[dwc-mixs] Draft DwC extension updated

Bill Duncan wdduncan at gmail.com
Mon Apr 19 13:35:18 UTC 2021


Hi Pier and Thomas,

No. The MIXS URIs are not live yet. ASIK, they should be live in a few
weeks. There is a GSC meeting on April 26. Hopefully, we will know more
after that.

Here a ticket you can follow regarding MIXS URIs:

https://github.com/tdwg/gbwg/issues/11

Bill


On Mon, Apr 19, 2021 at 6:03 AM Pier Luigi Buttigieg <pier.buttigieg at awi.de>
wrote:

> 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?
>
> Best,
> 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/>
> >
> >
> > _______________________________________________
> > dwc-mixs mailing list
> > dwc-mixs at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/dwc-mixs
>
> --
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>
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