From raissa.meyer at awi.de Wed Mar 3 12:47:11 2021 From: raissa.meyer at awi.de (Raissa Meyer) Date: Wed, 3 Mar 2021 13:47:11 +0100 Subject: [dwc-mixs] DwC-MIxS TG third meeting follow-up and next steps Message-ID: <67CE52EF-BDC3-40A8-95EE-D53A23ED1422@awi.de> Dear all, Thank you all, once again, for the productive meeting. Our next meeting will be on March 16th at 4 pm UTC, following our fortnightly rhythm. The link is available in the previous calendar invite and will be used consistently for all recurring meetings. Below, please find sections with a summary of yesterday?s meeting and next steps. == SUMMARY == For extended meeting notes, please see our running minutes document [1]. We discussed any comments and reactions that came up on review of the first-pass mappings. Major outcomes based on this were: For this TG we will focus on the mapping direction of DWC ?> MIxS (Related issues: Issue 12 and Issue 28 ) For mappings that relate two terms which have an associative rather than a hierarchical match, we will use skos:relatedMatch (in such cases skos:broadMatch would be inappropriate as it implies that skos:narrowMatch is the inverse). Our mappings should be exhaustive, so if there are multiple possible mappings (including one-to-many, many-to-many, and many-to-one mappings), we will capture all of them in the SSSOM matrix. (Related issues: Issue 12 , Issue 13 , and Issue 15 ) We decided that the choice of mapping predicates will be based on semantics only (i.e. are the fields about the same things in the world), and will not consider syntax recommendations (this is in contrast to what we had decided last week for the ?elevation? use case). If we do stick with this, we?ll have to make it very clear in our report and when sharing the mapping in the future. We must further ensure that this is compliant with the specification of SKOS semantic relations and SKOS mapping properties (Related issues: Issue 28 and SSSOM#15 ) Bill has kindly generated term lists of all non-MIxS-core-redundant MIxS environmental packages terms (see here for the notebooks and files). This sets us up to approach the mapping of MIxS environmental package terms to DwC terms. We anticipate that few will qualify for this mapping, as most MIxS environmental package terms are quite specific. This does, however, suggest that DwC could reuse MIxS IRIs for these terms if it needs to extend in that direction, and if the term is appropriate to their application cases. == NEXT STEPS == In preparation for our next meeting, please 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 . look through any MIxS environmental packages (see tabs in the SSSOM mapping spreadsheet ) of interest to you or your organisation, and highlight any fields that could be mapped to DwC terms. To avoid duplicating efforts, please capture your activity on our issue tracker . Thank you and best wishes, Ra?ssa and Pier [1] Running notes document https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kUnMZ4/edit#heading=h.nya8uz97plgv [2] DwC-MIxS mapping spreadsheet https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSIXEbqXDpA/edit?usp=sharing [3] Issue tracker https://github.com/tdwg/gbwg/issues ? https://orcid.org/0000-0002-2996-719X -------------- next part -------------- An HTML attachment was scrubbed... URL: From raissa.meyer at awi.de Fri Mar 5 06:48:31 2021 From: raissa.meyer at awi.de (Raissa Meyer) Date: Fri, 5 Mar 2021 07:48:31 +0100 Subject: [dwc-mixs] Emerging mapping efforts Message-ID: <50D965B3-1124-4CEC-8EE9-D795C87935AF@awi.de> Dear all, Part of the GBWG interest group, that we are also under, is interested in building a mapping for ABCD-MIxS . 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, Ra?ssa ? https://orcid.org/0000-0002-2996-719X -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsjeppesen at gbif.org Fri Mar 5 12:33:22 2021 From: tsjeppesen at gbif.org (Thomas Stjernegaard Jeppesen) Date: Fri, 5 Mar 2021 12:33:22 +0000 Subject: [dwc-mixs] DwC extension in the GBWG repository Message-ID: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> Dear all We have now added the work-in-progress DwC extension to the GBWG repository. Issues related to questions and TODOs for the extension should/will be tagged DwC-A Extension. Best, Thomas Stjernegaard Jeppesen Web developer orcid.org/0000-0003-1691-239X Global Biodiversity Information Facility Universitetsparken 15, 2100 K?benhavn ? www.gbif.org | www.catalogueoflife.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pier.buttigieg at awi.de Fri Mar 5 12:54:14 2021 From: pier.buttigieg at awi.de (Pier Luigi Buttigieg) Date: Fri, 5 Mar 2021 13:54:14 +0100 Subject: [dwc-mixs] DwC extension in the GBWG repository In-Reply-To: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> References: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> Message-ID: <51c23a26-a53f-b804-560e-2ff1ae23b6ce@awi.de> Dear Thomas, Many thanks - would you mind adding the intention of this content and some words on the relation to the mapping we're doing in the TG to the README? I'd also add its status to the README - Is this to be ratified by TDWG? Has it already been ratified? etc. Best, Pier Luigi On 05/03/2021 13:33, Thomas Stjernegaard Jeppesen wrote: > > Dear all > > We have now added the work-in-progress DwC extension > to the GBWG > repository. > > Issues related to questions and TODOs for the extension should/will be > tagged DwC-A Extension > . > > Best, > > *Thomas Stjernegaard Jeppesen* > > Web developer > > orcid.org/0000-0003-1691-239X > > *Global Biodiversity Information Facility* > > Universitetsparken 15, 2100 K?benhavn ? > > www.gbif.org | 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 From trobertson at gbif.org Fri Mar 5 15:19:05 2021 From: trobertson at gbif.org (Tim Robertson) Date: Fri, 5 Mar 2021 15:19:05 +0000 Subject: [dwc-mixs] DwC extension in the GBWG repository In-Reply-To: <51c23a26-a53f-b804-560e-2ff1ae23b6ce@awi.de> References: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> <51c23a26-a53f-b804-560e-2ff1ae23b6ce@awi.de> Message-ID: <5531E697-8878-4F39-9FB1-DDC67073A633@gbif.org> Thanks Pier I'll reply here for the benefit of all the group members too, so we can capture ideas before putting them into the READMEs. The intention of this extension is to allow data exchange within the GBIF, OBIS and ALA infrastructures specifically using the Darwin Core Archive standard. Being an extension to DwC this only draws in the terms not covered by Darwin Core, and also only brings in fields that would complement the kinds of information that the Darwin Core provides. Therefore the cross-mapping work of the group is not fully relevant to this extension, although any changes in MIxS would be followed now, or in the future. The background for how this extension came to be is described in section 2 of the forthcoming guide (in draft) for exchanging DNA-derived data in GBIF https://doi.org/10.35035/doc-vf1a-nr22 The question on ratification is really one for the members of the task group to consider. It would be useful to have the task group approve that this was a sensible route for Darwin Core Archive use. Ratification by TDWG isn't strictly necessary for GBIF/ALA/OBIS but would be desirable. GBIF have committed to having DwC-A support during Q2 2021 so there are time pressures to consider and we believe this is nearly ready. What GBIF are really seeking from the group is guidance on: 1. Is it correct use of MIxS in this specific application profile? 2. Are there considerations that OBIS would like to bring forward? 3. Is there scope to split the MIxS fields Thomas identified? 4. What should the name of this extension be? (bearing in mind 5 below) 5. Is it reasonable to supplement the MIxS fields with the additional ones to accommodate more use cases We'll open github issues specifically for some of these, but I thought I'd share here for context. Thanks, Tim ?On 05/03/2021, 13.58, "dwc-mixs on behalf of Pier Luigi Buttigieg" wrote: Dear Thomas, Many thanks - would you mind adding the intention of this content and some words on the relation to the mapping we're doing in the TG to the README? I'd also add its status to the README - Is this to be ratified by TDWG? Has it already been ratified? etc. Best, Pier Luigi On 05/03/2021 13:33, Thomas Stjernegaard Jeppesen wrote: > > Dear all > > We have now added the work-in-progress DwC extension > to the GBWG > repository. > > Issues related to questions and TODOs for the extension should/will be > tagged DwC-A Extension > . > > Best, > > *Thomas Stjernegaard Jeppesen* > > Web developer > > orcid.org/0000-0003-1691-239X > > *Global Biodiversity Information Facility* > > Universitetsparken 15, 2100 K?benhavn ? > > www.gbif.org | 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 _______________________________________________ dwc-mixs mailing list dwc-mixs at lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/dwc-mixs From pier.buttigieg at awi.de Mon Mar 8 22:10:54 2021 From: pier.buttigieg at awi.de (Pier Luigi Buttigieg) Date: Mon, 8 Mar 2021 23:10:54 +0100 Subject: [dwc-mixs] DwC extension in the GBWG repository In-Reply-To: <5531E697-8878-4F39-9FB1-DDC67073A633@gbif.org> References: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> <51c23a26-a53f-b804-560e-2ff1ae23b6ce@awi.de> <5531E697-8878-4F39-9FB1-DDC67073A633@gbif.org> Message-ID: <02da18af-14b7-6f8f-7e79-e3cb6f714751@awi.de> Hi Tim > [...] > The intention of this extension is to allow data exchange within the GBIF, OBIS and ALA infrastructures specifically using the Darwin Core Archive standard. Thanks for the clarification; however, does this occur outside of the standards space (i.e. TDWG/GSC)? This is then ad hoc? And is the DC-A standard is more about how to package (meta)data rather than the specification of the fields right (asking from ignorance here)? I still can't really understand the long-term role/utility of extensions if the fields they specify are not coordinated with the standards groups / used to extend the core standards "officially". > Being an extension to DwC this only draws in the terms not covered by Darwin Core, and also only brings in fields that would complement the kinds of information that the Darwin Core provides Brings them in from where? These are made up ad hoc? > Therefore the cross-mapping work of the group is not fully relevant to this extension, although any changes in MIxS would be followed now, or in the future. The background for how this extension came to be is described in section 2 of the forthcoming guide (in draft) for exchanging DNA-derived data in GBIFhttps://doi.org/10.35035/doc-vf1a-nr22 Is this an internal way of handling this information outside of TDWG and GSC processes? This sets off all kinds of alarm bells, especially if they are marketed widely as a sort of parallel de facto standard. > The question on ratification is really one for the members of the task group to consider. It would be useful to have the task group approve that this was a sensible route for Darwin Core Archive use. If it's outside the standardisation processes of TDWG/GSC (as imperfect as they are), I don't really see how that's sensible in a global sense. In a local sense, working against time constraints, it does make sense; however, only with a declared intent and plan to fold advancements into the global processes/standards. I don't fully understand the nuances, probably, but this just doesn't sound like good strategy. > Ratification by TDWG isn't strictly necessary for GBIF/ALA/OBIS but would be desirable. GBIF have committed to having DwC-A support during Q2 2021 so there are time pressures to consider and we believe this is nearly ready. Indeed, it isn't - anyone can do anything anytime - the question here is if this is creating more silos and not going through a process that the community at large (aside from GBIF users) can also use. It feels like this is creating more work downstream, where we will then have three entities to map (GBIF/TDWG/MIxS) all with different ways of doing things. Does OBIS also want to create its own thing? > What GBIF are really seeking from the group is guidance on: > > 1. Is it correct use of MIxS in this specific application profile? Given that the MIxS standards are mainlined into the INSDC, it makes sense to use this for anything omic. My hesitation of using MIxS because it was basically a spreadsheet is more or less removed thanks to Bill et al.'s work moving them into the linked open data world and giving each term an IRI. That being said, many of the MIxS terms in the environmental packages (many being biogeochemical parameters etc) should be replaced by IRIs of terms from standards bodies in those communities, once we find good parallels. > 2. Are there considerations that OBIS would like to bring forward? This would be very good to know. I think my concerns above would carry over. > 3. Is there scope to split the MIxS fields Thomas identified? MIxS v6 is almost out, but we can lodge issues on the GSC tracker to this effect, cross-linking them to those in our GBWG tracker. > 4. What should the name of this extension be? (bearing in mind 5 below) I'm not sure what you're referring to. > 5. Is it reasonable to supplement the MIxS fields with the additional ones to accommodate more use cases The best way to go about this is to post issues on the MIxS tracker to get them in there (they accept new environmental packages or extensions all the time, recently one from a global consortium of food agencies and one for the COVID response) > > We'll open github issues specifically for some of these, but I thought I'd share here for context. Thanks - I still feel like I don't get the relationship between these actors over the archives, vs the core standards, vs the unilateral move, etc. Is there somewhere where these things are explained? Best, Pier Luigi -- https://orcid.org/0000-0002-4366-3088 From p.provoost at unesco.org Thu Mar 11 13:28:44 2021 From: p.provoost at unesco.org (Provoost, Pieter) Date: Thu, 11 Mar 2021 13:28:44 +0000 Subject: [dwc-mixs] DwC extension in the GBWG repository In-Reply-To: <02da18af-14b7-6f8f-7e79-e3cb6f714751@awi.de> References: <35B00515-6770-4255-8EE1-D31EA6E91852@gbif.org> <51c23a26-a53f-b804-560e-2ff1ae23b6ce@awi.de> <5531E697-8878-4F39-9FB1-DDC67073A633@gbif.org> <02da18af-14b7-6f8f-7e79-e3cb6f714751@awi.de> Message-ID: <98CCA156-AD59-4034-B917-20F7D8C2F24B@unesco.org> Hi Pier Luigi, Maybe I'm missing the point, but I assume we are not questioning the existence of Darwin Core extensions, as creating a Darwin Core extension is exactly what this group set out to do? If the concern is with where some of the earlier discussions have happened, I can't speak for other communities but from the OBIS perspective we are happy with how things have progressed and we have had ample opportunity to contribute. I'm not sure this creates another silo, as far as I'm aware data formatting is outside the scope of the Darwin Core standard (although it offers some guidelines, https://dwc.tdwg.org/text/), and Darwin Core archives merely complement the standardized vocabularies by offering a flexible way to package vocabulary aligned data elements and metadata documents. Our main interest in this group is to be able to bring MIxS described datasets into our data model which is mostly Darwin Core based, so from a practical standpoint it makes sense to only include MIxS terms which have no Darwin Core equivalent into the extension (hence "extension"). Best, Pieter Pieter Provoost OBIS Data Manager Intergovernmental Oceanographic Commission (IOC) of UNESCO IOC Project Office for IODE Wandelaarkaai 7/61 - 8400 Oostende - Belgium +32 478 574420 ?On 08/03/2021, 23:15, "dwc-mixs on behalf of Pier Luigi Buttigieg" wrote: CAUTION: This email is external from UNESCO. Please be vigilant on its sender and content. ATTENTION : Cet e-mail est externe ? l'UNESCO. Soyez vigilant sur son exp?diteur et contenu. Hi Tim > [...] > The intention of this extension is to allow data exchange within the GBIF, OBIS and ALA infrastructures specifically using the Darwin Core Archive standard. Thanks for the clarification; however, does this occur outside of the standards space (i.e. TDWG/GSC)? This is then ad hoc? And is the DC-A standard is more about how to package (meta)data rather than the specification of the fields right (asking from ignorance here)? I still can't really understand the long-term role/utility of extensions if the fields they specify are not coordinated with the standards groups / used to extend the core standards "officially". > Being an extension to DwC this only draws in the terms not covered by Darwin Core, and also only brings in fields that would complement the kinds of information that the Darwin Core provides Brings them in from where? These are made up ad hoc? > Therefore the cross-mapping work of the group is not fully relevant to this extension, although any changes in MIxS would be followed now, or in the future. The background for how this extension came to be is described in section 2 of the forthcoming guide (in draft) for exchanging DNA-derived data in GBIFhttps://doi.org/10.35035/doc-vf1a-nr22 Is this an internal way of handling this information outside of TDWG and GSC processes? This sets off all kinds of alarm bells, especially if they are marketed widely as a sort of parallel de facto standard. > The question on ratification is really one for the members of the task group to consider. It would be useful to have the task group approve that this was a sensible route for Darwin Core Archive use. If it's outside the standardisation processes of TDWG/GSC (as imperfect as they are), I don't really see how that's sensible in a global sense. In a local sense, working against time constraints, it does make sense; however, only with a declared intent and plan to fold advancements into the global processes/standards. I don't fully understand the nuances, probably, but this just doesn't sound like good strategy. > Ratification by TDWG isn't strictly necessary for GBIF/ALA/OBIS but would be desirable. GBIF have committed to having DwC-A support during Q2 2021 so there are time pressures to consider and we believe this is nearly ready. Indeed, it isn't - anyone can do anything anytime - the question here is if this is creating more silos and not going through a process that the community at large (aside from GBIF users) can also use. It feels like this is creating more work downstream, where we will then have three entities to map (GBIF/TDWG/MIxS) all with different ways of doing things. Does OBIS also want to create its own thing? > What GBIF are really seeking from the group is guidance on: > > 1. Is it correct use of MIxS in this specific application profile? Given that the MIxS standards are mainlined into the INSDC, it makes sense to use this for anything omic. My hesitation of using MIxS because it was basically a spreadsheet is more or less removed thanks to Bill et al.'s work moving them into the linked open data world and giving each term an IRI. That being said, many of the MIxS terms in the environmental packages (many being biogeochemical parameters etc) should be replaced by IRIs of terms from standards bodies in those communities, once we find good parallels. > 2. Are there considerations that OBIS would like to bring forward? This would be very good to know. I think my concerns above would carry over. > 3. Is there scope to split the MIxS fields Thomas identified? MIxS v6 is almost out, but we can lodge issues on the GSC tracker to this effect, cross-linking them to those in our GBWG tracker. > 4. What should the name of this extension be? (bearing in mind 5 below) I'm not sure what you're referring to. > 5. Is it reasonable to supplement the MIxS fields with the additional ones to accommodate more use cases The best way to go about this is to post issues on the MIxS tracker to get them in there (they accept new environmental packages or extensions all the time, recently one from a global consortium of food agencies and one for the COVID response) > > We'll open github issues specifically for some of these, but I thought I'd share here for context. Thanks - I still feel like I don't get the relationship between these actors over the archives, vs the core standards, vs the unilateral move, etc. Is there somewhere where these things are explained? Best, Pier Luigi -- https://orcid.org/0000-0002-4366-3088 _______________________________________________ dwc-mixs mailing list dwc-mixs at lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/dwc-mixs From raissa.meyer at awi.de Tue Mar 30 10:08:26 2021 From: raissa.meyer at awi.de (Raissa Meyer) Date: Tue, 30 Mar 2021 12:08:26 +0200 Subject: [dwc-mixs] DwC-MIxS TG meeting follow-up and next steps Message-ID: <48468A78-1E50-403C-B5B1-802EAE31D906@awi.de> 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 ) 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 ) 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 ). 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 ). Further outputs: We may include a mapping of the upcoming biome term in DwC with controlled vocabulary (Related Issue: DwC Issue 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 , SSSOM issue 22 ). == NEXT STEPS == In preparation for our next meeting, please add syntax predicates to the newly added columns 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 . Thank you and best wishes, Ra?ssa and Pier [1] Running notes document https://docs.google.com/document/d/1569Q7D0Tm03vRQmu2L2WykI63Uk8Aa20GJBC7kUnMZ4/edit#heading=h.h1e3u14gjm5p [2] DwC-MIxS mapping spreadsheet https://docs.google.com/spreadsheets/d/1k6Xe1OREUVISLjw1XLrtLqWsE7QgvWf7lSIXEbqXDpA/edit?usp=sharing [3] Issue tracker https://github.com/tdwg/gbwg/issues ? https://orcid.org/0000-0002-2996-719X -------------- next part -------------- An HTML attachment was scrubbed... URL: