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@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

6. 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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-- https://orcid.org/0000-0002-4366-3088

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Hi all,

Pier wrote: ...the report, which will outline what this extension is, what it's not, and how it relates to other related extensions...

This seems to be the most urgent aspect here.

I suspect it is clear to all that "extension to Darwin Core" needs to focus on the management of the identifiers, definitions, multilingual aspects, release policies, decision making processes, resolution services, overlap etc around the terms themselves (i.e. sustainable governance aspects).

What remains unclear - to me at least - is our scope with relation to application schemas that make use of those terms.

The DwC-A extension is just an example of an application schema, of which there will likely be many. It is primarily (only?) for GBIF/OBIS/ALA data infrastructures that aim to use MIxS along with other terms to supplement observation data.

One option could be that the task group simply refer to in the report as an example of the correct use of MIxS terms for this kind of purpose but not consider it part of any request for ratification. This would be helpful to others generating e.g. FrictionlessData, ro-crate or following W3C CSV on the web guidelines to annotate tabular data as a reference to copy, and provide the "peer-review" needed that GBIF/OBIS are using MIxS terms correctly.

Thanks, Tim

On 19/04/2021, 15.37, "dwc-mixs on behalf of Pier Luigi Buttigieg" <dwc-mixs-bounces@lists.tdwg.org on behalf of pier.buttigieg@awi.de> wrote:

Thanks Bill - as you can see - this is really key to getting things working across the stakeholders involved (and much further). We can paste that issue into the references of the report to track the evolution of this convergence.

On 19/04/2021 15:35, Bill Duncan wrote: > 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 > https://github.com/tdwg/gbwg/issues/11 > > Bill > > > On Mon, Apr 19, 2021 at 6:03 AM Pier Luigi Buttigieg > <pier.buttigieg@awi.de mailto:pier.buttigieg@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 > 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 > 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 > > <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 > > <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/ > 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/ > 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 > http://orcid.org/0000-0003-1691-239X > <https://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 http://www.gbif.org <https://www.gbif.org/ > https://www.gbif.org/>|www.catalogueoflife.org/ > http://www.catalogueoflife.org/ > > <https://www.catalogueoflife.org/ > https://www.catalogueoflife.org/> > > > > > > _______________________________________________ > > dwc-mixs mailing list > > dwc-mixs@lists.tdwg.org mailto:dwc-mixs@lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/dwc-mixs > http://lists.tdwg.org/mailman/listinfo/dwc-mixs > > -- > https://orcid.org/0000-0002-4366-3088 > https://orcid.org/0000-0002-4366-3088 > > _______________________________________________ > dwc-mixs mailing list > dwc-mixs@lists.tdwg.org mailto:dwc-mixs@lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/dwc-mixs > http://lists.tdwg.org/mailman/listinfo/dwc-mixs > -- https://orcid.org/0000-0002-4366-3088

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