[tdwg-humboldt] Humboldt Extension Public Review preparations

Yanina Sica yanina.sica at gmail.com
Tue Aug 15 08:57:45 UTC 2023 

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_dmnBMqs/edit>,
   I included and suggested edits for the terms proposed by John
   - State of the Hierarchical document
   <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit#heading=h.a0hj80sigtm6>
   :
      - 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-A0mcjj98hbk/edit#heading=h.l89l0grun7cp>,
      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_8iIe3RvRnNYKDJcmSX3ii4S5hCznEA0/edit#heading=h.rr2lqlf80rn0>

*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


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On Mon, Aug 14, 2023 at 7:14 PM John Wieczorek <tuco at 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 at 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 at lists.tdwg.org> on behalf
>> of Kate Ingenloff <kathryn.ingenloff at gmail.com>
>> *Sent:* 14 August 2023 16:00
>> *To:* tuco at berkeley.edu <tuco at berkeley.edu>
>> *Cc:* Wesley M. Hochachka <wmh6 at cornell.edu>; Markus Döring (GBIF) <
>> mdoering at gbif.org>; Peter Desmet <peter.desmet.work at gmail.com>; Humboldt
>> Core TG <tdwg-humboldt at 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 at 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 at 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 at 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 at 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
>>
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