Data and Information Management for EOVs

The GOOS approach to data management is aligned with open data and FAIR (Findable, Accessible, Interoperable, Reusable)¹ practices. All EOV data and information is valuable, thus effective data management practices are essential to ensure it remains accessible and (re)usable for now and future generations. This document explains how to contribute EOV data to the global ocean observing system across different scenarios: an individual researcher submitting data, or an existing data centre connecting to the system.

Please follow these practices carefully, as EOV data FAIRness relies on compliance² with the guidelines below.

Please note the differentiation between the EOV datasets and the EOV data producers throughout this document (see Glossary). This distinction is made to emphasize that both the data and its source - the data producer - need to be managed and made visible.

Figure 1. High-level example of data and metadata flows to ensure A) EOV data producers and B) EOV datasets become visible in the IOC Digital Ecosystem.

1a. Become Discoverable: Confirm Visibility

Before initiating data flow, you must ensure that key metadata about the EOV data producer (i.e. the project, programme, or organisation) is up to date, verifiable, and FAIR within the BioEco Portal. Follow these steps:

1. Check if record already exists: Search the BioEco Portal
   • A record exists? Verify information is up to date (see Part 2: Submit Data Producer Metadata), then skip to step 3
   • Not found? Continue to step 2.
2. Register in IOC’s Ocean Expert (OE): Create a personal and/or organisational account in OE. OE allows you to link persistent identifiers (e.g. ORCiD or ROR), which ensure data traceability.
   • Note: Account approval takes 1-2 business days. Complete your profile once approved.
     • OE accounts are email based and thus can only be managed by the person it describes, or through an organisational email for organisations.
3. Register your data producer: Submit or update a record using the EOV Metadata Application (see Part 2 for guidance). This automatically makes your entry visible in the BioEco Portal, but a GitHub account is required.

1b. Become Discoverable: Submit Data Producer Metadata

Detailed metadata about the data producer is essential to help others find and understand the EOV monitoring work being done around the world, assess its relevance, credit the right people, and identify collaboration opportunities. The GOOS BioEco Portal uses this information to map who is monitoring which EOVs and where, and is being developed to also display EOV datasets published to OBIS.

Minimum required metadata

How to Submit

Use the EOV Metadata Application — it walks you through the required fields, generates the necessary JSON-LD file, and submissions become visible directly in BioEco Portal. No technical knowledge is required but a GitHub account is required to use the tool. You may contact helpdesk@obig.org for assistance.

If you’re technically savvy and comfortable with JSON-LD files and sitemaps, you can create the metadata files yourself. See the ODIS Book for detailed guidance.

Have an existing entry in the BioEco Portal? The BioEco Portal has recently migrated to a new submission workflow, so existing entries may need to be transferred. Please contact helpdesk@obis.org with the GitHub usernames that should have edit access, and we’ll get you set up.

Dataset metadata (as opposed to data producer metadata) should be submitted directly to the repository where the data is hosted (e.g. OBIS). Dataset metadata may include but is not limited to information about the taxonomic coverage, temporal and geographic area, sampling methods used, people involved, and the project producing the data (including identifiers to link the dataset with the data producer).

2. Prepare and Publish EOV Data

We encourage the “Publish once harvest many times” principle: publish your data to one trusted repository, and it will flow automatically to connected systems. Where you publish depends on your data type, but the repository must be interoperable with the data systems used by GOOS, IODE, and other IOC entities. OBIS is the recommended repository for all BioEco EOV observation-based data.

There are three main scenarios for BioEco observational data:

1. Publish BioEco data directly to OBIS
2. Connect an existing data portal to OBIS
3. Publish non-BioEco data

2a. Publish BioEco Data to OBIS

OBIS (Ocean Biodiversity Information System) can host observation-based datasets such as those derived from field samples, acoustic surveys, satellite imaging, animal tracking, DNA sequencing, etc. (Figure 2).

Figure 2. Diagram indiciating what kind of observational data can be published to OBIS. Arrows indicate which Darwin Core table particular information can be stored in.

Note: Data published to OBIS can also be simultaneously published to GBIF (Global Biodiversity Information Facility), so you do not need to submit separate datasets!

Dataset metadata aligns with Ecological Metadata Language (https://manual.obis.org/eml.html), however you do not need knowledge of the metadata language because the publishing tool used by OBIS, called the Integrated Publishing Toolkit (IPT), uses a form-based interface to create the necessary files for you.

Minimum metadata required for OBIS datasets:

Minimum data required for OBIS datasets:

How Darwin Core structures data

DwC organises data into linked tables. Tables are connected by shared identifiers (eventIDs and occurrenceIDs), so data from different tables can be reliably combined. See Figure 3 for an example. The tables currently implemented by OBIS are:

• Sampling-Event Where, when, and how sampling occurred (e.g. location, depth, methods, etc.)
• Occurrence What was observed (biological records, sequence-based detections, historical observations)
• ExtendedMeasurementOrFacts Any biotic/abiotic measurements, sampling facts, environmental conditions, or relevant information
• DNADerivedData Sequences, primers, and other molecular information

Figure 3. A simplified example of the Darwin Core structure, demonstrating how data in Sampling-Event, Occurrence, and extendedMeasurementOrFact (eMoF) tables can be linked by eventIDs and occurrenceIDs. Note the example does not show all required fields.

Getting help with OBIS

The OBIS Manual, OBIS Nodes, or the OBIS helpdesk (helpdesk@obis.org) can assist with formatting and publishing. We recommend identifying a regional or thematic Node to help you (Figure 4). If your dataset is incomplete or historical, don’t be discouraged - OBIS Nodes can also help assess what’s usable and how to handle gaps! For historical data, the Oceans Past Initiative is a thematic OBIS Node that specifically handles historical marine data.

The EOV Metadata Application is also under development to offer the option of uploading a file aligned to a user-friendly “EOV-format”, and guide you through the process of converting your data into DwC tables.

Figure 4. Map of OBIS Node Network

Data licensing

All data published to OBIS is open-access. However datasets may select one of three Creative Commons licenses: CC0, CC BY, CC BY-NC. For details on the data policy of OBIS, see the OBIS website and the OBIS Manual.

2b. Connect Existing Data Portals with OBIS

If your institution already publishes data through its own portal or repository, it may be possible to connect that system to OBIS. To do this, the data must be structured in Darwin Core format, and the portal needs to be connected to an Integrated Publishing Toolkit (IPT) - the software OBIS uses to harvest data.

If your portal isn’t already connected, this typically involves a workflow that:

1. Extracts the data from your institutional repository,
2. Formats it to align with DwC, and
3. Transfers it to an IPT, which OBIS can then harvest

For help setting this up, contact the OBIS Secretariat at (helpdesk@obis.org), or a regional/thematic OBIS Node. If you publish data from systems like NCEI or ERDDAP, becoming an OBIS Node (or partnering with one) may be the best path forward. The OBIS Secretariat can guide you through the process, or connect you with an appropriate OBIS node (Figure 4).

2c. Publish Non-BioEco Data

Non biological data collected must also be made FAIR. As a reminder, we encourage any non-BioEco data that was taken at the same time as BioEco data to be published together in OBIS. To do this, you can utilise the ExtendedMeasurementOrFact table. Using this approach will avoid datasets being split into several separate datasets, which are then difficult to combine again. Ensure identifiers for the associated projects, people, institutions, etc. are included in all metadata so they can be connected. Specific details on using this table are outlined in the OBIS Manual.

For guidance on data flows for physical or biochemical data not collected alongside BioEco data, please refer to the relevant EOV specification sheet.

Metadata about observing platforms should be made available through the GOOS OceanOPS. See https://www.ocean-ops.org/metadata/ for guidance.

Verify Visibility

To verify that your (meta)data are Findable (the F of FAIR), check that the name of your entry appears in the GOOS BioEco Portal.

To verify that BioEco datasets published to OBIS are accessible (the A of FAIR), search by dataset name through the OBIS Mapper (https://mapper.obis.org/) or the Homepage portal (https://obis.org/search?entity=dataset).

Help Resources

• Ocean Best Practices System – Search for best practices: https://search.oceanbestpractices.org/

OBIS

• OBIS Manual: https://manual.obis.org/
• OBIS YouTube data formatting and publishing videos: https://www.youtube.com/playlist?list=PLlgUwSvpCFS4TS7ZN0fhByj_3EBZ5lXbF
• Darwin Core term reference list: https://dwc.tdwg.org/terms/
• WoRMS taxonomy: https://www.marinespecies.org/
• DwC spreadsheet template generator https://www.nordatanet.no/aen/template-generator/config%3DDarwin%20Core
• BioData Guide with example code for transforming datasets to DwC: https://ioos.github.io/bio_data_guide/

GOOS BioEco Portal

• EOV Metadata Application: https://eovmetadata.obis.org/
• Access the Portal: https://bioeco.goosocean.org/

ODIS

• General help: https://book.odis.org/index.html
• Connecting to ODIS: https://book.odis.org/gettingStarted.html
• ODIS Catalogue of Sources: https://catalogue.odis.org/
• Ocean Info Hub: https://oceaninfohub.org/