obis-network-datasets

What is this repository?

As reported at the 10th meeting of the IODE Steering Group for OBIS (SG-OBIS-10) Document link, see Section 3.1, pgs 39–40, OBIS and GBIF both host large volumes of marine biodiversity data. However, this overlap can lead to duplication and confusion for users.

To address this, the OBIS Secretariat created this repository to track marine datasets that are tagged in GBIF as part of the OBIS network but are not yet available in OBIS. Each dataset is represented as a GitHub issue so that OBIS nodes can review and endorse them.

History

In November 2021, GBIF released IPT version 2.5.2, which introduced the ability for publishers to link datasets to networks such as OBIS. Datasets marked with the OBIS network tag automatically appear on the OBIS network page in GBIF. However, not all of these datasets were flowing into OBIS.

To close this gap, the OBIS Secretariat developed a Python package that uses the GBIF API to detect “missing” datasets and create GitHub issues for nodes to review.

Workflow

• Each dataset appears here as an issue.
• OBIS nodes are expected to:
  • Monitor these issues.
  • Endorse appropriate datasets.
  • Coordinate with publishers to resolve any quality concerns.
• Once endorsed, the OBIS Secretariat harvests the dataset directly from the source IPT and lists it on the endorsing node’s OBIS page.

This process ensures that:

• The same, best-quality “master copy” of each dataset flows to both GBIF and OBIS.
• Duplicate records are avoided.
• OBIS is recognized within GBIF as the global marine biodiversity network.

All OBIS node managers and data managers are encouraged to watch this repository and stay engaged in reviewing and endorsing new datasets.

Assignments

GitHub accounts per OBIS node used to assign datasets:

• AntOBIS: @ymgan
• IndOBIS: @johnny3125
• Caribbean OBIS: @diodon, @cperaltab
• OBIS Japan: @hosonot
• EurOBIS: @cyrilrader
• OBIS Australia: @obisau
• OBIS Deepsea: @haniehsaeedi
• AfrOBIS: @TRasehlomi
• OBIS China: @ZhaocuiMeng
• OBIS Canada: @cornthwaitem
• OBIS Ecuador: @vechocho, @gbif-ec
• OBIS UK: @dblear
• Ocean Tracking Network: @jdpye
• OBIS Canada: @cornthwaitem

To view all open issues not currently assigned to a node, use this filter.

Python Package

This repository also includes the Python package that creates issues for datasets linked to the OBIS network in the GBIF registry.

Run

1. Create a .env file with environment variables GITHUB_USER and GITHUB_ACCESS_TOKEN.

2. Run:

   python -m obisnd