ### eDNA is already in OBIS — and being used OBIS currently holds around 128 datasets containing eDNA-derived occurrences, totaling roughly 44.5 million records and about 2 million distinct sequences. That's only ~2% of all datasets in OBIS, but they contribute **25% of all occurrence records** — eDNA datasets tend to be large. Real eDNA datasets already published include eDNA surveys from Monterey Bay, 16S rRNA metabarcoding of pico- to mesoplankton, and fish eDNA surveys across multiple ocean basins. This data is being used for species distribution modeling, biodiversity assessments, MPA baseline studies, and global meta-analyses. You can query these records directly from R using the [`robis`](https://iobis.github.io/robis/) package, filtering for the DNA extension: ```{r} #| eval: false library(robis) # occurrence records that include the DNA Derived Data extension occurrence( hasextensions = "DNADerivedData", taxonid = 127160 # e.g. Actinopteri ) ``` ::: {.callout-caution icon=false} ## 🧪 Exercise 2.1: Explore DNA-derived occurrences in OBIS Using `robis::occurrence()`, retrieve DNA-derived occurrence records for a marine group you're interested in (look up its WoRMS AphiaID first, or search by `scientificname` instead of `taxonid`). How many records do you get back, and which datasets do they come from? ::: {.callout-caution icon=false collapse=true} ## Solution ```{r} #| eval: false library(robis) recs <- occurrence( scientificname = "Actinopteri", hasextensions = "DNADerivedData" ) nrow(recs) unique(recs$datasetName) ``` Try changing `scientificname` to a taxon of your own interest — the AphiaID or scientific name both work with `occurrence()`. ::: ::: --- ## Resources and community | Resource | Link | |---|---| | OBIS Manual (DNA chapter) | [manual.obis.org/dna_data.html](https://manual.obis.org/dna_data.html) | | GBIF DNA publishing guide | [doi.org/10.35035/DOC-VF1A-NR22](https://doi.org/10.35035/DOC-VF1A-NR22) | | OBIS helpdesk | helpdesk@obis.org | The OBIS community is genuinely welcoming to beginners, and the helpdesk responds quickly if you get stuck formatting your own dataset. --- ::: {.instructor-only} ::: {.callout-warning icon=false} ## {{< fa chalkboard-teacher >}} Instructor notes **Estimated time:** 60 minutes **Pacing notes:** - Spend more time on "why publish through OBIS" than on OBIS trivia — the NCBI-is-not-enough argument (no space/time link) is the point learners most need to internalize before the standards episode. - If running Exercise 2.1 live, warn learners that `robis::occurrence()` requires an internet connection and can be slow for very common taxa; suggest picking a narrower group. **Common errors:** - Confusing an AphiaID with a GBIF taxon key — `robis` wants the AphiaID (or a plain scientific name). - Expecting `occurrence()` results to already contain sequence data — the DNA sequences themselves live in the DNADerivedData extension, fetched separately with `occurrence(..., extensions = "DNADerivedData")` if needed. **Discussion prompts:** - What biodiversity questions could *not* be answered if eDNA data stayed only in NCBI/GenBank? - Why might publishing through a regional OBIS node be easier than running your own IPT? ::: ::: --- ::: {.callout-tip icon=false} ## {{< fa key >}} Key points - OBIS is a global, UNESCO IOC-endorsed system for marine biodiversity data that also feeds data to GBIF; you publish once and reach both. - Raw sequences in NCBI alone can't answer *where* or *when* a species was detected — publishing through OBIS links sequences to space, time, and method. - eDNA datasets are a small fraction of OBIS's holdings by dataset count, but a large fraction of its records, and are already used in real biodiversity assessments. - `robis::occurrence(hasextensions = "DNADerivedData")` lets you query existing DNA-derived occurrence records directly from R. :::