User Request: Document the data management leading practices for IFCB

[MathewBiddle]

Who is requesting this?

NERACOOS

What is being requested?

Documentation about how to align IFCB data to DarwinCore and publish to OBIS. Include a space for other details such as archiving at NCEI, required metadata to collect, etc.

How would this request improve your current workflow?

We don't have a workflow. So, this will improve consistency across the community.

How can we get in contact with you to follow up on this request?

ping this issue

[MathewBiddle]

xref:

• [dataset] align IFCB data to DwC and produce notebook to demonstrate process bio_data_guide#277
• https://github.com/CeNCOOS/OBIS_workshop_2024_IFCB

[MathewBiddle]

additional documentation https://dx.doi.org/10.1575/1912/27377

[laurabrenskelle]

From SMBD Working Group meeting on 8 Jan 2025:

• https://repository.oceanbestpractices.org/handle/11329/1917
• Possible focus for 2025 Marine Biological Data Standardization Workshop?

There was a module in the IOC Marine Biological Data Management training last year about this. The generalized workflow is below.

Workflow to format datasets obtained from imagery:

1. Raw images and metadata are retrieved from the instrument.
2. Images are processed manually or with specialised software. The user could use tools such as BIIGLE, EcoTaxa, or FathomNet.
3. Derived data is formatted to the Darwin Core OBIS-ENV-DATA format, according to the best practices. This includes the necessary Darwin core terms in the Occurrence table and details about the instrumentation, calculations and methods in the Extended Measurements or Facts table.
4. The dataset is submitted to the GBIF Integrated Publishing Toolkit (IPT).
5. Formatted dataset undergoes quality control.
6. The dataset can flow to GBIF, OBIS or other initiatives.

Step 2 could be a step where image data is archived at NCEI (FathomNet; possibly a US version of EcoTaxa that gets archived?). Submitting these data to OBIS-USA would also result in archiving at NCEI.

[MathewBiddle]

Thanks for capturing this @laurabrenskelle!

I think one of the questions @aalloilla posed during the meeting was focused around step 2. Are there recommendations as to how the raw images, metadata, and processed data can be shared on ERDDAP or other places? What are the current recommendations?