April 2021 - dwc-mixs - lists.tdwg.org

DwC-MIxS TG sixth meeting follow-up and next steps
by Raissa Meyer 26 Apr '21

26 Apr '21

Dear all, Thank you all for another productive meeting. Below, please find sections with a summary of our last meeting and next steps. == SUMMARY == For extended notes please see our running notes document [1]. We’ve used the meeting to discuss the developments on the extension and the TG report. TSJ introduced the draft extension which has already been successfully tested (see Issue 53 <https://github.com/tdwg/gbwg/issues/53>). We took some dedicated time to add to and review the TG’s draft report <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…> sections. The editorial process for the TG report has been outlined as follows: Please make sure to be logged in as you suggest changes and comment. If you agree with an addition please add a “+1” in the edit message. If you have a concern please raise it right away in the edit message. Try to resolve concerns bilaterally in the comments (independently of any high order editorial control). Changes will be accepted as they are agreed upon (e.g., shown by the “+1”s). Any rejected changes will be accompanied with a comment on the edit message explaining why. Please feel free to also reopen comments or suggestions if you disagree with the editorial decisions. == NEXT STEPS == Add suggestions and comments to the report <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…>. Review open issues (now including syntax predicate suggestions) on our tracker <https://github.com/tdwg/gbwg/issues> to wrap up the mapping <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…>. We’re looking forward to our next meeting on Tuesday, 27.04.2021, at 3 pm UTC. Best regards, Raïssa and Pier [1] Running Notes Document https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU… <https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU…> [2] DwC-MIxS mapping spreadsheet https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI… <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…> [3] Issue tracker https://github.com/tdwg/gbwg/issues <https://github.com/tdwg/gbwg/issues> — https://orcid.org/0000-0002-2996-719X

1 1

Draft DwC extension updated
by Thomas Stjernegaard Jeppesen 20 Apr '21

20 Apr '21

Dear all I have now applied all the changes to the extension I can; please can you see this<https://tdwg.github.io/gbwg/dwc-mixs/dwc/extension/dna_derived_data.xml>? I updated this pilot 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 we will get real datasets that we can refer to when seeking ratification. We worry that a standard should not be ratified without significant testing, but this approach would alleviate that concern and would strengthen our task report. We believe this is the outstanding tasks and 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 ? 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). 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? * pcr_primer_name_forward * pcr_primer_name_reverse * pcr_primer_reference 5. Based on outputs from GBIFs 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? * concentration * concentrationUnit * methodDeterminationConcentrationAndRatios * ratioOfAbsorbance260_230 * ratioOfAbsorbance260_280 1. Based on outputs from GBIFs draft data publishing guide<https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/>, we have additionally included the following MIQE terms. Is this reasonable? * annealingTemp * annealingTempUnit * probeReporter * probeQuencher * ampliconSize * thresholdQuantificationCycle * baselineValue * quantificationCycle * automaticThresholdQuantificationCycle * automaticBaselineValue * contaminationAssessment * partitionVolume * partitionVolumeUnit * estimatedNumberOfCopies * amplificationReactionVolume * amplificationReactionVolumeUnit * 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/>

4 4

DwC-MIxS TG meeting time
by Raissa Meyer 13 Apr '21

13 Apr '21

Dear all, Many thanks for adding to the poll for rescheduling our DwC-MIXS TG meeting time after the daylight savings time change. Based on the output from the poll and our last meeting, we’ll have our upcoming meetings at 3 pm UTC (5 pm CEST, 8 am PDT). Looking forward to our meeting tomorrow! Best, Raïssa P.S. We’ll use the same link as always. — https://orcid.org/0000-0002-2996-719X

2 1

DwC-MIxS TG fifth meeting follow-up and next steps
by Raissa Meyer 07 Apr '21

07 Apr '21

Dear all, Thank you all for another productive meeting. Due to the daylight saving time change, we’ve been asked to move the UTC time of our meeting forward by one hour to 3 pm UTC (5 pm CEST, 8 am PDT). Please add to the doodle poll <https://doodle.com/poll/w34ag83zvu4mrk3d?utm_source=poll&utm_medium=link> until Thursday to indicate whether this would work for you. Below, please find sections with next steps and a summary of our last meeting. == NEXT STEPS == In our next meetings we’re planning to go through and resolve open issues on our tracker <https://github.com/tdwg/gbwg/issues> to wrap up the mapping and to start building the extension. In preparation, please add syntax predicates to the newly added columns <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…> in our SSSOM mapping spreadsheet and review existing mappings. == SUMMARY == For extended notes please see our running notes document [1]. We’ve continued to review our mapping and started to shape the extension. The main outputs were: To capture both semantics and syntax in the mapping, we'll use SKOS predicates in a separate syntax_predicate column <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…>. When the SSSOM team introduces official syntax mapping predicates (the SKOS predicates are intended for mapping concepts rather than syntax) we’ll update accordingly (Related issues: Issue 28 <https://github.com/tdwg/gbwg/issues/28> and 54 <https://github.com/tdwg/gbwg/issues/54>, SSSOM issue 56 <https://github.com/mapping-commons/SSSOM/issues/56#issuecomment-801575819> and 52 <https://github.com/mapping-commons/SSSOM/issues/52>). MIxS:url is currently mapped to DC:references. We’ll keep that mapping because the DC term is the most widely interoperable, but will additionally map to the relevant DwC terms (Related issue: Issue 23 <https://github.com/tdwg/gbwg/issues/23>). We’ll prioritise developing an extension anchored in Occurrence core, which is also a superset of Event core. We’ll additionally comment on an Event core extension in our report (the implementation of which may be challenging due to star schema restrictions), as the Event core can be decoupled from taxonomy and may thus be more appropriate for reporting on molecular approaches. A single extension for all DNA-related terms across standards would allow for the most implementation cases. We could officially engage the relevant standards organisations (e.g. GGBN) once we’ve identified the gaps that their terms could fill in the extension. Thank you and best wishes, Raïssa and Pier [1] Running Notes Document https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU… <https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU…> [2] DwC-MIxS mapping spreadsheet https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI… <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…> [3] Issue tracker https://github.com/tdwg/gbwg/issues <https://github.com/tdwg/gbwg/issues> — https://orcid.org/0000-0002-2996-719X

1 0