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<p class="MsoNormal"><span style="color:black">Dear all<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">I have now applied all the changes to the extension I can; please can you see<span class="apple-converted-space"> </span><a href="https://tdwg.github.io/gbwg/dwc-mixs/dwc/extension/dna_derived_data.xml"><span style="color:#0563C1">this</span></a>?<o:p></o:p></span></p>
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<span style="color:black">I updated this<span class="apple-converted-space"> </span><a href="https://github.com/tdwg/gbwg/issues/53#issuecomment-806515780"><span style="color:#0563C1">pilot dataset</span></a><span class="apple-converted-space"> </span>accordingly.<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">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.<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">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 we<span class="apple-converted-space"> </span>will get real datasets that we can<span class="apple-converted-space"> </span>refer to when seeking ratification. We worry that a standard should not be ratified without significant testing,<span class="apple-converted-space"> </span>but<span class="apple-converted-space"> </span>this
approach would alleviate that<span class="apple-converted-space"> </span>concern<span class="apple-converted-space"> </span>and would strengthen our task report.<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">We<span class="apple-converted-space"> </span>believe this is the outstanding tasks<span class="apple-converted-space"> </span>and decisions to be made are:<o:p></o:p></span></p>
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<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level1 lfo1">
The extension is called “DNA Derived Data”. Is this reasonable?<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level1 lfo1">
Is this the correct format for the URIs, e.g.<span class="apple-converted-space"> </span><a href="https://w3id.org/gensc/terms/MIXS:0000074"><span style="color:#0563C1">https://w3id.org/gensc/terms/MIXS:0000074</span></a><span class="apple-converted-space"><span lang="DA"> </span></span><span lang="DA">?</span><o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level1 lfo1">
We have added atomized (forward, reverse) fields for pcr_primers – these are currently GBIF name spaced (e.g.<span class="apple-converted-space"> </span><a href="http://rs.gbif.org/terms/pcr_primer_name_forward"><span style="color:#0563C1">http://rs.gbif.org/terms/pcr_primer_name_forward</span></a>).
Should we rather have MIXS IRIs for those, and what would they be?<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level1 lfo1">
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?<o:p></o:p></li><ol style="margin-top:0cm" start="1" type="a">
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level2 lfo1">
pcr_primer_name_forward<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level2 lfo1">
pcr_primer_name_reverse<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level2 lfo1">
pcr_primer_reference<o:p></o:p></li></ol>
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l1 level1 lfo1">
Based on outputs from<span class="apple-converted-space"> </span><a href="https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/"><span style="color:#0563C1">GBIFs draft data publishing guide</span></a>, we have included the following GGBN terms in addition.
Is this reasonable?<o:p></o:p></li></ol>
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<ol style="margin-top:0cm" start="1" type="a">
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level2 lfo2">
concentration<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level2 lfo2">
concentrationUnit<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level2 lfo2">
methodDeterminationConcentrationAndRatios<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level2 lfo2">
ratioOfAbsorbance260_230<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level2 lfo2">
ratioOfAbsorbance260_280<o:p></o:p></li></ol>
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l2 level1 lfo2">
Based on outputs from<span class="apple-converted-space"> </span><a href="https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/"><span style="color:#0563C1">GBIFs draft data publishing guide</span></a>, we have<span class="apple-converted-space"> </span>additionally<span class="apple-converted-space"> </span>included
the following MIQE terms. Is this reasonable?<span class="apple-converted-space"> </span><o:p></o:p></li></ol>
<ol style="margin-top:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px" start="6" type="1">
<ol style="margin-top:0cm" start="1" type="a">
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
annealingTemp<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
annealingTempUnit<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
probeReporter<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
probeQuencher<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
ampliconSize<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
thresholdQuantificationCycle<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
baselineValue<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
quantificationCycle<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
automaticThresholdQuantificationCycle<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
automaticBaselineValue<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
contaminationAssessment<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
partitionVolume<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
partitionVolumeUnit<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
estimatedNumberOfCopies<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
amplificationReactionVolume<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
amplificationReactionVolumeUnit<o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;mso-list:l0 level2 lfo3">
pcr_analysis_software<o:p></o:p></li></ol>
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<span style="color:black"> <o:p></o:p></span></p>
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<span style="color:black">Best<o:p></o:p></span></p>
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<span style="color:black"> <o:p></o:p></span></p>
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<b><span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:gray">Thomas Stjernegaard Jeppesen</span></b><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:gray">Web developer</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:black"><a href="https://orcid.org/0000-0003-1691-239X"><span style="color:#0563C1">orcid.org/0000-0003-1691-239X</span></a></span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:gray"> </span><span style="color:black"><o:p></o:p></span></p>
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<b><span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:gray">Global Biodiversity Information Facility</span></b><span style="color:black"><o:p></o:p></span></p>
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<span lang="DA" style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:gray">Universitetsparken 15, 2100 København Ø</span><span style="color:black"><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:"Verdana",sans-serif;color:black"><a href="https://www.gbif.org/"><span style="color:#0563C1">www.gbif.org</span></a><span class="apple-converted-space"> </span>|<span class="apple-converted-space"> </span><a href="https://www.catalogueoflife.org/"><span style="color:#0563C1">www.catalogueoflife.org/</span></a></span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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