Skip to content

User Guide

Why We Created This Catalog

The Challenge

As the Ocean Biodiversity Information System (OBIS) network has grown to encompass 38 regional and thematic nodes, with data published by thousands of institutions worldwide, researchers have created an incredible variety of data products from OBIS-mediated marine biodiversity data. Examples include:

  • Scientific publications and reports
  • Interactive maps and dashboards
  • Statistical models and analyses
  • Data visualizations and infographics
  • Derived and aggregated datasets
  • Software tools and applications
  • Educational materials

However, these products were scattered across repositories and platforms, making it difficult for the community to discover and access them. This challenge was flagged by the OBIS Products Coordination Group as important for mitigation.

The Solution

The OBIS Products Catalog provides a centralized metadata registry that serves as a focal point for discovering OBIS-related data products. Rather than requiring researchers to maintain metadata in multiple places, the catalog:

  • Aggregates metadata from existing sources (Zenodo, institutional repositories)
  • Links to authoritative sources (OBIS nodes, Ocean Expert institutions)
  • Exposes machine-readable metadata via JSON-LD for semantic web integration
  • Provides a unified search interface with faceted filtering

This approach minimizes the maintenance burden on product creators while maximizing discoverability.

Community Governance

The catalog is developed and maintained by the OBIS Products Coordination Group (PCG), which coordinates data and information products that synthesize and generate new information from OBIS-hosted data. The PCG meets bimonthly and welcomes participation from the OBIS community.

For more information, see the OBIS Manual or contact helpdesk@obis.org.

Signing In

ORCID Login

The catalog supports signing in with your ORCID iD. Click "Sign in with ORCID" on the login page to authenticate using your existing ORCID account.

Access is controlled by an approved ORCID whitelist. If your ORCID iD is not on the list, you'll see a message directing you to contact helpdesk@obis.org to request access.

On your first approved login, the catalog will:

  • Create a catalog account linked to your ORCID iD
  • Add you to the OBIS Community organization as an editor
  • Use your name and email from your ORCID profile

What You Can Do

Once signed in, you can:

Action Available to
Browse and search all products Everyone (no login required)
Edit any public dataset Any logged-in user
Create new datasets Any logged-in user
Import datasets from DOIs Any logged-in user
Delete datasets Organization admins only
Change a dataset's organization Organization admins only

This means any researcher can improve metadata across the entire catalog — adding thematic tags, linking institutions, correcting descriptions — without needing to be a member of the owning OBIS node.

Organization Membership

When you create a new dataset, it will be assigned to one of your organizations. By default, all new users belong to OBIS Community. If you need to create datasets under a specific OBIS node, contact helpdesk@obis.org to request membership.

When editing an existing dataset, you cannot change its owning organization — it stays with the node that originally created it. Only organization admins can reassign datasets.

Understanding the Data Model

The catalog organizes metadata using three main entities that reflect the OBIS organizational structure:

OBIS Nodes (Organizations)

What they are: The 38 regional and thematic nodes that form the OBIS network.

Examples: - EurOBIS (European node) - Antarctic OBIS - Caribbean OBIS - Ocean Tracking Network (OTN)

How they work in the catalog: - Each node is represented as an Organization. The OBIS Secretariat and OBIS Community (non-nodes) are represented as organizations. - Products are associated with the node(s) that stewarded the underlying data - Node metadata is synchronized from the OBIS API - In the database, Organizations are prefixed with node- (e.g., node-obis-usa) to avoid naming conflicts

Data Source: https://api.obis.org/v3/node

OBIS Institutions (Groups)

What they are: The 668+ research institutions, universities, and organizations that contribute data to OBIS and are registered in Institutes in Ocean Expert.

Examples: - CSIRO National Collections - Flanders Marine Institute (VLIZ) - Ocean Tracking Network - Alfred Wegener Institute

How they work in the catalog: - Each institution is represented as a Group in CKAN - Products can be tagged with relevant institutions - OBIS Institution metadata is enriched with data from Ocean Expert, including: - Contact information (email, phone, address) - Geographic location and region - Institution type and activities - Website and social media links - Acronyms and alternative names

Data Sources: - https://api.obis.org/v3/institute - https://oceanexpert.org/api/v1/institute/

Relationship Between Nodes and Institutions

Nodes (Organizations) are the data stewardship entities—they manage, curate, and publish datasets to OBIS. Products in the catalog are owned by nodes.

Institutions (Groups) are the research entities that produce the data and products. Products can be tagged with multiple institutions to show all contributors.

Example: A publication analyzing Arctic fish distributions might be: - Owned by: node-arctic-obis (the steward of Arctic data) - Tagged with: University of Alaska Fairbanks, Norwegian Polar Institute (the research institutions)

This structure mirrors how OBIS itself organizes data and reflects real-world collaborations.

Product Types

The catalog uses Zenodo's resource type vocabulary, which is based on DataCite's ResourceType standard. Products are classified into nine main types:

Dataset

Description: Derived, aggregated, or processed datasets created from OBIS data.

Examples: - Species distribution models - Aggregated occurrence data for a specific region or taxon - Gridded biodiversity data products - Quality-controlled subsets of OBIS data

Publication

Description: Peer-reviewed articles, research reports, and technical documents.

Examples: - Journal articles citing OBIS data - Technical reports on biodiversity assessments - Book chapters on marine biodiversity - Conference papers

Software

Description: Code, applications, and tools for analyzing or visualizing OBIS data.

Examples: - R packages for OBIS data access - Python libraries for biodiversity analysis - Web applications and dashboards - Analysis scripts and workflows

Presentation

Description: Slides and materials from conference presentations and talks.

Examples: - Conference presentations - Webinar slide decks - Workshop materials

Poster

Description: Scientific posters presented at conferences and meetings.

Examples: - Conference posters - Poster presentations at workshops

Image

Description: Maps, visualizations, infographics, and other visual products.

Examples: - Distribution maps - Biodiversity heatmaps - Infographics on marine species - Data visualization galleries

Video

Description: Animated visualizations, educational videos, and multimedia content.

Examples: - Animated species distribution changes over time - Educational videos about OBIS data - Video tutorials

Lesson

Description: Educational materials, tutorials, and training resources.

Examples: - Training materials for OBIS data use - Educational modules - Online courses featuring OBIS data

Other

Description: Products that don't fit the above categories.

Examples: - Interactive web experiences - Data management plans - Citizen science projects

Thematic Areas

Products can be tagged with thematic areas that describe the scientific domains or applications:

Current Themes

  • Biodiversity Assessment - Species richness, diversity indices, community composition
  • Climate Change - Climate impacts on marine life, range shifts, phenology
  • Conservation Planning - Protected area design, threat assessment, priority setting
  • Ecosystem Health - Indicators, monitoring, environmental quality
  • Fisheries Management - Stock assessment, bycatch, sustainable fishing
  • Invasive Species - Non-native species distribution, impacts, management
  • Ocean Acidification - pH impacts on marine organisms
  • Pollution - Marine debris, chemical contaminants, impacts
  • Species Distribution - Range maps, ecological niche models, habitat suitability
  • Near-Realtime - Products providing near-realtime data streams or monitoring, such as live species tracking, sensor networks, or rapid biodiversity assessments

Adding New Themes

Themes are managed as CKAN vocabulary tags and can be expanded by the community. To suggest new themes, contact helpdesk@obis.org.

Searching and Browsing

Use the search bar at the top of any page to search across: - Product titles - Descriptions - Author names - Keywords - Organizations and institutions

Faceted Filtering

Narrow your results using filters on the left sidebar:

  • Product Type - Filter by dataset, publication, software, etc.
  • Thematic Area - Filter by conservation, climate change, etc.
  • Organization - Filter by OBIS node
  • Institution - Filter by research institution
  • Tags - Filter by keywords
  • License - Filter by usage rights

Browse by Organization

Visit /organization to see all OBIS nodes and the products they steward.

Browse by Institution

Visit /group to see all OBIS institutions and their associated products.

Use the CKAN API for programmatic access:

# Search for datasets
curl "https://products.obis.org/api/3/action/package_search?q=biodiversity"

# Filter by product type
curl "https://products.obis.org/api/3/action/package_search?fq=product_type:publication"

# Get specific dataset
curl "https://products.obis.org/api/3/action/package_show?id=dataset-name"

Contributing Products

Ways to Contribute

  1. Zenodo Import — Import a product from its DOI (recommended)
  2. Direct Entry — Create a record directly in the catalog

Both methods are available to any logged-in user.

We recommend publishing products to Zenodo first, then importing to the catalog:

Benefits: - Zenodo provides a permanent DOI - Metadata is maintained in one place - Automatic updates when you revise on Zenodo - Zenodo provides long-term preservation

Process: 1. Create account on Zenodo 2. Upload your product and fill in metadata 3. Obtain the DOI 4. Log in to the catalog and use the DOI import form, or contact helpdesk@obis.org to add your DOI to the harvest registry

Editing Existing Products

Any logged-in user can edit the metadata of any public product in the catalog. Common curation tasks include:

  • Adding or correcting thematic area tags
  • Linking products to the correct institutions (groups)
  • Improving descriptions and titles
  • Adding spatial coverage information
  • Correcting author information

When editing, the product remains under its original owning organization — your edits will not change which OBIS node owns the product.

Importing from a DOI

  1. Sign in with your ORCID
  2. Click "Add Product" and choose "Import from DOI"
  3. Paste the DOI URL (e.g., https://doi.org/10.5281/zenodo.11464531)
  4. Select the owning organization (OBIS node)
  5. Optionally select contributing institutions
  6. Click Import

The system fetches metadata from Zenodo automatically — title, description, authors, files, and license.

Re-importing a DOI: If the product already exists in the catalog, it will be updated from the source. Curated fields (organization, tags, thematic areas, contributing institutions) are preserved. You'll see a yellow notice confirming this.

Blacklisted DOIs: Some DOIs have been reviewed and excluded from the catalog. If you try to import one, you'll see a warning with the reason. Contact helpdesk@obis.org if you believe this is an error.

Catalog Manifest

The catalog maintains a version-controlled record of all products:

  • catalog_whitelist.csv — Exported nightly from the database. Contains DOI, title, source URL, and catalog URL for every product. This file is committed to git automatically, providing a full audit trail.
  • catalog_blacklist.csv — Manually curated list of DOIs that have been reviewed and excluded. Contact helpdesk@obis.org to request additions or removals.

These files can be archived in Zenodo as a citable record of the catalog's contents.

Metadata Best Practices

When creating product metadata:

  • Use ORCID for author identification
  • Include spatial coverage (bounding box or place names)
  • Specify temporal coverage (time period of data used)
  • Add keywords relevant to marine biodiversity
  • Choose appropriate license (we recommend CC-BY or CC0 for data)
  • Link to source datasets when possible
  • Include funding information to acknowledge support

Required Metadata

At minimum, products should include:

  • Title
  • Description
  • Author(s)
  • Publication date
  • Product type
  • License
  • Identifier (DOI preferred)

Getting Help

This user guide is maintained by the OBIS Products Coordination Group. Last updated: February 2026.