August 2023 - tdwg-humboldt

Humboldt Implementation Report
by Kate Ingenloff 28 Aug '23

28 Aug '23

Hi all, I've completed my review of the Implementation Report <https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>. I think I've resolved all the major issues but would be grateful for others to have a look to ensure I didn't miss anything glaring. I have one outstanding question in 'Properties of Hierarchical Events' in the 'Unresolved Issues/Remaining Challenges Section': Is there a reason for using 3 different terms in the examples? It works, but it's just not as easy to read as using a single term to make the case (e.g., targetTaxonomicScope would work for all 3 points). Thanks! Kate ------------------------------ Kate Ingenloff, PhD Pronouns: she/her(s) (+45) 51 44 13 23 "When one tugs at a single thread in nature, he finds it attached to the rest of the world." ~John Muir

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Summary of meeting and next steps
by Yanina Sica 25 Aug '23

25 Aug '23

Hi all, We had a great discussion today, thanks for being so flexible and staying longer! We arrived at the conclusion that we will include 'bycatch' terms. One of the main issues with these terms was that the scopes were unclear (species out of taxonomic scope vs species out of lifeStage, growthForm scopes, etc). It became apparent that we needed to differentiate those cases so we propose 4 terms, 3 terms related to Taxa out of scope and 1 term related to Organisms out of organismal scopes. See here <https://docs.google.com/document/d/184BjPL-Kd9lv_x39sVGNxFKFlb4hY_Xsli5_dmn…> the 4 terms and their definitions.* Please review the 'bycatch' terms and share your thoughts before Friday 18. *Unless any of you has a strong feeling against it, John will include these terms as part of the main vocabulary. We ran out of time, and were not able to discuss the Hierarchical document <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…>. Ming, John, Ani and Kate will meet on Friday or Monday to finish it.* Please let me know if you would like to join our discussion.* We reviewed the List of Authors <https://github.com/tdwg/hc/blob/main/build/authors_configuration.yaml> and there was no major opposition. Basically our criteria of inclusion was to include every Task Group member that joined a considerable number of meetings and discussions plus the 3 authors of the original publication. *Please let me know If you have any thoughts regarding the inclusion and order of authors or if we forgot somebody!* We also assigned people (mostly Kate) responsible for: - Reviewing isLeastSpecificTargetCategoryQuantityInclusive <https://github.com/tdwg/hc/blob/main/docs/inclusive/index.md> - Yani and John will review - Reviewing Implementation report <https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>, making sure latest advances are captured in the text (e.g. Bycatch or non-target species recorded section) - Kate will clean up the doc - Reviewing Landing Page <https://github.com/tdwg/hc/blob/main/docs/index.md> - Kate will write an abstract for this and the rest of the documents (e.g. https://tdwg.github.io/hc/list/) - Reviewing User Guide <https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…> - Kate and Ani will revise and accept main changes *We aim to have everything revised for Wednesday 23. So, now is the time to wear your editor's hat!!* Really looking forward to our next meeting and submitting the extension!! All the best 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 Extension Public Review preparations
by John Wieczorek 25 Aug '23

25 Aug '23

Hi folks, Steve and I have been working through and finished (to the extent we can) the preparations of the documents needed for the public review of the Humboldt Extension. The idea is that the basic entry point to the review would be this landing page <https://github.com/tdwg/hc/blob/main/docs/index.md> and that everything to review would be accessible from there. We need the Task Group to finalize all documents to be included and to authorize the Darwin Core Maintenance Group to initiate the review. When authorized, the Darwin Core Task Group will send a message introducing the submission and how people should review it. It would be great to have a brief statement presenting the proposal from the Task Group to have at the beginning of that message. The DwC Maintenance Group will also solicit the TDWG Outreach folks to publicize the public review via various channels and social media. Anyone will be welcome to further publicize it in any community that TDWG misses. The issue of new terms for by-catch came up late in last Wednesday's meeting after several people had to leave. I don't feel comfortable including anything official from that conversation without the Task Group making decisions. There are a few reasonable options. The first option for the "by-catch" terms is to add those terms now and include them in the proposal. That means work up front to make sure the terms are well-defined and thought through. Think of this ratification process very much as if it was the publication of a manuscript with peer review. As such, an important goal is to try to avoid avoidable public discussion, which has the potential to slow things down or even derail ratification. A second option might be to propose the new terms during public review and see if there is buy-in. This strategy is likely to make the ratification process slower, and runs a risk (that I might be inventing) that if such an added proposal came from people in the Task Group, reviewers might view that our work was submitted unfinished. A third option might be to leave the proposal as is without additional terms, get it through ratification, and sometime afterwards propose new terms. This follows the normal evolution process of Darwin Core, so there would not be anything odd about it. It would also guarantee that there is demand for such terms, as that is a prerequisite for accepting new term proposals. It isn't for the Darwin Core Maintenance Group to decide the strategy the Task Group should take, but rather to advise and facilitate in the search for a successful proposal I hope this feels like we are getting close. Cheers, John and Steve on behalf of the Darwin Core Maintenance Group

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Fwd: Humboldt Extension Public Review preparations
by Yanina Sica 15 Aug '23

15 Aug '23

>From Wesley! ---------- Forwarded message --------- From: Wesley M. Hochachka <wmh6(a)cornell.edu> Date: Wed, Aug 16, 2023 at 4:26 AM Subject: Re: [tdwg-humboldt] Humboldt Extension Public Review preparations To: Yanina Sica <yanina.sica(a)gmail.com>, tuco(a)berkeley.edu < tuco(a)berkeley.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> CC: Yi Ming Gan <ymgan(a)naturalsciences.be>, Markus Döring (GBIF) < mdoering(a)gbif.org>, Peter Desmet <peter.desmet.work(a)gmail.com> Hi everyone, I expect that, as usual, my attempt to send this message to the Humboldt Extension listserv will fail, so someone please forward this on to the list. I think that I will *not* be attending this Wednesday's meeting, unfortunately, because Wednesday is the last of my 3 days in Ithaca before travelling again...and I do not feel that I have everything under control. I was able to look at the new "bycatch" terms, because I think that this is the document that would be most useful for me to read. As general thoughts, I think that these terms are not absolutely essential, because the same information could be derived from looking at the taxonomic scope. However, I also think that they are useful "convenience" terms. Basically, I do not have a strong opinion either way about whether to include the terms. If the number of terms balloons beyond these three, because the same information is added for other scopes, then I'm thinking that I would tend towards not wanting to include any new terms. Regarding the terms themselves I have added a small number of questions to the document about the descriptions of the terms, such as whether eco:hasNonTargetTaxa mybe could be logically turned into a true Boolean, because leaving the term blank when no taxonomic scope is specified is the same as saying that every reported taxon is outside of the bounds of the taxonomic scope. There are also multiple places in which it looks like terms from the TDWG controlled vocabulary (i.e. "SHOULD", "MUST") need to be added to replace the general English-language words that are in the current text. Finally, the current wording is vague enough to suggest that if the eco:Event is an observation of an individual species, then the new terms could/should be applied to each individual record of each independent taxon (i.e. to each observationID). Was this the intent, or would it be appropriate to only apply these terms within the structure at levels about the observationID (i.e. the first "parent" above the level of the individual observation)? I expect that there is no correct answer to this question, so I am only asking it to see whether this issue had been considered yet. I think that these are the main questions/comments that came to mind while I was reading the descriptions of the new terms. Wesley P.S. While I will be reading my e-mail at least twice daily for the remainder of August, I probably will not have any larger blocks of time to devote to any work until 1 September, when I finally stop moving for a little while and I'm no longer in darkened conference rooms. ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 ******************* ------------------------------ *From:* Yanina Sica <yanina.sica(a)gmail.com> *Sent:* Tuesday, August 15, 2023 04:57 *To:* tuco(a)berkeley.edu <tuco(a)berkeley.edu>; Humboldt Core TG < tdwg-humboldt(a)lists.tdwg.org> *Cc:* Yi Ming Gan <ymgan(a)naturalsciences.be>; Wesley M. Hochachka < wmh6(a)cornell.edu>; Markus Döring (GBIF) <mdoering(a)gbif.org>; Peter Desmet < peter.desmet.work(a)gmail.com> *Subject:* Re: [tdwg-humboldt] Humboldt Extension Public Review preparations Thank you all for this lively discussion! It seems we are moving towards including "bycatch" terms. To keep up with the proposed timeline for ratification, I will urge *everybody to attend tomorrow's meeting, if possible. Otherwise, provide your comments regarding these terms before tomorrow's meeting. * The rest of the Humboldt Extension documents should be reviewed by the end of this week (*let's try to finish everything by Wed 22!*). Agenda: - Discuss 'bycatch' terms. Please share your opinion here <https://docs.google.com/document/d/184BjPL-Kd9lv_x39sVGNxFKFlb4hY_Xsli5_dmn…>, I included and suggested edits for the terms proposed by John - State of the Hierarchical document <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9g…> : - discuss examples provided by Ming. Please see section 4 - discuss comments in the text. Please see section 3 - Review List of Authors <https://github.com/tdwg/hc/blob/main/build/authors_configuration.yaml> (thanks Steve!) - Assign people responsible* for: - Reviewing isLeastSpecificTargetCategoryQuantityInclusive <https://github.com/tdwg/hc/blob/main/docs/inclusive/index.md> - Reviewing Implementation report <https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj9…>, making sure latest advances are captured in the text (e.g. Bycatch or non-target species recorded section) - Reviewing Landing Page <https://github.com/tdwg/hc/blob/main/docs/index.md> - Reviewing User Guide <https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCz…> *If you are not able to attend the meeting but are willing to critically review any document please reply to this email saying so. If people are available and willing, I suggest we consider extending the meeting for 30-45min. Final push!! we got this! 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…> <#m_-3994289178551888878_x_m_5260918668296950599_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Aug 14, 2023 at 7:14 PM John Wieczorek <tuco(a)berkeley.edu> wrote: Herein lies the problem of not having eco:nonTargetTaxa: "Assuming everything that is not the target is non-target..." That assumption isn't supportable because the taxonomic opinions applied to the taxa (target, excluded, and nonTarget) can differ over time and between people. Thus, a taxon that might have been out of scope at the time of the Event could come into scope later analysis by virtue of changes in taxonomy. It seems to me never safe to make any assumptions in this respect and that would mean that the eco:nonTargetTaxa is actually required in order to make inferences if any non-target Occurrences are reported. These terms are in support of post-facto use of the data, and it's becoming clear thinking about it that inventory data can be very fragile for some purposes, and the down-stream researcher will have to do a lot of due diligence to be able use them wisely. On Mon, Aug 14, 2023 at 11:48 AM Yi Ming Gan <ymgan(a)naturalsciences.be> wrote: Thank you so much everyone! John I appreciate your attempt to jump-start the term definition. In my humboldt opinion, eco:hasNontargetTaxa and eco:areNontargetOrganismsFullyReported are certainly helpful! eco:hasNontargetTaxa + eco:isTaxonomicScopeFullyReported can also help to differentiate whether an Event caught something vs nothing. Assuming everything that is not the target is non-target, eco:nonTargetTaxa is helpful, but I feel like it could get complicated - for example, taking into account of lifeStageScope etc. (adult fish is *not* a target, but larvae and juvenile are) User can look in the Occurrences to search for whatever not in eco:targetTaxonomicScope (and other scopes) to determine which of those Organisms are non-target. So I suggest to have this implicit, instead of having every non-target listed out in eco:nonTargetTaxa. It is much easier to have those non-target in Occurrence, because they have their own lifeStage, degreeOfEstablishment etc field. I hope this makes sense. Thanks again! Cheers Ming ------------------------------ *From:* tdwg-humboldt <tdwg-humboldt-bounces(a)lists.tdwg.org> on behalf of Kate Ingenloff <kathryn.ingenloff(a)gmail.com> *Sent:* 14 August 2023 16:00 *To:* tuco(a)berkeley.edu <tuco(a)berkeley.edu> *Cc:* Wesley M. Hochachka <wmh6(a)cornell.edu>; Markus Döring (GBIF) < mdoering(a)gbif.org>; Peter Desmet <peter.desmet.work(a)gmail.com>; Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> *Subject:* Re: [tdwg-humboldt] Humboldt Extension Public Review preparations Ahh, good point on that John. I will amend my vote to support option 2. :) On Mon, Aug 14, 2023 at 3:38 PM John Wieczorek <tuco(a)berkeley.edu> wrote: Hi folks, Thanks for this input, Kate. It seems we are of divided opinions about when to address non-target organisms than whether to do so. Assuming it will be done eventually, here is an attempt to get the issues on the table. Kate is proposing terms from the Occurrence perspective in the sense that they would be populated for child-most Occurrence Events (I'll use eco: isNonTargetOrganism). That is, The Event record associated with the Occurrence would have a Humboldt extension term eco:isNonTargetOrganism populated). Last Wednesday Anahita was proposing terms at a parent Event level (I'll use eco:hasNontargetTaxa, eco:areNontargetOrganismsFullyReported, and eco:nonTargetTaxa). This parent Event perspective alerts a user about what to expect among the children. It should be possible to confirm the expectations among the children by investigating them. These two approaches are very different. The first approach seems like a bit of a contorsion to me in that the term really ought to be an Occurrence term, and yet it would be going into the Event extension. A second problem I see is that it would be a challenge for users to know whether a data set, or a particular Event within a data set, is potentially fit for their purpose because all of the child Occurrences would have to be investigated to see if there were relevant non-target taxa. The second approach circumvents the issues mentioned above. The term eco:hasNontargetTaxa for an Event would be a single boolean that could immediately alert a user about what to expect among the child Occurrences. It could also be populated for the Occurrence Events, serving the role intended for eco:isTargetOrganism. The term eco:nonTargetTaxa could actually list those taxa so the user would know what was considered non-target. The term eco:areNontargetOrganismsFullyReported seems extremely important, but it is also extremely problematic, the problem being that it seems like the value of this term would almost ALWAYS have to be 'false'. So, there are clearly things to discuss, but here is an attempt to jump-start term definitions at least. eco:hasNontargetTaxa - definition: One or more dwc:Organisms of taxa outside the target taxonomic and organismal scopes were detected and reported for this dwc:Event. - comments: Should be empty if no taxonomic scope is declared. Should be 'true' if Occurrences of taxa outside the taxonomic and organismal scopes as defined at the time of the dwc:Event are included for the dwc:Event. Should be 'false' if no Occurrences of taxa outside the taxonomic and organismal scopes as defined at the time of the dwc:Event are included for the dwc:Event. - examples: 'true'; 'false' eco:nonTargetTaxa - definition: A list (concatenated and separated) of taxa reported during the dwc:Event that are outside of the eco:targetTaxonomicScope. - comments: Non-target taxa can be reported at any taxonomic level. Recommended best practice is to separate multiple values in a list with space vertical bar space ( | ). - examples: `Parabuteo unicinctus | Geranoaetus melanoleucus`; `Cetoniinae | Aclopinae | Cyclocephala modesta` eco:areNontargetOrganismsFullyReported - definition: Every dwc:Organism that was outside the eco:targetTaxonomicScope, and was detected during the dwc:Event, and was detectable using the given protocol, was reported. - comments: This term is only relevant if the dwc:Event used restricted search or open search methods and the value should otherwise be empty. If all dwc:Organisms not included within the eco:targetTaxonomicScope and detected during the dwc:Event were reported, the value should be 'true'. If all dwc:Organisms not included within the eco:targetTaxonomicScope and detected during the dwc:Event were not reported, the value should be 'false'. - examples: 'true; 'false' Cheers, John On Mon, Aug 14, 2023 at 5:09 AM Kate Ingenloff <kathryn.ingenloff(a)gmail.com> wrote: Hi John, Steve, Yani, et al., Thank you so much John and Steve. The landing page looks great! I'll be happy to help look over documentation this week. As for bycatch, as Yani said, we've discussed this several times and I think it's important to include a couple of the obvious terms for data providers to denote if individual occurrences within a survey are bycatch (e.g., isBycatch or isNonTargetOrganism,) or perhaps to identify is a separate dataset (Event) of some level is nothing but bycatch (e.g., allBycatchReported or allNonTargetOrganismsReported). I think we would be remiss to not include a couple of relevant terms prior to public review. Discussion shouldn't have to take too long and feedback from the first round of review can help fill in the rest (if more than those two terms are necessary). Just my two cents :) Cheers, Kate On Sat, Aug 12, 2023 at 2:43 AM John Wieczorek <tuco(a)berkeley.edu> wrote: Hi folks, Steve and I have been working through and finished (to the extent we can) the preparations of the documents needed for the public review of the Humboldt Extension. The idea is that the basic entry point to the review would be this landing page <https://github.com/tdwg/hc/blob/main/docs/index.md> and that everything to review would be accessible from there. We need the Task Group to finalize all documents to be included and to authorize the Darwin Core Maintenance Group to initiate the review. When authorized, the Darwin Core Task Group will send a message introducing the submission and how people should review it. It would be great to have a brief statement presenting the proposal from the Task Group to have at the beginning of that message. The DwC Maintenance Group will also solicit the TDWG Outreach folks to publicize the public review via various channels and social media. Anyone will be welcome to further publicize it in any community that TDWG misses. The issue of new terms for by-catch came up late in last Wednesday's meeting after several people had to leave. I don't feel comfortable including anything official from that conversation without the Task Group making decisions. There are a few reasonable options. The first option for the "by-catch" terms is to add those terms now and include them in the proposal. That means work up front to make sure the terms are well-defined and thought through. Think of this ratification process very much as if it was the publication of a manuscript with peer review. As such, an important goal is to try to avoid avoidable public discussion, which has the potential to slow things down or even derail ratification. A second option might be to propose the new terms during public review and see if there is buy-in. This strategy is likely to make the ratification process slower, and runs a risk (that I might be inventing) that if such an added proposal came from people in the Task Group, reviewers might view that our work was submitted unfinished. A third option might be to leave the proposal as is without additional terms, get it through ratification, and sometime afterwards propose new terms. This follows the normal evolution process of Darwin Core, so there would not be anything odd about it. It would also guarantee that there is demand for such terms, as that is a prerequisite for accepting new term proposals. It isn't for the Darwin Core Maintenance Group to decide the strategy the Task Group should take, but rather to advise and facilitate in the search for a successful proposal I hope this feels like we are getting close. Cheers, John and Steve on behalf of the Darwin Core Maintenance Group _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt(a)lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt -- ------------------------------ Kate Ingenloff, PhD Pronouns: she/her(s) (+45) 51 44 13 23 "When one tugs at a single thread in nature, he finds it attached to the rest of the world." ~John Muir -- ------------------------------ Kate Ingenloff, PhD Pronouns: she/her(s) (+45) 51 44 13 23 "When one tugs at a single thread in nature, he finds it attached to the rest of the world." ~John Muir _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt(a)lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt -- Yani

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Inferring non-detection of target taxa of presence-only data using Humboldt Extension | Test dataset with updated terms good to go
by Yi Ming Gan 14 Aug '23

14 Aug '23

Hi all, I have done the exercise mentioned in subject. Please see the rendered html with this link: https://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/s… The repository is public: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data I hope some of the remarks and questions are useful! I think the guiding principles are fine after last Wednesday long meeting (special thanks to Yani, Ani and Wesley). The dataset based on latest term name (from last Wednesday) is good to go. I can update the dataset in test IPT<https://ipt.gbif.org/resource?r=brokewest-fish> when the new terms are up in the sandbox. Cheers Ming

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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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