Expanding Metadata Standards for Environmental and ToL Extensions - eDNAquaPlan T3.2

[camilababo]

We are going to build on your DwC-MIxS alignment and are seeking further guidance beyond what is documented in your paper.

Dear GBWG,

My name is Camila, and I'm a Bioinformatician at BIOPOLIS-CIBIO, based in Portugal. As a research institution focused on biodiversity, we are collaborating with several EU partners on the eDNAqua-Plan project. This three-year initiative is dedicated to developing a comprehensive digital ecosystem for eDNA reference libraries aimed at marine and freshwater environments.

In this project, we serve as task leaders for Task T3.2. Our role involves providing a model that aligns eDNA (meta)data standards for all aquatic biodiversity biomonitoring workflow stages, such as MIxS, ToL, and DwC. We aim to achieve this by building on the existing work already available in this repository, as outlined in our project proposal and encouraged by Pier Luigi (@pbuttigieg), a member of the GBWG and the project's International Advisory Board.

Given that GBWG's work has focused on the MIxS core, we have discussed the possibility of expanding such an effort by mapping MIxS environmental package terms to standards in Earth and environmental sciences (ENVOs, SWEET, EOVs, GOOS, MoF?) and the ToL standards. We recognize and have reviewed the recommendation from the "Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability" paper and intend to consider them in our work going forwards, particularly the suggestions outlined in "Recommendations for using the SSSOM mapping matrix" (inclusion of syntax_predicate_id, syntax_comment to capture syntax meaning along with the semantics, "or even definitions [subject_definition, object_definition], syntax requirements [subject_valueSyntax, object_valueSyntax"); and "Recommendations for the mapping of MIxS environmental package terms".

To make sure we are aligned with best practices, we would like to invite members of the GBWG to share any additional recommendations, insights, or cautionary advice you may have before we begin this task.

I'm looking forward to your insights and sharing what we do back to you and the wider community.

Best regards,
Camila Babo

[pbuttigieg]

@camilababo thank you for the description

In this project, we serve as task leaders for Task T3.2. Our role involves providing a model that aligns eDNA (meta)data standards for all aquatic biodiversity biomonitoring workflow stages, such as MIxS, ToL, and DwC. We aim to achieve this by building on the existing work already available in this repository...

As noted at the GA in Spala, this approach is strongly advised - working with standards bodies like the GSC and TDWG to persist such alignments will help sustain outcomes from your work, and allow quality control

Given that GBWG's work has focused on the MIxS core, we have discussed the possibility of expanding such an effort by mapping MIxS environmental package terms to standards in Earth and environmental sciences (ENVOs, SWEET, EOVs, GOOS, MoF?) and the ToL standards.

Extensions of the current mapping are welcome, but note that the resources listed above cannot and should not be considered standards in the same manner as GSC or TDWG standards. It is therefore important that the maps you create do not convolute very different resources.

We recognize and have reviewed the recommendation from the "Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability" paper and intend to consider them in our work going forwards, particularly the suggestions outlined in "Recommendations for using the SSSOM mapping matrix" (inclusion of syntax_predicate_id, syntax_comment to capture syntax meaning along with the semantics, "or even definitions [subject_definition, object_definition], syntax requirements [subject_valueSyntax, object_valueSyntax"); and "Recommendations for the mapping of MIxS environmental package terms".

The reuse of mapping conventions like SSSOM is welcome. The statement above, however, is somewhat unclear. Currently, the GBWG mapping described in the paper you referenced has very particular conventions which the standards bodies have agreed to operate with. Any extensions must be compatible. We can reconvene the working group to ensure your project outputs contribute effectively.

To make sure we are aligned with best practices, we would like to invite members of the GBWG to share any additional recommendations, insights, or cautionary advice you may have before we begin this task.

There are several things to consider, that go beyond a single GitHub issue.

The most pressing concern for the moment is that we establish how your work can extend the existing DwC-MixS map (the other resources need more thought, and are generally outside of this group's remit).

My suggestion is that you create new SSSOM files for each extension/package that you wish to map and generate PRs that a GBWG team can assess and ratify.

[sformel-usgs]

@camilababo thanks for sharing this info! I'm the US node manager for OBIS and GBIF, and there are a few similar efforts going on, so I'm tagging those folks, in case you haven't already crossed paths. @tobiasgf is the main contact for DNA publishing at GBIF. I think you might already be working with @eboulanger from OBIS and eDNAqua-Plan. @ksilnoaa is leading the development of Omics workflows at NOAA AOML. @miwa582 at CSIRO is leading the development of an eDNA checklist for MixS/DwC that might overlap quite a bit with what you're proposing.