[tdwg-humboldt] Fwd: Humboldt Extension Public Review preparations
Yanina Sica
yanina.sica at gmail.com
Wed Aug 16 05:32:55 UTC 2023
>From Wesley!
---------- Forwarded message ---------
From: Wesley M. Hochachka <wmh6 at 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 at gmail.com>, tuco at berkeley.edu <
tuco at berkeley.edu>, Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>
CC: Yi Ming Gan <ymgan at naturalsciences.be>, Markus Döring (GBIF) <
mdoering at gbif.org>, Peter Desmet <peter.desmet.work at 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 at gmail.com>
*Sent:* Tuesday, August 15, 2023 04:57
*To:* tuco at berkeley.edu <tuco at berkeley.edu>; Humboldt Core TG <
tdwg-humboldt at lists.tdwg.org>
*Cc:* Yi Ming Gan <ymgan at naturalsciences.be>; Wesley M. Hochachka <
wmh6 at cornell.edu>; Markus Döring (GBIF) <mdoering at gbif.org>; Peter Desmet <
peter.desmet.work at 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_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
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
Virus-free.www.avast.com
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
<#m_-3994289178551888878_x_m_5260918668296950599_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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
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--
------------------------------
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 at lists.tdwg.org
https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
--
Yani
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