[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
>
> --
> https://orcid.org/0000-0002-4366-3088
>
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