[dwc-mixs] Draft DwC extension updated

Pier Luigi Buttigieg pier.buttigieg at awi.de
Mon Apr 19 09:58:35 UTC 2021

Dear Thomas,

Thanks for the application case - we still need to work on the report, 
which will outline what this extension is, what it's not, and how it 
relates to other related extensions which may pop up. We should make 
sure these questions are addressed therein.

The mandate of this group is to create a MIxS extension with the GSC and 
TDWG synced - that's what will make this sustainable for partners across 
the board. I would strongly hesitate to call our primary output 
something as general as the DNA Derived Data extension (or similar) as 
that's a mandate we don't have.

We can certainly extend it into a more general direction, but after 
we've anchored the GSC and TDWG standards. In this frame, the "right" 
way to get the fields you listed in (which make sense) is to propose the 
GBIF terms to the GSC to extend MIxS.

For the GGBN terms, I'm not sure what kind of processes / stability / 
technology they have to make this work sustainably. I note they're 
emulating our work in the GBWG tracker. Perhaps the follow up action of 
this group would be to merge with them to sync further.

Ultimately, if all these groups and ad hoc standards bodies get their 
metadata into linked data, extensions can be developed on the fly, but 
their sustainability still depends on some kind of process and 
multilateral community.

@Bill - would you have guidance on using MIxS IRIs? Are they live yet?

Pier Luigi

On 19/04/2021 10:07, Thomas Stjernegaard Jeppesen wrote:
> Dear all
> I have now applied all the changes to the extension I can; please can 
> you seethis 
> <https://tdwg.github.io/gbwg/dwc-mixs/dwc/extension/dna_derived_data.xml>?
> I updated thispilot dataset 
> <https://github.com/tdwg/gbwg/issues/53#issuecomment-806515780>accordingly.
> We discussed the use of the extension for both Event and Occurrence, 
> therefore I set the dwc:subject to <nothing> in order to make the 
> extension available for all cores. It might also be useful for a 
> reference sequence for a Taxon.
> We wonder if it would be prudent to resolve the outstanding issues and 
> then move this into use in GBIF with a clear statement that the 
> extension is pending ratification by TDWG and subject to change. GBIF 
> can then coordinate early adopters so that wewill get real datasets 
> that we canrefer to when seeking ratification. We worry that a 
> standard should not be ratified without significant testing,butthis 
> approach would alleviate thatconcernand would strengthen our task report.
> Webelieve this is the outstanding tasksand decisions to be made are:
>  1. The extension is called “DNA Derived Data”. Is this reasonable?
>  2. Is this the correct format for the URIs,
>     e.g.https://w3id.org/gensc/terms/MIXS:0000074
>     <https://w3id.org/gensc/terms/MIXS:0000074>?
>  3. We have added atomized (forward, reverse) fields for pcr_primers –
>     these are currently GBIF name spaced
>     (e.g.http://rs.gbif.org/terms/pcr_primer_name_forward
>     <http://rs.gbif.org/terms/pcr_primer_name_forward>). Should we
>     rather have MIXS IRIs for those, and what would they be?
>  4. We have also added the following primer related fields that are
>     currently GBIF name spaced. Should they rather have MIXS IRIs, and
>     what would they be?
>      1. pcr_primer_name_forward
>      2. pcr_primer_name_reverse
>      3. pcr_primer_reference
>  5. Based on outputs fromGBIFs draft data publishing guide
>     <https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/>,
>     we have included the following GGBN terms in addition. Is this
>     reasonable?
>      1. concentration
>      2. concentrationUnit
>      3. methodDeterminationConcentrationAndRatios
>      4. ratioOfAbsorbance260_230
>      5. ratioOfAbsorbance260_280
>  5. Based on outputs fromGBIFs draft data publishing guide
>     <https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/>,
>     we haveadditionallyincluded the following MIQE terms. Is this
>     reasonable?
>      1. annealingTemp
>      2. annealingTempUnit
>      3. probeReporter
>      4. probeQuencher
>      5. ampliconSize
>      6. thresholdQuantificationCycle
>      7. baselineValue
>      8. quantificationCycle
>      9. automaticThresholdQuantificationCycle
>     10. automaticBaselineValue
>     11. contaminationAssessment
>     12. partitionVolume
>     13. partitionVolumeUnit
>     14. estimatedNumberOfCopies
>     15. amplificationReactionVolume
>     16. amplificationReactionVolumeUnit
>     17. pcr_analysis_software
> Best
> *Thomas Stjernegaard Jeppesen*
> Web developer
> orcid.org/0000-0003-1691-239X <https://orcid.org/0000-0003-1691-239X>
> *Global Biodiversity Information Facility*
> Universitetsparken 15, 2100 København Ø
> www.gbif.org <https://www.gbif.org/>|www.catalogueoflife.org/ 
> <https://www.catalogueoflife.org/>
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