April 2023 - tdwg-humboldt

Humboldt Task Group Meeting Wed 19 April 2023, 08:00 EST/12:00 UTC
by ys628 03 May '23

03 May '23

Hi all, I am very sorry for the short notice. I will not be able to join our meeting. I had to travel to Argentina last minute to help my family. My mom had an emergency but now she is recovering very well so there is nothing to worry about. I will kindly ask you to discuss and review the following documents so we can finally submit the extension. * Implementation report (please review and add yourself as an author here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>) * List of terms (please review all eco: terms here<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…>, tab: complete_term_list_from_JW) * Additional document to better explain eco:isLeastSpecificTargetCategoryQuantityInclusive (please add content, examples, links to other terms, etc. to this <https://docs.google.com/document/d/11fPW4JibRWUnrtTOZwDkAcxo5d-lwnATXyh3xmO…> document). * This will be added as an official document to the list of terms. The idea here, is that all the comments and relations of other terms will be better captured in a separate document instead of making a terribly long Comments section. * Humboldt Extension Documentation (please review here<https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…>) * This will not be an official document but will probably need to be linked in our presentation. Basically, I took our testing guide and removed all the parts related to the testing. We will need to update this document and polish it. When to meet Wednesdays 8 am EST (see your time here<https://www.timeanddate.com/worldclock/converter.html?iso=20230419T120000&p…>) Where to meet Zoom link: https://yale.zoom.us/j/97318391101<https://www.google.com/url?q=https://yale.zoom.us/j/97318391101&sa=D&source…> Thank you and sorry for missing the meeting All the best, Yanina V. Sica, PhD Lead Data Team Map of Life<https://mol.org/> | Center for Biodiversity and Global Change<https://bgc.yale.edu/> Yale University pronouns: she/her/hers If you are receiving this email outside of your working hours, I am not expecting you to read or respond.

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Fwd: Humboldt Task Group Meeting Wed 19 April 2023, 08:00 EST/12:00 UTC
by Yi Ming Gan 02 May '23

02 May '23

Thank you so much Wesley, really appreciate it! Maybe dummy was not the right word to use. The isLeastSpecificTargetCategoryQuantityInclusive is specific for Occurrence (I think), but Humboldt extension is extending Event (not Occurrence) in Darwin Core Archive. Darwin Core Archive follows star schema. 1 Event can be associated with multiple Occurrences and Humboldt extension extends the Event (not Occurrence). If isLeastSpecificTargetCategoryQuantityInclusive is true for certain Occurrences and false for the other Occurrences in an Event, then the Event has to be duplicated in order to have a Humboldt record with isLeastSpecificTargetCategoryQuantityInclusive = true and another with isLeastSpecificTargetCategoryQuantityInclusive = false, with corresponding Occurrences link to each Event extended by Humboldt with such values. If my understanding is correct, then I am not sure if I understand the merit of having this term in the Humboldt Extension, when the examples in comment can be expressed in a simpler manner with existing Darwin Core terms. It is a different story in the new data model. However, people will not evaluate its usefulness based on the new data model in the public review, but in the context of Darwin Core. Anyway, I will try to express my thoughts better in the next meeting, then you all can correct me if I am wrong :) Thank you all so much for discussing it in the meeting yesterday! PS: Wesley, you are always essential to the team. Thank you for the email! Have a good trip! Sincerely Ming Begin forwarded message: From: "Wesley M. Hochachka" <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Task Group Meeting Wed 19 April 2023, 08:00 EST/12:00 UTC Date: 19 April 2023 at 15:31:25 CEST To: Yi Ming Gan <ymgan(a)naturalsciences.be>, "Sica, Yanina" <yanina.sica(a)yale.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Hi Ming, First, I still cannot sent e-mail messages to the listserv, so could either you or Yani forward this message to the entire group? Oh, and I have added Yani as a direct recipient so that I know that she will receive this message too. Anyway, there was only a small group of us at today's meeting (Zach, Steve, and myself), and one of the things that we talked about was the message that you had sent earlier today. We are not sure what you meant when you write about the need to create a "dummy Event", and why one would need to create a dummy event. What I am speculating is that something in the documentation is leading you and I (and I assume Steve and Zach) to assume different things about the use of the term isLeastSpecificTargetCategoryQuantityInclusive. It may not be efficient to use e-mail messages to ensure that all of us know understand the reason for what you wrote, so could you make certain to bring this up at the next meeting for discussion? Oh, and I'm afraid that I won't be able to attend the meeting next Wednesday, because I will be inside a winged tube flying west over the Atlantic. Zach and Steve should be able to explain my own questions about what you wrote, so I do not think that it is essential that I am at the meeting when this is discussed. Oh...gotta run...I've got another meeting now! Wesley ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 ******************* ________________________________ From: Yi Ming Gan <ymgan(a)naturalsciences.be> Sent: Wednesday, April 19, 2023 05:09 To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Cc: Wesley M. Hochachka <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Task Group Meeting Wed 19 April 2023, 08:00 EST/12:00 UTC Hi all, I have a deadline today, so I can’t attend the meeting. However, I tried to put isLeastSpecificTargetCategoryQuantityInclusive into tables (Darwin Core) based on the examples in the comment, so here are my thoughts: 1. It looks much simpler without isLeastSpecificTargetCategoryQuantityInclusive (Darwin Core Archive, not the new Unified Model) If isLeastSpecificTargetCategoryQuantityInclusive = true Use case without “isLeastSpecificTargetCategoryQuantityInclusive” Occurrence occurrenceID eventID taxonID lifeStage organismQuantity organismQuantityType occ_01 event_01 taxon_01 adult 1 individual occ_02 event_01 taxon_01 juvenile 2 individual occ_03 event_01 taxon_01 1 individual eventID Total individual of taxon_01 event_01 4 = 1 adult + 2 juvenile + 1 no lifestage If isLeastSpecificTargetCategoryQuantityInclusive = false use case without “isLeastSpecificTargetCategoryQuantityInclusive” Occurrence occurrenceID eventID taxonID lifeStage organismQuantity organismQuantityType occ_01 event_01 taxon_01 adult 1 individual occ_02 event_01 taxon_01 juvenile 2 individual occ_03 event_01 taxon_01 4 individual eventID Total individual of taxon_01 event_01 7 = 1 adult + 2 juvenile + 4 no lifestage 2. Dummy Event needs to be created if isLeastSpecificTargetCategoryQuantityInclusive differs in each Taxon per sampling event (Darwin Core Archive, not the new Unified Model) Multiple taxa per event with isLeastSpecificTargetCategoryQuantityInclusive If this will lead to user creating dummy Event to use this term, I feel like people will not use it. I also think that then what is the point of using Event core this way? Occurrence occurrenceID eventID taxonID lifeStage organismQuantity organismQuantityType occ_01 event_01 taxon_01 adult 1 individual occ_02 event_01 taxon_01 juvenile 2 individual occ_03 event_01 taxon_01 4 individual occ_04 event_02 taxon_02 4 individual Humboldt eventID isLeastSpecificTargetCategoryQuantityInclusive Total individual of taxon event_01 true taxon_01 = 1 adult + 2 juvenile + 1 no lifestage event_02 false taxon_02 = 4 no lifeStage Multiple taxa per event without isLeastSpecificTargetCategoryQuantityInclusive Occurrence occurrenceID eventID taxonID lifeStage organismQuantity organismQuantityType occ_01 event_01 taxon_01 adult 1 individual occ_02 event_01 taxon_01 juvenile 2 individual occ_03 event_01 taxon_01 1 individual occ_04 event_01 taxon_02 4 individual eventID Total individual of taxon event_01 * taxon_01 = 1 adult + 2 juvenile + 1 no lifeStage * taxon_02 = 4 no lifeStage Maybe I missed something but I am not sure what is the merit of having isLeastSpecificTargetCategoryQuantityInclusive in Darwin Core (not the new unified model)? I also put all the examples above in the slides in Humboldt google drive: https://docs.google.com/presentation/d/1lsCqdh_OeAFPgJYT9nqP82wqZgVNaDQpWpq… Thanks a lot!! Sincerely Ming On 19 Apr 2023, at 04:01, ys628 <yanina.sica(a)yale.edu> wrote: Hi all, I am very sorry for the short notice. I will not be able to join our meeting. I had to travel to Argentina last minute to help my family. My mom had an emergency but now she is recovering very well so there is nothing to worry about. I will kindly ask you to discuss and review the following documents so we can finally submit the extension. * Implementation report (please review and add yourself as an author here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>) * List of terms (please review all eco: terms here<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…>, tab: complete_term_list_from_JW) * Additional document to better explain eco:isLeastSpecificTargetCategoryQuantityInclusive (please add content, examples, links to other terms, etc. to this <https://docs.google.com/document/d/11fPW4JibRWUnrtTOZwDkAcxo5d-lwnATXyh3xmO…> document). * This will be added as an official document to the list of terms. The idea here, is that all the comments and relations of other terms will be better captured in a separate document instead of making a terribly long Comments section. * Humboldt Extension Documentation (please review here<https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…>) * This will not be an official document but will probably need to be linked in our presentation. Basically, I took our testing guide and removed all the parts related to the testing. We will need to update this document and polish it. When to meet Wednesdays 8 am EST (see your time here<https://www.timeanddate.com/worldclock/converter.html?iso=20230419T120000&p…>) Where to meet Zoom link: https://yale.zoom.us/j/97318391101<https://www.google.com/url?q=https://yale.zoom.us/j/97318391101&sa=D&source…> Thank you and sorry for missing the meeting All the best, Yanina V. Sica, PhD Lead Data Team Map of Life<https://mol.org/> | Center for Biodiversity and Global Change<https://bgc.yale.edu/> Yale University pronouns: she/her/hers If you are receiving this email outside of your working hours, I am not expecting you to read or respond. _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt

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Humboldt Task Group Meeting Wed 11 April 2023, 08:00 EST/13:00 UTC
by ys628 12 Apr '23

12 Apr '23

Hi all, Thank you so much Wesley for last week's summary and everybody for advancing with the report! Here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…> is the latest version of the report. John and I have also been discussing the term isLeastSpecificTargetCategoryQuantityInclusive. There was a confusion between the previous name (sumQuantities) and the current name (isLeastSpecificTargetCategoryQuantityInclusive) because when sumQuantities is TRUE then isLeastSpecificTargetCategoryQuantityInclusive is FALSE. For example, in eBird, where ebird_target_1 (H. rustica, did not include the subspecies), we have to add organismQuantity to get the total detected quantity for the Taxon (H rustica at the species level). Or the opposite, for OBIS, where bw_target_3 (E. antarctica without lifestage distinction) is inclusive of the more specific lifeStage targets (is already the sum of organismQuantity for lava and postmeta) so we cannot add organismQuantity to get the total detected quantity for the Taxon (E. antarctica without lifestage distinction). Now, this is resolved, please take a look at this new definition/comments: * Term name: isLeastSpecificTargetCategoryQuantityInclusive * Definition: The total detected quantity of Organisms for a Taxon in an Event is given explicitly in a single record (dwc:organismQuantity value) for that Taxon. * Comments: "Recommended values are 'true' and 'false'. If 'true', the dwc:organismQuantity values for a Taxon in an Event is inclusive of all Organisms of the Taxon (including more specific scopes such as different life stages or lower taxonomic ranks) and the total detected quantity of Organisms for that Taxon in the Event cannot be determined by summing the dwc:organismQuantity values for the Taxon in the Event. Instead, the total detected quantity of Organisms for the Taxon in an Event would have to be reported in a single record for the Taxon in the Event that had no further specific scopes. In this case the sum of dwc:organismQuantity values for the reported subsets of the Taxon must not exceed the value of dwc:organismQuantity for the single record for the Taxon without subsets (i.e., the total). If 'false', the dwc:organismQuantity values for a Taxon in an Event can be added to get the total detected quantity of Organisms for that Taxon in the Event. For example, suppose there are three records with dwc:organismQuantity for a Taxon for an Event. One record is for adults of the Taxon with dwc:organismQuantity = 1 and dwc:organismQuantityUnit = 'individuals', one record is for juveniles of the Taxon with dwc:organismQuantity = 2 and dwc:organismQuantityUnit = 'individuals', and one record is for the Taxon without specifying the lifeStage and with dwc:organismQuantity = 4 and dwc:organismQuantityUnit = 'individuals'. If isLeastSpecificTargetCategoryQuantityInclusive is 'true', the total number of individuals of the Taxon for the Event is 4 (the least specific Taxon record - the one with no more specific scopes - includes all individuals of the Taxon). This means there was 1 adult, 2 juveniles and 1 individual whose lifeStage was not recorded. If isLeastSpecificTargetCategoryQuantityInclusive is 'false', the total number of individuals of the Taxon for the Event is 7 (the least specific Taxon record - the one with no more specific scopes - does not include all individuals of the Taxon, rather, it is a separate category that must also be added to get the total). This means there was 1 adult, 2 juveniles and 4 individuals whose lifeStage was not recorded. This term is only relevant if dwc:organismQuantity is a number. * We could point to the DwC definition of Taxon<http://rs.tdwg.org/dwc/terms/Taxon> == A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit. Should we do this adding dwc:Taxon? or since it is a class adding the nameSpace is not correct. * Tomorrow, we can discuss this term, review the report and assign the next step (public review??)😁 All the best! Yani Yanina V. Sica, PhD Lead Data Team Map of Life<https://mol.org/> | Center for Biodiversity and Global Change<https://bgc.yale.edu/> Yale University pronouns: she/her/hers If you are receiving this email outside of your working hours, I am not expecting you to read or respond. ________________________________ From: Wesley M. Hochachka <wmh6(a)cornell.edu> Sent: Wednesday, April 5, 2023 10:15 AM To: ys628 <yanina.sica(a)yale.edu>; Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Subject: Re: Humboldt Task Group: Please review implementation report Hi Yani, First, while I am trying to send this message to the Humboldt Core group in TDWG, I suspect that it will bounce, so could you forward the contents of the message to the group? Anyway... Ming, Zach, Steve and I met today, and here's a brief summary of what we discussed: * regarding the term isLeastSpecificTargetCategoryQuantityInclusive, we agreed that we should keep this name, which is a clear description of the intend of the term even though it's long. There did not seem to be an obvious way to substantially shorten the term and still maintain clarity of meaning. If there are comments during public review, then we can always revisit the name, but for now it did not seem worth holding up the process of going to public review in order to try to find a better alternative to the current name. * Also regarding this term, we discussed that its Definition and Comments need a little more work, mostly or entirely associated with the use of "Taxon", which currently is used in a way that means that organisms of different sexes or age classes below to different taxa. I'll try to create time before next Wednesday to suggest changes to wording, and I believe that Ming will look at the Definition and Comments as well. * We also discussed the Implementation Report, and none of us felt that there were any topics missing from the current version (thanks for all of the work that you put into the report!). * Personally, I am still wondering whether I will suggest one or two additional minor changes. You should assume that if I make any changes, then I will have made these changes before next Wednesday. I don't want to get in the way of wrapping up work on the report. There, I think that's a complete summary of our discussions today. Let me know if you have any questions! Wesley ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 ******************* ________________________________ From: ys628 <yanina.sica(a)yale.edu> Sent: Monday, April 3, 2023 20:56 To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org>; Wesley M. Hochachka <wmh6(a)cornell.edu> Subject: Humboldt Task Group: Please review implementation report Dear all, We have made a lot of progress with the Implementation report. Please have a look and edit here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>. I would like to thank Wesley, Ming, Zach and Steve for pushing this forward! I really appreciate it! Here is a brief description of the document, the goal is to convince TDWG people that this extension is useful an that it would work! - Authors will include the people writing the report and participating in the testing (we may even publish this as a paper in BISS) - Introduction and background will be the basis of the Feature report as it already includes the rationale behind building this extension. This means that this Implementation report will include the information needed in the Feature report. For more info on TDWG required documents see here: http://rs.tdwg.org/vms/doc/specification/#421-feature-report<https://www.google.com/url?q=http://rs.tdwg.org/vms/doc/specification/%2342…> - Development of the vocabulary includes some description of what is considered an inventory, a basic description of the terms, and a link to the final table with the terms - Use cases will include a description of the datasets and how the mapping was done - Lessons learned will include all the challenges identified during the mapping and testing that were addressed using the Humboldt extension - Unresolved issues/remaining challenges will include all the challenges identified during the mapping and testing that were NOT addressed using the Humboldt extension - Conclusions will be some sort of summary stating that we are ready to go to public review I will not be able to join our next meeting, but it would be great if you can meet and discuss how the document is looking otherwise please take the time to review the document. The sooner we finish this the faster we can start the public review. We also need to review the documentation and the list of terms<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> that will accompany the implementation report. I would also ask you to discuss line 41 of that sheet. Hope everybody is good and we got this! All the best! Yanina V. Sica, PhD Lead Data Team Map of Life<https://mol.org/> | Center for Biodiversity and Global Change<https://bgc.yale.edu/> Yale University pronouns: she/her/hers If you are receiving this email outside of your working hours, I am not expecting you to read or respond.

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Humboldt Task Group: Please review implementation report
by ys628 11 Apr '23

11 Apr '23

Dear all, We have made a lot of progress with the Implementation report. Please have a look and edit here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>. I would like to thank Wesley, Ming, Zach and Steve for pushing this forward! I really appreciate it! Here is a brief description of the document, the goal is to convince TDWG people that this extension is useful an that it would work! - Authors will include the people writing the report and participating in the testing (we may even publish this as a paper in BISS) - Introduction and background will be the basis of the Feature report as it already includes the rationale behind building this extension. This means that this Implementation report will include the information needed in the Feature report. For more info on TDWG required documents see here: http://rs.tdwg.org/vms/doc/specification/#421-feature-report<https://www.google.com/url?q=http://rs.tdwg.org/vms/doc/specification/%2342…> - Development of the vocabulary includes some description of what is considered an inventory, a basic description of the terms, and a link to the final table with the terms - Use cases will include a description of the datasets and how the mapping was done - Lessons learned will include all the challenges identified during the mapping and testing that were addressed using the Humboldt extension - Unresolved issues/remaining challenges will include all the challenges identified during the mapping and testing that were NOT addressed using the Humboldt extension - Conclusions will be some sort of summary stating that we are ready to go to public review I will not be able to join our next meeting, but it would be great if you can meet and discuss how the document is looking otherwise please take the time to review the document. The sooner we finish this the faster we can start the public review. We also need to review the documentation and the list of terms<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> that will accompany the implementation report. I would also ask you to discuss line 41 of that sheet. Hope everybody is good and we got this! All the best! Yanina V. Sica, PhD Lead Data Team Map of Life<https://mol.org/> | Center for Biodiversity and Global Change<https://bgc.yale.edu/> Yale University pronouns: she/her/hers If you are receiving this email outside of your working hours, I am not expecting you to read or respond.

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