May 2023 - tdwg-humboldt - lists.tdwg.org

Humboldt Task Group Meeting Wed 31 May 2023, 08:00 EST/12:00 UTC
by ys628 02 Jun '23

02 Jun '23

Hi all, I am sorry but I did not finish reviewing the document on inheritance. I also wanted to reach out individually to Walter and Robert, official Parent Events of the Humboldt Core. So I do not think we are ready to 'submit' tomorrow. Maybe, we can briefly meet and confirm that all documents needed are there. As a summary of what we have so far: * Implementation report<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>. The main document to submit to Darwin Core maintenance group stating that this extension is awesome! * should be ready * List of terms<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> (tab complete_term_list_ACTIVE). The most important document including all terms to include in the Humboldt extension for ecological inventories * should be ready (can we already update the Humboldt Extension Quick Reference Guide<https://tdwg.github.io/hc/terms/>?) * Additional official document to better explain eco:isLeastSpecificTargetCategoryQuantityInclusive<https://github.com/tdwg/hc/blob/main/docs/inclusive/index.md> * should be ready (check is all Event and Taxon now include their name spaces) * Additional official document to better explain hierarchical events and inheretance<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> * still need some revision, before it gets transformed into a markdown doc Please review the documents, particularly the authorship, until the end of the week. Ideally, we would start the official process next week!! * The Humboldt Extension Documentation or user guide (here<https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…>) will not be an official document but will be linked in our presentation. It still needs some revision, but it should not delay our presentation. Best! Yani 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…>

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Humboldt Task Group Meeting Wed 24 May 2023, 08:00 EST/12:00 UTC
by ys628 24 May '23

24 May '23

Dear Humboldties, In our last meeting, we decided to develop yet another piece of documentation that describes the "Properties of hierarchical Events in Humboldt Extension". This topic was briefly covered in the Implementation report and in the User guide but many of us felt the need for more information about this. I volunteered to start this document; you can take a look at it here<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…>. You will see that it needs more development but at least it is a start. In tomorrow's meeting it would be great to talk about this document as well as any advances on the Users Guide (here<https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…>), the list of terms (here<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…>) and the mardown doc on isLeastSpecificTargetCategoryQuantityInclusive (https://github.com/tdwg/hc/blob/main/docs/inclusive/index.md) See you! 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…> Yani

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Meeting!
by ys628 18 May '23

18 May '23

Hi all, Thank you all for working on the documents; I saw many of you made comments and revised both the general HE documentation and the implementation report. Much appreciated! Wesley, the documentation on isLeastSpecificTargetCategoryQuantityInclusive looks great! You really improved it, thank you so much! Unfortunately, I do not think I will be able to join the meeting today (I am in Frankfurt with lots of in person meetings...) I will kindly ask you to discuss and the following points. * Update the Humboldt Extension Quick Reference Guide<https://tdwg.github.io/hc/terms/> with updated terms * 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). Markdown version? As usual, * 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) * 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 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.

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Markdown version of isLeastSpecificTargetCategoryQuantityInclusive Guidelines
by Baskauf, Steven James 17 May '23

17 May '23

Hi folks, I’ve done a conversion of the isLeastSpecificTargetCategoryQuantityInclusive Guidelines to Markdown. You can see the draft at: https://github.com/baskaufs/msc/blob/master/docs/inclusive.md When it’s good enough, I’ll submit it as a pull request to somewhere in the Humboldt repo. Notes: 1. In the Google Doc, some text earlier in the doc repeated what was in the Examples section, so I deleted it. 2. I added the standard status (1.1) and RFC 2119 keyword section (1.2) section. After reading the doc, it seems that only section 3 is normative, so I stated that, and labeled all of the major sections as to whether they were normative or not. I made a few changes to section 3 so that the RFC 2119 keywords were include where I though they needed to be, so please read that section again to make sure that these prescriptive wordings make sense. 3. I can’t remember who did the work of writing the doc, so please check the contributors section at the top to make sure I got it right. 4. I made up an abstract from info in the introduction. 5. I split the Introduction and Rationale into 2 separate sections to follow the pattern of other TDWG documents: having an initial introductory section, the technical sections (1.1-1.3) then the main text. This seemed to work out if I split the first paragraph out and used it for the intro and put the rest into rationale. IMPORTANT: I was rigorous in distinguishing between text that referred to abbreviated term IRIs (like dwc:Event) and colloquial use of terms (like “organism”) by putting the abbreviated term IRIs (and literal values) in code markup as has been standard practice in other documents. However, there were many places in the document where it straddled the fence by using capitalized words like “Event”, “Taxon”, or “Organism”. These either were term IRIs or they weren’t. Since they weren’t prefixed by a namespace abbreviation, I assumed they were just nouns and not term IRIs and I changed them to lower case. If that was not the intention and “dwc:Event”, “dwc:Taxon”, and “dwc:Organism” were intended, then they should all be re-capitalized and prepended with a namespace abbreviation. We can discuss what was intended at our meeting tomorrow and I’ll change them as necessary. See you in the morning. Steve -- Steven J. Baskauf, Ph.D. he/him/his Data Science and Data Curation Specialist / Librarian III Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA Biodiversity Information Standards (TDWG) Executive Committee/Technical Architecture Group Chair https://baskauf.github.io/

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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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Final steps for submitting the Humboldt Extension??
by ys628 02 May '23

02 May '23

Hi all, Hopefully you are as excited as I am! We are very close to submitting! There are a few questions to discuss: * Update the Humboldt Extension Quick Reference Guide<https://tdwg.github.io/hc/terms/>? * allow multiple values in samplingEffortValue and samplingEffortUnit? (separated values with |) * include isLeastSpecificTargetCategoryQuantityInclusive? A usual, please revise the 'official' documents to present: * list of terms<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> * Implementation report<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…> 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…> See you soon! All the best, Yani

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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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