[Taxacom] A question for GBIF regarding data harvests from iNaturalist (Alec McClay)

Sun Dec 26 17:19:18 CST 2021

Sure - in general principle. But I make no judgment myself about "wrong
attitude" and "undermining other people's work" in this particular case
since I am no party to it. These are also problematic assertions in general
since any critique or opposition to a particular position or viewpoint in
science could be characterized as having the 'wrong attitude', or
'undermining other people's work'. In fact I obviously have the 'wrong
attitude' when it comes to panbiogeography or others would not attempt to
suppress my work, and definitely my critiques and alternative models
'undermine' other people's work. Personally I don't see anything wrong with
that.

Cheers, John

On Sun, Dec 26, 2021 at 5:20 PM Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:

> Oops! Replied to wrong email!
>
> On Monday, 27 December 2021, 11:19:13 am NZDT, Stephen Thorpe via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>
> It is ok to be wrong about facts, as long as you are prepared to correct
> your mistakes. It is not ok to have the wrong attitude, one of undermining
> other people's work, as Hegg has fone
>     On Sunday, 26 December 2021, 12:18:17 pm NZDT, John Grehan <
> calabar.john at gmail.com> wrote:
>
> Sometimes there is just help for a situation, especially one involving an
> independent organization involving 'community' input. Perhaps you should
> start your own website. I did that for my group so I would have total
> control. But my former institution ('science' museum) would not keep it
> going and I could not afford to maintain the website cost after retirement.
> But there are other cost effective or cost free options for the Web savvy
> individual.
> Cheers, John
> On Sat, Dec 25, 2021 at 4:24 PM Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> wrote:
>
> John,Presumably it is all about finding an appropriate trade off between
> data quality and amount of data. If you only addmit the absolutely most
> reliable (however that can be defined!) data, then you are only going to
> have a tiny bit of data to work with. Is it better to have 1% of available
> data, but with 99% reliability, or is it better to have 50% of the
> available data at 80% reliability? The actual numbers are not relevant
> here, I am just trying to make a general point. In a way, this point was
> Danilo Hegg's big mistake: he rolled back "my identifications" (MPI's
> identifications) of Balta bicolor, because they are not 100%
> reliable/certain. He was imposing an unrealistically high standard of
> certainty. Our official government biosecurity authority (MPI) is not
> infallible, but has a high enough level of reliability for iNat and GBIF
> purposes. It isn't quite that simple though, as Hegg seemed convinced
> ("100% certain") that the roaches belong to genus Ellipsidion, so I'm not
> quite sure why his judgement is seen by him as certain while the judgement
> of MPI and myself isn't reliable enough for him!Cheers, Stephen
>     On Sunday, 26 December 2021, 09:33:54 am NZDT, John Grehan <
> calabar.john at gmail.com> wrote:
>
> All this points to what everyone recognizes - that broad databases are
> only as good as the data, and some more than others. But in the end one has
> to make their informed judgment about the data. I have used GBIF at times
> to get a quick impression of a distribution, but try not to rely on it. So
> far, my best experiences are with websites on particular groups (e.g.
> reptiles) where an effort is made to provide distribution maps based on
> taxonomic works. But nothing is foolproof of course.
> John Grehan
> On Sat, Dec 25, 2021 at 2:52 PM Kerry Ford via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> Harvesting all would be scary, just thinking of the grasses and sedges
> here and my NZ experience of iNat.
> Kerry
>
> Get Outlook for iOS<https://aka.ms/o0ukef>
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Stephen
> Thorpe via Taxacom <taxacom at mailman.nhm.ku.edu>
> Sent: Saturday, December 25, 2021 11:37:50 AM
> To: taxacom at mailman.nhm.ku.edu <taxacom at mailman.nhm.ku.edu>; Richard Pyle
> <deepreef at bishopmuseum.org>
> Cc: INaturalist Support <help at inaturalist.org>
> Subject: Re: [Taxacom] A question for GBIF regarding data harvests from
> iNaturalist (Alec McClay)
>
> Hi Rich,The issues you raise do have some relevance, but it is a bit more
> complicated. I could write volumes about all this, but, if I could only
> maake one short point in this connection, it would be this: I have been
> repeatedly told over the years by iNat California (specifically Tony Iwane
> and/or Don Loarie) that everyone in the world must use a single name and
> classification for every taxon (even if all N.Z. botanists, for example
> disagree with overseas botanists about NZ taxa!). While this is not
> directly relevant to multiple identifications, it isn't hard to see how the
> former might influence the latter! GBIF would actually be better off
> harvesting all iNat observations, not just "RG" ones. That would certainly
> mitigate the damage in cases like Balta bicolor.Cheers, Stephen
>     On Saturday, 25 December 2021, 11:19:30 am NZDT, Richard Pyle via
> Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
>
>  It sounds like a big part of this kerfuffle (would that be the right word
> to describe it?) involves a current limitation of GBIF (and iNat?) in that
> only *one* identification per Occurrence instance can be
> presented/stored/represented.  GBIF harvests content through the DarwinCore
> Archive (DwCA) template, which is essentially a flattened version of the
> DarwinCore standard.  The good news is that the full standard accommodates
> an unlimited number of taxonomic identifications associated with each
> Occurrence instance, and the better news is that the good folks at GBIF and
> TDWG (specifically, the guy who basically invented DwCA and the guy who is
> widely regarded as the ultimate guru of DarwinCore) are developing a new
> protocol for how GBIF ingests content, which will be much more effective at
> leveraging the non-flat capabilities of DarwinCore (watch this space early
> next year).  So, in the not-too-distant future, it should be possible to
> accommodate multiple alternative identifications for the same Occurrence
> instance.
>
> In that paradigm, each Occurrence of the relevant roach in NZ could have
> one identification from Stephen asserting it to be Balta bicolor, and
> another from Danilo asserting to be [whatever he reckons it is]. And it
> would be discoverable through searches of either name.
>
> "But...", you might ask, "...how does the 'correct' identification get
> flagged?"  To which I would answer: "There is no such thing."
>
> Aloha,
> Rich
>
> Richard L. Pyle, PhD
> Senior Curator of Ichthyology | Director of XCoRE
> Bernice Pauahi Bishop Museum
> 1525 Bernice Street, Honolulu, HI 96817-2704
> Office: (808) 848-4115;  Fax: (808) 847-8252
> eMail: deepreef at bishopmuseum.org
> BishopMuseum.org
> Our Mission: Bishop Museum inspires our community and visitors through the
> exploration and celebration of the extraordinary history, culture, and
> environment of Hawaiʻi and the Pacific.
>
> > -----Original Message-----
> > From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of
> > Stephen Thorpe via Taxacom
> > Sent: Friday, December 24, 2021 10:27 AM
> > To: taxacom at mailman.nhm.ku.edu; Mark Egger <m.egger at comcast.net>
> > Subject: Re: [Taxacom] A question for GBIF regarding data harvests from
> > iNaturalist (Alec McClay)
> >
> >  Hi Mark,You are correct, but please be aware than in cases of
> misidentified RG
> > observations, they will drop back out of GBIF if the misidentification is
> > subsequently corrected on iNat. This can be seen as an improvement in
> data
> > quality over time. What I am talking about, however, is the reverse.
> GBIF did
> > have (maybe still does have, for the moment) a solid portfolio of RG
> Balta
> > bicolor observations, sourced from iNat, and due largely to my work.
> Danilo
> > Hegg, however, unilaterally decided that both I and our official
> government
> > biosecurity authority (MPI) were wrong, and so rolled back all the IDs,
> without
> > any prior discussion. He was not even aware of the relevant facts when
> he did
> > this! He interpreted those facts, when I informed him of them, in a
> highly
> > biased way, having already made up his mind on the matter. Nobody else on
> > iNat has the relevant knowledge of the taxa concerned, to make a
> meaningful
> > judgement. It really comes down to whether or not I was justified in
> following
> > the ID by MPI, and I suggest this is a perfectly reasonable thing to do,
> in the
> > absence of any convincing evidence to the contrary (and merely looking
> > superficially like a roach in the genus Ellipsidion is not convincing
> evidence!) So,
> > here we have a problem in which good, solid data, already on GBIF, can be
> > removed by the actions of a single stubborn and misguided iNat user.
> This does
> > not lead to an improvement in data quality over time, quite the
> > reverse!Cheers, Stephen
> >    On Saturday, 25 December 2021, 09:11:10 am NZDT, Mark Egger via
> > Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
> >
> >  As a “curator” for a few genera of flowering plants of iNaturalist, I
> would urge
> > great caution in assessing the reliability of “data harvests” from the
> site,
> > even/especially for “Research Grade” observations. In the genera I
> monitor, I
> > very frequently come across RG identifications that are clearly
> incorrect. This
> > stems from the fact that one inexperienced user can “confirm” a machine-
> > generated suggestion, and then this faulty identification can be
> confirmed by
> > an equally inexperienced observer, often a friend of the original
> poster. That’s
> > all that is needed to make an observation RG! I’ve seen cases where an
> > obviously incorrect identification has been confirmed by as many as 4 or
> 5
> > users. Of course, herbarium specimens are subject to incorrect
> identifications
> > as well and still end up in public databases, but the sheer number of
> > observations coming  in daily to iNaturalist makes it particularly
> subject to
> > these sorts of errors, especially when a certain percentage of the
> posters don’t
> > seem able to distinguish a red fall leaf from a red-colored
> inflorescence. While
> > curators find and correct many such cases, many more undoubtedly escape
> > timely detection.
> >
> > That being said, iNaturalist is a wonderful tool for collecting
> observations from
> > regions that are understudied, and real discoveries can be made there.
> For
> > instance, I’ve seen posts of what are clearly undescribed or little-known
> > species, especially from Mexico. But the fact remains that bulk data
> imports
> > from iNat should be analyzed carefully prior to using them, especially
> for
> > distributional studies. And it is also vital to understand that the
> label of RG
> > does not at all mean that the identification has been made by experts in
> the
> > given group. Sometimes this is the case, but in many others it is
> definitely not.
> >
> > Mark
> >
> > > On Dec 24, 2021, at 10:00 AM, taxacom-request at mailman.nhm.ku.edu
> > wrote:
> > >
> > > Daily News from the Taxacom Mailing List
> > >
> > > When responding to a message, please do not copy the entire digest into
> > your reply.
> > > ____________________________________
> > >
> > >
> > > Today's Topics:
> > >
> > >  1. Re: A question for GBIF regarding data harvests from
> > >      iNaturalist (Alec McClay)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Fri, 24 Dec 2021 12:17:47 -0500
> > > From: Alec McClay <alec.mcclay at shaw.ca>
> > > To: taxacom at mailman.nhm.ku.edu
> > > Subject: Re: [Taxacom] A question for GBIF regarding data harvests
> > >    from    iNaturalist
> > > Message-ID: <eccd6f76-0c80-8ea0-8ce2-6a09189a75b3 at shaw.ca>
> > > Content-Type: text/plain; charset=UTF-8; format=flowed
> > >
> > > According to this discussion on the iNaturalist forum
> > >
> https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforum.inaturalist.org%2Ft%2Fobservations-of-cultivated-plants-on-g&data=04%7C01%7Cfordk%40landcareresearch.co.nz%7C4dfd9ae9c2714f0495dd08d9c72e1127%7C43050530b3c74cd2a11cb826b2604b5b%7C0%7C0%7C637759822955406554%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=8izqVncvv%2BMR1x1B4R3TkwxYSK5eBlZWOo3HfuCUQ6E%3D&reserved=0
> > > bif/5296/4 (from someone who works for GBIF) "For the record, the good
> > > iNat folks control what goes in the dataset that we ingest. If they
> > > add/update/delete a record, we do the same when ingesting".
> > >
> > > Merry Christmas and Happy New Year to all.
> > >
> > > Alec.
> > >
> > > On 2021-12-23 1:00 p.m., taxacom-request at mailman.nhm.ku.edu wrote:
> > >> Date: Wed, 22 Dec 2021 20:35:02 +0000 (UTC)
> > >> From: Stephen Thorpe<stephen_thorpe at yahoo.co.nz>
> > >> To:"jmiller at gbif.org"  <jmiller at gbif.org>,  Taxacom
> > >>    <taxacom at mailman.nhm.ku.edu>
> > >> Subject: [Taxacom] A question for GBIF regarding data harvests from
> > >>    iNaturalist
> > >> Message-ID:<1223057220.1448512.1640205302753 at mail.yahoo.com>
> > >> Content-Type: text/plain; charset=UTF-8
> > >>
> > >> Hi Joe,
> > >> As you know, GBIF periodically harvests Research Grade observations
> from
> > iNaturalist. What isn't quite clear, but which I think would be well
> worth
> > clarifying, if you could, please, is what happens to observations which
> drop
> > back out of Research Grade? Do they drop out of GBIF at the next
> harvest? This
> > is important for the reason that there are two types of cases, and the
> > consequences are very different for observations of each type: (1)
> observations
> > of well-known species; and (2) observations reliant on expert IDs.
> > >> For type (1) observations, it can be reasonably assumed that dropping
> back
> > out of RG will rarely happen, and if it does happen for inadequate
> reasons,
> > then the community ID will be restored fairly quickly, since it involves
> a well-
> > known species that many iNat users are familiar with.
> > >> For type (2) observations, however, IDs may be based on just a couple
> of
> > experts. An RG observation of this kind can be dropped out of RG by any
> iNat
> > user, who chooses to disagree for whatever reason, be it scientific or
> personal
> > or whatever. The lack of further experts means that RG is likely not to
> be able
> > to be restored very easily!
> > >> So, my question is, for type (2) observations that were RG long
> enough to
> > have been harvested by GBIF, if they subsequently drop out of RG on
> iNat, do
> > they drop out of GBIF at the next data harvest? If so, then data already
> in GBIF,
> > harvested from iNat, is vulnerable to the whims of single users on iNat,
> which,
> > to my mind at least, is a concern!
> > >> Cheers, Stephen
> > >
> > > --
> > > Alec McClay
> > > 12 Roseglen Private
> > > Ottawa, ON K1H 1B6
> > > Canada
> > > 613-739-8499 (home)
> > > 343-988-4077 (mobile)
> > >
> > >
> > >
> > > ------------------------------
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> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
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> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
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