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[Hierarchical Events doc] Example for implementation principles added | Proofread of 3.2.3 Principle of inference needed
by Yi Ming Gan 13 Aug '23

13 Aug '23

Hi all, Apology for sending email in the weekend. 1. I have added a figure to illustrate the implementation principles in 4 Examples (non-normative) in the Hierarchical Events document<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…>. Figure is slide 21 here<https://docs.google.com/presentation/d/1NWFCYmv_nJNYnhhJ1CPQSh1ZkIpIHUOquWd…>. Please modify if necessary. @John, can you please check if I have the examples right? 2. Can someone please proofread 3.2.3 Principle of inference again? * When I was reading it, I feel like Occurrence is described as child Event, but I am not sure if it is just me. * I commented on a paragraph<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> which I feel unsure about and would like to suggest to move that part to User Guide instead. Please correct me if I am wrong. 3. It will be public holiday for me on Monday and Tuesday and I have another meeting at the same time as Humboldt's on Wednesday, so I would not be able to join the Humboldt meeting. Thanks a lot for all the hard work!! Cheers Ming

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Humboldt Extension update 2023-08-08
by John Wieczorek 09 Aug '23

09 Aug '23

Hi folks, I've cc'ed you all as well as sending to the list in case the latter is still misbehaving. I have just pushed a new version of the Humboldt Extension XML file <https://github.com/gbif/rs.gbif.org/blob/master/sandbox/extension/Humboldt_…> to rs.gbif.org where Matt Blissett has kindly merged it, making it available in the sandbox for installing and mapping in test IPTs. This should enable Yi Ming to proceed with the publishing exercise. Still to be done are to make updated documents such as the Quick Reference Guide, List of terms, landing page, etc. I have started to look into these. The technology for making these was upgraded in Darwin Core processing, and it is not entirely clear the state the code to produce these documents is in. I'll try to figure that out next. Cheers, John

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Re: [tdwg-humboldt] How to populate/interpret eco:isTaxonomicScopeFullyReported if dwc:Event caught nothing/something outside of eco:targetTaxonomicScope?
by Yi Ming Gan 04 Aug '23

04 Aug '23

Thank you so much Wesley! I appreciate your perspectives! I agree with your interpretation of eco:isAbsenceReported and eco:isTaxonomicScopeFullyReported. That means the definition of the terms are clear (if the values are true or false), yay! However, I am still looking for the answer of my first question - If nothing was caught in a trawl Event. Should eco:isTaxonomicScopeFullyReported (defined as "Every dwc:Organism that was included within the taxonomic scope, and was detected during the dwc:Event, was reported.”) be true, false or null? Is “nothing” considers as “within" eco:targetTaxonomicScope? If “nothing" is not considered as part of eco:targetTaxonomicScope, then eco:isTaxonomicScopeFullyReported will receive a false. If that’s the case, the user cannot make inference of non-detection of taxa within the eco:targetTaxonomicScope. The reason I included eco:isAbsenceReported in the table I made was because this term is not restricted to the scopes. If there is only one Occurrence associated with the Event that says Animalia, occurrenceStatus=absent, hence eco:isAbsenceReported=true, it MAY be interpreted as none of my taxa in eco:targetTaxonomicScope (if they all belong to Animalia) and by-catch that is animal was caught. Thanks again!! Cheers Ming > On 3 Aug 2023, at 19:49, Wesley M. Hochachka <wmh6(a)cornell.edu> wrote: > > Hi Ming, > > If I am correctly understanding the use of eco:isAbsenceReported, then the value of eco:isAbsenceReported should be irrelevant to whether eco:isTaxonomicScopeFullyReported is set to be "true" or "false". I am assuming thateco:isAbsenceReported and eco:isTaxonomicScopeFullyReported are independent of each other, such that all four combinations of conditions can occur: > eco:isAbsenceReported = false and eco:isTaxonomicScopeFullyReported = false: in this case the absence of the report of a taxon within the taxonomic scope cannot be interpreted. > eco:isAbsenceReported = true and eco:isTaxonomicScopeFullyReported = false: in this case the absence of the report of a taxon within the taxonomic scope cannot be interpreted, because the combination of these two conditions says that "some counts of zero are being reported, but not necessarily for all of the species within or outside of the taxonomic scope. > eco:isAbsenceReported = false and eco:isTaxonomicScopeFullyReported = true: in this case the absence of the report of a taxon within the taxonomic scope can be interpreted to mean that the species was not detected, but these non-detections will need to be inferred because they are not explicitly entered as records of counts of zero. > eco:isAbsenceReported = true and eco:isTaxonomicScopeFullyReported = true: in this case, the absence of the report of a taxon within the taxonomic scope can be interpreted to mean that the species was not detected, and there is no need to infer these absences because counts of zero will be present for all taxa that were not detected. > Again, what I have written above is based on the assumption that I fully understand the use of eco:isAbsenceReported. If this assumption is wrong, then I think that the definition should be tweaked to make its interpretation unambiguous, because my interpretation is consistent with the definition, as far as I can tell. > > > I do not think that there is any way to differentiate between a sampling event in which only by-catch was detected but it was not reported, and a sampling even detected literally no organisms of any taxon (within the constraints of the sampling methods). > From an ecological perspective, the distinction could be important, because the two extreme alternatives are the difference between "our target taxa were not detected but there were still organisms (i.e. the by-catch) detected", and "the sampling area was devoid of detected life". So, these extreme alternatives could only be differentiated of at least one by-catch taxon was reported for the sampling event. However, this feels somewhat dis-satisfying to me, because it's still not possible to tell the difference between "none of the target taxa were detected and just a single organism of any taxon was detected", and "lots of different non-target taxa were detected, but we only bothered to report one of them". > Reports of by-catch (which I'd generically call "presence-only data") is just massively limited in its interpretability. > > > So, anyway, those are my answers to your questions. You might want to forward my reply on to the Humboldt Extension listserv, because it's almost certain that my attempt to send my reply to this listserv is going to fail. > > Wesley > > > > ******************* > Wesley Hochachka > Senior Research Associate > Cornell Lab of Ornithology > ph. (607) 254-2484 > ******************* > > From: Yi Ming Gan <ymgan(a)naturalsciences.be> > Sent: Thursday, August 3, 2023 06:10 > To: tdwg-humboldt(a)lists.tdwg.org <tdwg-humboldt(a)lists.tdwg.org>; Rob Stevenson <rdstevenson10(a)gmail.com> > Cc: Wesley M. Hochachka <wmh6(a)cornell.edu> > Subject: How to populate/interpret eco:isTaxonomicScopeFullyReported if dwc:Event caught nothing/something outside of eco:targetTaxonomicScope? > > Hi all, > > In my attempt to use Humboldt Extension to infer non-detection, I arrived at this question because it is not clear to me how to use null in the following situation. > > Should eco:isTaxonomicScopeFullyReported (previously eco:isTaxonomicScopeComplete) be "true", "false" or null if an dwc:Event do not catch anything within the eco:targetTaxonomicScope and eco:isAbsenceReported == "false"? > > I illustrate my understanding in the table below: > assume that all the catch are reported in the Occurrence extension > eventID catch eventRemarks targetTaxonomicScope (taxa are pipe-separated) isAbsenceReported isTaxonomicScopeFullyReported can infer non-detection of taxa within targetTaxonomicScope? > event_001 A > A | B false true true > event_002 A > A | B false false false > event_003 A, C > A | B false true true > event_004 > by-catch only A | B false true true > event_005 > by-catch only A | B false false false > event_006 > by-catch only A | B false > false > event_007 > caught nothing A | B false true true > event_008 > caught nothing A | B false false false > event_009 > caught nothing A | B false > false > > How can I distinguish: > an dwc:Event caught by-catch only, but did not report it (no dwc:Occurrence record associates with the dwc:Event) > an dwc:Event caught nothing at all > Is this distinction important? Can someone with ecology or relevant background please comment? @Rob Stevenson <mailto:rdstevenson10@gmail.com>maybe? > Thanks a lot! > > > Cheers > Ming

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How to populate/interpret eco:isTaxonomicScopeFullyReported if dwc:Event caught nothing/something outside of eco:targetTaxonomicScope?
by Yi Ming Gan 03 Aug '23

03 Aug '23

Hi all, In my attempt to use Humboldt Extension to infer non-detection, I arrived at this question because it is not clear to me how to use null in the following situation. Should eco:isTaxonomicScopeFullyReported (previously eco:isTaxonomicScopeComplete) be "true", "false" or null if an dwc:Event do not catch anything within the eco:targetTaxonomicScope and eco:isAbsenceReported == "false"? I illustrate my understanding in the table below: * assume that all the catch are reported in the Occurrence extension eventID catch eventRemarks targetTaxonomicScope (taxa are pipe-separated) isAbsenceReported isTaxonomicScopeFullyReported can infer non-detection of taxa within targetTaxonomicScope? event_001 A A | B false true true event_002 A A | B false false false event_003 A, C A | B false true true event_004 by-catch only A | B false true true event_005 by-catch only A | B false false false event_006 by-catch only A | B false false event_007 caught nothing A | B false true true event_008 caught nothing A | B false false false event_009 caught nothing A | B false false How can I distinguish: * an dwc:Event caught by-catch only, but did not report it (no dwc:Occurrence record associates with the dwc:Event) * an dwc:Event caught nothing at all Is this distinction important? Can someone with ecology or relevant background please comment? @Rob Stevenson<mailto:rdstevenson10@gmail.com> maybe? Thanks a lot! Cheers Ming

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Humboldt next steps!
by Yanina Sica 02 Aug '23

02 Aug '23

Hi all, *Sorry about the listserve errors, duplicate emails, and event cancellations*..the universe conspired against us today. Despite this, we managed to meet today and had a very good and productive meeting. We have resolved our latest doubts regarding the principles in the hierarchical doc and summarized our next steps: - John will finish some small edits to the list of terms and update the IPT - Ming will map again the BROKE-West campaign with the latest eco: terms and guiding principles - John and Ming will populate some good examples in the hierarchical document - Dmitry will try to track GBIF's attention (and funding?) to push the Humboldt User Guide to the next level and transform it into a nice format that allows easy updates. I cleaned and edited some of the previous documents and organized the Drive. - Ratification-related documents are in this folder <https://drive.google.com/drive/u/0/folders/1XI1P07lgGRpVyTWiCiA7yJcs9tD_L0ma> : - Implementation Experience Report for Humboldt extension for ecological inventories <https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…> - Hierarchical Events in Humboldt Extension for ecological inventories <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> - isLeastSpecificTargetCategoryQuantityInclusive <https://docs.google.com/document/d/11fPW4JibRWUnrtTOZwDkAcxo5d-lwnATXyh3xmO…> - List of <https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> terms <https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d…> in Humboldt Extension for ecological inventories - Humboldt Extension for ecological inventories User Guide <https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…> *Next week, we will take a look at the examples from Ming and John and, if we all agree, we could formally submit the extension!* We are getting there! Thank you all for your last efforts! All the best! PS: You should have received a calendar invite for next week. In case you did not, please let me know. You can also find the info below: *When to meet* Wednesdays 8 am EST (see your time here <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.timea…> ) *Where to meet* Zoom link: https://yale.zoom.us/j/97318391101 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Yani <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Humboldt Task Group Meeting Wed 26 June 2023, 08:00 EST/14:00 CET
by ys628 26 Jul '23

26 Jul '23

[Apologies if this email is duplcate] Hi all, Hope everybody is doing well. Today, we will discuss the document of hierarchical events (here<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…>). I feel we have advanced and discussed a lot about this so I am very hopeful we can finish it quite soon (if possible in this meeting). This is the last document we need to formally start the ratification process and we should start that process ASAP if we want to have any advances before TDWG 2023. Somehow, I lost the calendar invites for the Humboldt meetings, did the same happen to you? If yes, I can create another invite but we can discuss it today. 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 see you in a bit! 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 Meeting Wed 26 June 2023, 08:00 EST/14:00 CET
by Yanina Sica 26 Jul '23

26 Jul '23

Hi all, Hope everybody is doing well. *Today, we will discuss the document of hierarchical events (here <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…>).* I feel we have advanced and discussed a lot about this so I am very hopeful we can finish it quite soon (if possible in this meeting). This is the last document we need to formally start the ratification process and we should start that process ASAP if we want to have any advances before TDWG 2023. Somehow, I lost the calendar invites for the Humboldt meetings, did the same happen to you? If yes, I can create another invite but we can discuss it today. *When to meet* Wednesdays 8 am EST (see your time here <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.timea…> ) *Where to meet* Zoom link: https://yale.zoom.us/j/97318391101 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Thank you and see you in a bit! All the best, Yani

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meeting this week
by ys628 25 Jul '23

25 Jul '23

Hi all, Lets discuss the Hierarchical Document <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> this week! With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps. See you! Yani [https://lh3.googleusercontent.com/docs/ADP-6oHMdd4mw25hw7lvSXn4ZCiwspb9cc28…]<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> Hierarchical Events in Humboldt Extension for ecological inventories<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ... docs.google.com 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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summer plans: ratifikation and ESA
by Dmitry Schigel 03 Jul '23

03 Jul '23

Hello all, Just to let you know that this week I will set my out of office reply for a couple of weeks. FYI Kate Ingenloff will be back to work on 24 July, and I - on 25 July. I would like to flag two things here: * From the GBIF work perspective, ratification in 2023 is a very positive move. We are happy to help, but neither Kate nor I are very experienced in TDWG formalities. John Wi or Steve, will one of you lead the work? Please count on us - from the dates mentioned above. We will certainly consult with Tim Robertson. * I will represent GBIF Secretariat at the ESA 2023, which is an interesting audience for the Humboldt thinking. GBIF will do two things: a Data dialogues session on Monday https://esa2023.eventscribe.net/agenda.asp?startdate=8/7/2023&enddate=8/7/2… (where Rob has a slot - for Humboldt maybe?) and I may also give a GBIF talk at one of the NEON session. Just mentioning also to check if other Humboldt people will be at ESA? We discussed that 2023 may be a bit early for proper "product placement" of the extension, but just checking if there is a chance to meet. Thanks, Dmitry Dmitry Schigel, PhD Scientific Officer GBIF | Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK Office +45 35 32 14 85 Mobile +45 30 45 02 25 E-mail dschigel(a)gbif.org<mailto:dschigel@gbif.org> Zoom https://ucph-ku.zoom.us/my/dschigel<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzMjZjOWE1ZGUyNGEyNzM2ND02M…> Web www.gbif.org<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTM4MT02M…> [cid:image001.png@01D9AD9C.FF87E5E0] DNA derived evidence in GBIF https://bit.ly/dnagbif<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGUyNWY2NTYwMD02M…> Biodiversity data for research and policy on human diseases http://bit.ly/gbifvectors<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTJkMD02M…> Join GBIF Biodiversity Open Data Ambassadors http://bit.ly/bodamba<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTJkMD02M…> Northern Eurasia: GBIF progress in the Cyrillic world http://bit.ly/cyrril<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTJkMD02M…> GBIF enabled research http://bit.ly/gbifsci<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTJkMD02M…>

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TDWG 2023 Abstract
by ys628 01 Jul '23

01 Jul '23

Hi all, I would like to ask you to take a look at the abstract one more time. Wesley did a major rearranging (OPTION 2, some description below). I want to make sure everybody agrees...also in regarding the authors. https://docs.google.com/document/d/1Yqz4pwRksvaL_pDVlXTnOZG6w5fEDKIO0FKV17a… [https://lh3.googleusercontent.com/docs/ADP-6oEiMin53Or6vohQ7FHBNAzVXHHxnfBr…]<https://docs.google.com/document/d/1Yqz4pwRksvaL_pDVlXTnOZG6w5fEDKIO0FKV17a…> Abstract - TDWG2023<https://docs.google.com/document/d/1Yqz4pwRksvaL_pDVlXTnOZG6w5fEDKIO0FKV17a…> Instructions! https://www.tdwg.org/conferences/2023/instructions-for-abstract-submission/ Title: Want to describe share biodiversity inventory and monitoring data? The Humboldt Extension for Ecological Inventories can help! Please complete your name and affiliation Authors: Yi-Ming Gan1, Kate In... docs.google.com I will submit later today or even tomorrow morning (July 1st) to give you more time to review Thanks a lot Yani ---mail and explanation from Wesley Hi Yani and Ming, If this message looks like something that is relevant for the entire group, could you please forward it to the Humboldt Extension listserv? I'm writing to both of you because Yani you should be aware of what I've done sooner rather than later, and Ming because I saw that you were viewing the document while I was also mucking around with it. Somehow, I ended up experimenting with a major reorganization of the material in the existing abstract, while (hopefully) not deleting any information, and adding little new information (the exception being the fourth and fifth sentences). I have pasted my experimental reoganization of the material below the current version, and I have written a long comment linked to the first word in my experiment. Unfortunately, it's impossible to see where the original text remained, where parts of the original text were moved, or where I made additions, because I made a local copy of the original and then copied the end result back...and all of the change-tracking colour information disappeared. Anyway, as I wrote at the end of my comment, you absolutely should treat what I did as an experiment in creating a new order of presentation of the ideas in the original version, and use the new organization, or not, to the extent that you see fit. Oh, and regarding English versus U.S. spelling, I'm definitely the worst person to ask, because the spelling all looks Canadian (i.e. a British-U.S. hybrid) to me. Wesley ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 *******************

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