- dwc-mixs - lists.tdwg.org

DwC-MIxS follow-up and next steps
by Raissa Meyer 27 May '21

27 May '21

Dear all, Many thanks for the productive meeting! You’ll shortly receive an updated calendar invite for the coming weeks to go back to our regular schedule of fortnightly meetings on Tuesdays, 3 pm UTC (after our rescheduled meeting yesterday). As always, please find sections with a summary of our last meeting and next steps below. == SUMMARY == For extended notes please see our running notes document <https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU…> [1]. We’ve taken the opportunity of this meeting to continue writing the TG report <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…> and close any remaining open issues regarding the mapping (SSSOM mapping TSV files have since been added to our GH repo <https://github.com/tdwg/gbwg/tree/main/dwc-mixs/mapping>). == NEXT STEPS == Finish and review TG report. Best regards, Raïssa and Pier [1] Running Notes https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU… <https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU…> [2] TG report https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi… <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…> [3] SSSOM mapping files on GH https://github.com/tdwg/gbwg/tree/main/dwc-mixs/mapping <https://github.com/tdwg/gbwg/tree/main/dwc-mixs/mapping> — https://orcid.org/0000-0002-2996-719X

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DwC-MIxS TG - reschedule, follow-up, and next steps
by Raissa Meyer 23 May '21

23 May '21

Dear all, Many thanks for the productive meeting last week! Unfortunately, we’ll have to reschedule our meeting next week because it overlaps with the upcoming GBWG meeting (which many of us are also a part of). Please fill out the doodle poll <https://doodle.com/poll/cufg6uwi88t4w6uh?utm_source=poll&utm_medium=link> by Friday to let us know when you’d be available. We’ll send an updated zoom link accordingly. To prepare, Pier Luigi and I will take some dedicated time the coming week to work on the TG report <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…> and are looking forward to discussing it and collectively contributing to it all together when we convene next (based on the doodle poll output). In case you won’t be able to make the alternative option, please feel free to asynchronously contribute to the TG report <https://docs.google.com/document/d/1zhb8m2nAahcWDdGtGm_z4Q8qqHbDibWRnPdfGFi…>. Below, please find sections with a summary of our last meeting and next steps. == SUMMARY == For extended notes please see our running notes document <https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kU…>. We’ve reviewed all DwC-MIxS mappings (semantic and syntactic) to wrap up the mapping. While most stayed as they were, changes for the following were discussed and logged in comments on the issues: Depth (Issue 13 <https://github.com/tdwg/gbwg/issues/13>): update syntactic predicate for mapping DwC:minimum/maximumDistanceAboveSurfaceInMeters to MIxS:depth (see here <https://github.com/tdwg/gbwg/issues/13#issuecomment-839548428> & here <https://github.com/tdwg/gbwg/issues/54#issuecomment-838988018>) geo_loc_name (Issue 16 <https://github.com/tdwg/gbwg/issues/16>): update semantic predicate for mapping DwC:country to MIxS:geo_loc_name, add additional mapping for DwC:waterBody (see comment <https://github.com/tdwg/gbwg/issues/16#issuecomment-839571040>) collection_date (Issue 17 <https://github.com/tdwg/gbwg/issues/17>): update semantic predicate for mapping DwC:eventDate (see comment <https://github.com/tdwg/gbwg/issues/17#issuecomment-838671641>) samp_mat_process (Issue 21 <https://github.com/tdwg/gbwg/issues/21>): update semantic predicate for mapping DwC:samplingProtocol (see comment <https://github.com/tdwg/gbwg/issues/21#issuecomment-838687231>) Tim and Thomas have also introduced the updates to our extensions based on previous conversations (see Tim’s email from 2021-05-11 for more). The extensions now include: MIxS-core extension to DwC (primary TG output, including MIxS core terms orthogonal to DwC) DNA extension (application example, building on the MIxS-core extension, but also including sequence-relevant terms from other standards or checklists) We’ve updated the report accordingly and briefly discussed the general state of the report. == NEXT STEPS == Write TG report. Close issues on the mapping after implementing updates based on the discussions of this meeting and the GH issue tracker. Best regards, Raïssa and Pier — https://orcid.org/0000-0002-2996-719X

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DwC-A Extension roadmap
by Tim Robertson 11 May '21

11 May '21

Hi all, We discussed the outstanding DwC-A extension questions with Pier and have a proposed way forward. The motivation here is to keep the scope of the TG well-defined, and to progress exploratory activities that complement the work here. 1. Create a MIxS specific DwC-A Extension - Within the TDWG github - Containing only the fields of MIxS not covered by DwC - We will maintain a SSSOM mapping for the "covered" terms - This extension will be the reference showcasing the use of DwC and MIxS within a DwC-A for the report - Expected that TDWG / GSC will commit to maintain this with future changes in standards 2. GBIF create an additional DNA extension - In the GBIF schema repository (rs.gbif.org) - based on the MIxS Extension, but bringing in the additional terms necessary to satisfy the exchange needs of the GBIF/OBIS network - Documented in the description that it extends the MIxS one with a link - GBIF/OBIS progress with early adopters in data exchange, to be referred to in the report as a “case study” / example of use 3. Consider documenting other formats in the report - Ideas include the Frictionless Data, W3C CSV approach including a conversion to RDF Please say if you have any comments or concerns, otherwise we’ll work through this in the coming weeks. Many thanks, Tim

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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

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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/>

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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

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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

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DwC-MIxS TG meeting follow-up and next steps
by Raissa Meyer 30 Mar '21

30 Mar '21

Dear all, Thank you all for the productive meeting and please excuse the delay in sending this summary around. Our next meeting will be today, on March 30th at 4 pm UTC, following our fortnightly rhythm. As you know the time change in some regions has occurred. The UTC time of our meeting stays the same, which will translate to an additional hour later for Europe (6 pm CEST). If the changed time should not work for you, please contact me privately and we’ll try to reschedule future meetings. 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 discussed some key aspects of this TG: The scope of this TG includes mapping of DwC terms to MIxS core terms developing an extension for sequence information to DwC with MIxS IRIs testing TG outputs in the implementation space (Related Issue: Issue 53 <https://github.com/tdwg/gbwg/issues/53>) capturing notes and recommendations in our report about any additional aspects option to extend this TG or convene a new one to capture MIxS environmental terms The sustainability of our work in part relies on our ability to reliably track and detect new releases of the standards. DwC is using GitHub releases coupled with a backup on Zenodo, which we could leverage for this. A similar process is being discussed for MIxS. (Related issue: GSC Issue 120 <https://github.com/GenomicsStandardsConsortium/mixs/issues/120>) Recommendations to be added to our report: MIxS environmental packages MD had previously passed through the environmental packages and identified one potential mapping. We will capture the scarcity of potential mappings in our report (Related issue: Issue 52 <https://github.com/tdwg/gbwg/issues/52>). We have also identified environmental package terms that could be captured in the DwC measurement of fact extension and will note this in our report. Additionally, we may add recommendations on possible other community vocabularies appropriate for capturing environmental parameter (e.g., NERC vocabularies) Licensing information Need for licensing information in the metadata as a requirement for FAIR data, recommend to use DC term (Related Issue: Issue 32 <https://github.com/tdwg/gbwg/issues/32>). Further outputs: We may include a mapping of the upcoming biome term in DwC with controlled vocabulary (Related Issue: DwC Issue 38 <https://github.com/tdwg/dwc/issues/38>). Based on input from CM, we’ve started to update the SSSOM spreadsheet to more closely follow the standard and add functionality (Related issues: Issue 54 <https://github.com/tdwg/gbwg/issues/54>, SSSOM issue 22 <https://github.com/mapping-commons/sssom-py/issues/22>). == NEXT STEPS == In preparation for our next meeting, please add syntax predicates to the newly added columns <https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSI…> in our SSSOM mapping spreadsheet review the existing mappings to see if any should be updated in response to the major outcomes of this meeting. Please capture any suggestions on our issue tracker <https://github.com/tdwg/gbwg/issues>. 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… <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

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DwC extension in the GBWG repository
by Thomas Stjernegaard Jeppesen 11 Mar '21

11 Mar '21

Dear all We have now added the work-in-progress DwC extension<https://github.com/tdwg/gbwg/tree/main/dwc-mixs/dwc> to the GBWG repository. Issues related to questions and TODOs for the extension should/will be tagged DwC-A Extension<https://github.com/tdwg/gbwg/labels/DwC-A%20Extension>. 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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Emerging mapping efforts
by Raissa Meyer 05 Mar '21

05 Mar '21

Dear all, Part of the GBWG interest group, that we are also under, is interested in building a mapping for ABCD-MIxS <https://github.com/tdwg/gbwg/issues/7#>. This is out of the scope of our working group, but may be interesting to know about. They're currently thinking of setting up another GBWG task group to officially map ABCD to MIxS, following a similar approach as we are - using the SSSOM matrix and SKOS predicates to perform the mapping. As we’re collectively working in the GBWG GitHub repo, just a heads up that issues for an ABCD-MIxS mapping may also be added there in the future. To keep the tracker organised, please continue to add tags that identify what TG the issues are related to. Best regards, Raïssa — https://orcid.org/0000-0002-2996-719X

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