Taxon Status #1805
Comments
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What are we trying to do here? I thought we were moving away from "someone at some point liked this for some purpose" and towards "use this for THAT." |
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I am trying to use standard language used by taxonomists. Apparently animal people use valid/invalid and plant people use accepted/unaccepted. From ITIS:
And I am trying to move away from "someone at some point liked this for some purpose" and towards "use this for THAT." See #1806 |
See #1136 - I've gone exactly the other way. Those things flip-flop around in the literature for decades (centuries??), and often it requires an "expert" to make sense of them - which of course opens the door for another "expert" to come up with a different conclusion. "This good, that bad" probably makes taxonomists twitchy, but it's also usable by we mere mortals!
That's not going to happen. (And FWIW attempts to implement "acceptedness" are a huge part of the reason we're where we are instead of plugged into something like ITIS.) The folks in some collections that use Arctos have reviewed the current literature (or pulled out the ouija board or whatever happens in taxonomy-land...) and decided that woodfrog is spelled "Rana." Other collections have performed their own rituals and decided that woodfrog is spelled "Lithobates." The situation isn't uncommon. I don't think Arctos should ever put itself in the position of trying to dictate taxonomy to Curators. |
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Well, we can go out on a limb and create all of our own versions of "acceptedness" and we will just add to the chaos. If we did this correctly, both Rana and Lithobates could be "valid/accepted" and labeled as synonyms of each other through the Taxon Relation table. |
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At least sometimes I think I hear ya'll saying that "useful" involves someone working for some collection knowing exactly what to do when handed a woodfrog. That's not in the literature - it flip-flops and some of us ignore some of that or something. Throwing "accepted!" on everything that woodfrogs have ever been called is functionally identical to not doing anything. If I'm understanding anything, and I'm not so sure of that, we need "accepted by ABC:ZYX." That of course has nothing to do with taxonomy, and not really even identifications, but I don't have a better place for "hey you, click here." |
Yes, I think we might need that in the shared taxonomy world. However, in Phyllis' case (and what I am attempting to use these code tables for), she isn't telling anyone what her collection accepts (she is not a malacologist) she is attempting to follow what appears to be accepted by the community (beyond Arctos) in order to bring some consistency to her use of taxonomy and make her data play well with others (GBIF, iDigBio). I think if you look at it as if she were choosing to use WoRMS for her taxonomy, then any time someone edited a taxon in WoRMS to change its "acceptedness", she would just get that from them, correct? (If we do some sort of linking with them this will happen as well...) There may be users in the Arctos community who are attempting to tell someone doing data entry which taxon to use in their collection. If that is the case, perhaps we do need a non-classification field that lets each collection select a preferred taxa when there are several variants. Not sure how this would work. It seems to be super complicated and maybe if a collection prefers certain terms the best option is for them to create and maintain their own taxonomy (but I'm pretty sure no one wants to do that...) |
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And FWIW in the case of
I'm pretty sure that they will be given the name "Rana" or "Lithobates" and not "woodfrog" so as long as both are in Arctos, data entry should not be a problem. |
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See how Lithobates catesbeianus and Rana catesbeiana are set up. |
Maybe "accepted by WoRMS" does what we need? Certainly more palatable than "accepted by the curator of some obscure collection that you've never heard of" and if the collections can just instruct their folks to use WoRMS over something else or similar maybe that gets us to the same place.
That is NOT what I'm hearing. IDK what's on the label, but CollectionA would do one thing and CollectionB the other for the same critter with the same data.
I think at least one collection in Arctos would just consider that wrong - they consider Rana valid/something they want to use, we have it marked as invalid. |
That's perfectly fine. Both can exist in Arctos and if the relationship is set, then anyone should be able to find/use both, correct?
Valid/invalid DOES NOT indicate whether you should use it or not, just that there is a community that has made that determination as indicated in the SOURCE_AUTHORITY. In taxonomy, there is no "wrong" apparently. Anyway, based upon what you have said above, we can't call ANY taxon "invalid" as there will almost assuredly be SOMEONE who thinks it is valid, otherwise it wouldn't be here... Shouldn't TAXON_STATUS be accompanied by the SOURCE_AUTHORITY and a DATE? And shouldn't they reflect the status from the source the classification was taken? ITIS lists Rana catesbeiana as "invalid" and that is where I took the term from. This SHOULD NOT be an arbitrary term set by whoever creates the classification (in my non-taxonomic professional opinion). If someone can find an authority that lists it as accepted, well then they can change this. It will, however, still be a synonym of Lithobates catebeianus. (At least it should be set that way if we want people to be able to find stuff that could be called either name, but are really the same thing.) |
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Taxon Status (or something like it) is for "us." Regardless of source or date, for whatever reason maybe I don't want my students using some name for data entry and you do. I don't think that's possible with binary acceptedness terms. We need something like status=preferred/accepted/whatever by me which will be visible in the taxa pick box, and a relationship to get everyone else to the specimens from either term. I don't care who created anything or where it came from, I just want a flag in the data entry app pointing my students to my preferred term.
Exactly - and anything that asserts such therefore has extremely limited usefulness. We are here talking about this instead of just using ITIS as a taxonomy source because they list Rana catesbeiana as "invalid." "Suitable for {use} according to {something}" seems to work, get more authoritative than that and it seems to always find a way to do something that some Curator isn't willing to deal with. |
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How about "accepted by: collection name"? That way MSB Herps can choose
Lithobates and MVZ can choose Rana, both can be accepted, and students can
choose the one that applies to their collection. Each collection can
choose which set of names they prefer, and the valid names are linked as
synonyms.
…On Thu, Nov 22, 2018, 9:44 AM dustymc ***@***.*** wrote:
At least sometimes I think I hear ya'll saying that "useful" involves
someone working for some collection knowing exactly what to do when handed
a woodfrog. That's not in the literature - it flip-flops and some of us
ignore some of that or something. Throwing "accepted!" on everything that
woodfrogs have ever been called is functionally identical to not doing
anything. If I'm understanding anything, and I'm not so sure of that, we
need "accepted by ABC:ZYX."
That of course has nothing to do with taxonomy, and not really even
identifications, but I don't have a better place for "hey you, click here."
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It seems like I am not making my point very well. The TAXON_STATUS field should be filled from the related field found in the SOURCE_AUTHORITY's data. It is not making ANY assertion about whether or not anyone in Arctos should or should not use it. We need something else to do
And I don't think it should refer to "accepted" . I like the term "preferred" but here's the rub. Where do you record that? Will each collection have to go through and select "preferred for all the taxa they want to use? This really seems like we are talking about something that just isn't going to happen. If a curator is giving a student stuff to catalog that is identified as "wood frog" then they aren't doing their job in the first place and they deserve whatever they get. Rana and Lithobates are both in Arctos, if the Curator applies a scientific name, then the student will select the name they have been asked to enter. Accepted is not something any of us decides, it comes from what is hopefully and expert who is maintaining the taxon at the SOURCE_AUTHORITY. We can always choose to ignore it, but I don't think we should assert it. |
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You are proposing a fundamental change to the nature of what we've discussed and done with that concept. We can add a new concept to hold "source's status flag" or whatever this is, perhaps we can even add things to cttaxon_status, but there's been a lot of discussion and code getting us to where we are and I'm not going to abandon that without good reason. |
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Is anyone opposed to changing "invalid" to "invalid/unaccepted" and "valid"
to "valid/accepted"?
I'm not.
I also don't understand most of what Dusty has been complaining about. I
thought we were all in agreement on this stuff, but apparently not?
It makes sense that a name's validity should have an 'according to' source
field (this is the very basis of the Taxon Concept approach), and also
makes sense that we should be able to have more than one of those for folks
who want to record a name as both valid according to X and invalid
according to Y.
Names are words and words are meaningless without their definitions (by
definition!). Some have multiple, even contradictory, definitions. We need
to know whose/which definitions were using when we use these words.
I would go so far as to say that *Nicrophorus vespilloides Herbst 1783
sensu Anderson & Peck 1985* should have a different SCINAME record
than *Nicrophorus
vespilloides Herbst 1783 sensu Sikes et al. 2016* since the definition of
the species (and distribution of the populations) is quite different. But I
haven't thought this through, and don't know what plans are afoot for
implementing taxon concepts in Arctos.
I should also add that most (90%+) junior synonyms (invalid) names have
been invalid for a long time and are likely to remain so. There is always a
small % of names flip flopping and competing classifications (eg Rana vs
Lithobates) in play but these are a pittance compared to the vast hoards of
old, invalid names. In my group of beetles there are over 300 species group
names for 70 species. After I published a catalog and cleaned up these
names there remains only 1 pair of names that the community still seems
confused about. Once those curators (or name servers) get the message that
they're using an invalid name and switch to the valid name (sensu Sikes et
al 2002) all those invalid names should become of historical interest only,
and not used for tracking current biodiversity data.
…-Derek
On Fri, Nov 23, 2018 at 7:54 AM dustymc ***@***.***> wrote:
You are proposing a fundamental change to the nature of what we've
discussed and done with that concept. We can add a new concept to hold
"source's status flag" or whatever this is, perhaps we can even add things
to cttaxon_status, but there's been a lot of discussion and code getting us
to where we are and I'm not going to abandon that without good reason.
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I'm just trying to pass on what I think I've heard from Curators. I think the conversation where I thought I finally "got it" was with @ccicero so maybe Carla can chime in here. The use case is a pair of names and a bunch of publications... A-->accepted variant of--->B etc. so that "current" (or accepted or whatever) isn't obvious from the literature - everything had a turn as "accepted." A flag in the data (code has been written around taxon_status) would then be used to flag one of those as "current" (or preferred or whatever we call it). In some cases (the Rana/Lithobates situation, I think) some Curators don't accept some of the literature while others do, and having more than a binary "accepted/unaccepted" in the flag facilitates that complexity. In the case of "A-->accepted variant of--->B" (that's it) I don't think we need taxon status at all - everything you need to pick one is in the literature/relationships. (But maybe the extra step of creating status has some value anyway - it's available there too if someone wants to use it.) Adding authors to names is #1803. In the current implementation, Nicrophorus vespilloides Herbst 1783 sensu Sikes et al. 2016 is the intersection of three things:
I think that's roughly the same end result as "taxon concepts" (the assertion is ~"that name under that classification as understood by author") but it does it with many fewer data objects. |
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We do need to hear from Carla and any other curators who might have an
opinion on this. However, I know of very few curators who are engaged with
the daily business of managing taxonomy and even fewer who are working to
manage taxonomy in Arctos. The task has fallen to the collection managers
who work daily with specimens and their data. It appears from the previous
threads and issues that all the collection managers who have responded are
in agreement, and we do not understand the difficulties in implementing the
changes being requested which are necessary to correct significant problems
in our current model that make our data unreliable and our jobs difficult.
We need solutions to these problems as soon as possible, even if they are
solutions in progress as we work all this out.
…On Fri, Nov 23, 2018 at 11:17 AM dustymc ***@***.***> wrote:
what Dusty has been complaining about
I'm just trying to pass on what I think I've heard from Curators. I think
the conversation where I thought I finally "got it" was with @ccicero
<https://github.com/ccicero> so maybe Carla can chime in here. The use
case is a pair of names and a bunch of publications...
A-->accepted variant of--->B
B-->accepted variant of--->A
(maybe some more going back and forth)
etc. so that "current" (or accepted or whatever) isn't obvious from the
literature - everything had a turn as "accepted." A flag in the data (code
has been written around taxon_status) would then be used to flag one of
those as "current" (or preferred or whatever we call it). In some cases
(the Rana/Lithobates situation, I think) some Curators don't accept some of
the literature while others do, and having more than a binary
"accepted/unaccepted" in the flag facilitates that complexity.
In the case of "A-->accepted variant of--->B" (that's it) I don't think we
need taxon status at all - everything you need to pick one is in the
literature/relationships. (But maybe the extra step of creating status has
some value anyway - it's available there too if someone wants to use it.)
Adding authors to names is #1803
<#1803>. In the current
implementation, Nicrophorus vespilloides Herbst 1783 sensu Sikes et al.
2016 is the intersection of three things:
- Nicrophorus vespilloides is a name (and might refer to jellyfish or
something as well as insects)
- Herbst 1783 comes from the collection's preferred classification
(which should exclude the jellyfish, at least most of the time)
- sensu Sikes et al. 2016 is part of Identification
I *think* that's roughly the same end result as "taxon concepts" (the
assertion is ~"that name under that classification as understood by
author") but it does it with many fewer data objects.
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That's often a useful tack and/or where I get lost - what are we trying to solve? I don't think any of this should be blocking anything else. Updating vocabulary (A-->B) is simple enough, even if it takes some time in taxon_term. That will cause complications with any data in the hierarchical editor as well and should be coordinated with anyone working there, but still not much of an issue (from my perspective anyway). I don't think anything about any vocabulary here precludes adding finer-grained terms later, but redefining taxon term (eg, to mean "thing from source") might. (And it's not clear to me how those data would be created or maintained, but that's a different problem.) |
Hallelujah! Hey @DerekSikes are all those updated names (and relationships to old names) in Arctos? If not, how can I facilitate getting them there? |
This pairs well with the Darwin Core definition:
I stand by my assertions that our TAXON_NAMES should include author and date. |
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DWC is dealing with identification.scientific_name. I have no problems with doing something different in identifications or mapping something different to DWC. (I suppose I don't have a problem with adding that stuff to taxon_name either, as long as we're all aware of the functional implications.) |
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Teresa,
Very few of the old names are in Arctos and I see no need to add them. I've
attached my 2002 catalog though, so you can see the work that would be
involved.
However, see the attached screenshot. The results of searching Arctos
taxonomy for name = Nicrophorus on the left and a list of Nicrophorus
species names on the right from my 2002 catalog.
Why not have the Arctos results return a little more information in those
search results? Why not add the taxon describer & year, and an indication
of whether the name is valid or not (and if not, what the senior name is),
or if unknown (like a nomen dubium) that could also be listed?
…-Derek
On Fri, Nov 23, 2018 at 11:54 AM Teresa Mayfield-Meyer < ***@***.***> wrote:
I know of very few curators who are engaged with the daily business of
managing taxonomy and even fewer who are working to manage taxonomy in
Arctos
Hallelujah!
Hey @DerekSikes <https://github.com/DerekSikes> are all those updated
names (and relationships to old names) in Arctos? If not, how can I
facilitate getting them there?
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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
dssikes@alaska.edu
phone: 907-474-6278
FAX: 907-474-5469
University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
<http://www.uaf.edu/museum/collections/ento/>
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Interested in Alaskan Entomology? Join the Alaska Entomological
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Your screenshot is MIA.
"Nobody's asked for it" is the usual answer. Issue please. |
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added screenshot |
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Agree - no reason to ADD any old names, but if any are already there, it would be good to create the appropriate relationships. Although, one day some collection will come into Arctos that is labeled with all the old names and whoever brings it in will decide to add them all (because like most of us they don't know the taxonomy, they are just tasked with "digitizing"). |
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Article in the last TREE on WoRMS might be of interest:
https://www.sciencedirect.com/science/article/pii/S0169534718301915
…-D
On Fri, Nov 23, 2018 at 2:57 PM Teresa Mayfield-Meyer < ***@***.***> wrote:
Agree - no reason to ADD any old names, but if any are already there, it
would be good to create the appropriate relationships.
Although, one day some collection will come into Arctos that is labeled
with all the old names and whoever brings it in will decide to add them all
(because like most of us they don't know the taxonomy, they are just tasked
with "digitizing").
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
dssikes@alaska.edu
phone: 907-474-6278
FAX: 907-474-5469
University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
<http://www.uaf.edu/museum/collections/ento/>
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It's behind a paywall. But the abstract is describing exactly what we need.... |
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It's just a promo piece on WoRMs but emphasizes some important traits of a good names database. I've attached the PDF. |
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And one of the authors, Andreas Kroh, is the person we're talking to tomorrow about accessing the entire WoRMS database to incorporate into Arctos. Thx Derek. |
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Derek, if you are interested in the WORMS call, it is through the Zoom link
at 8 am PST tomorrow.
…On Mon, Nov 26, 2018 at 2:39 PM Phyllis Sharp ***@***.***> wrote:
And one of the authors, Andreas Kroh, is the person we're talking to
tomorrow about accessing the entire WoRMS database to incorporate into
Arctos. Thx Derek.
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thanks, I'll pass
On Mon, Nov 26, 2018 at 2:46 PM Mariel Campbell <notifications@github.com>
wrote:
… Derek, if you are interested in the WORMS call, it is through the Zoom link
at 8 am PST tomorrow.
On Mon, Nov 26, 2018 at 2:39 PM Phyllis Sharp ***@***.***>
wrote:
> And one of the authors, Andreas Kroh, is the person we're talking to
> tomorrow about accessing the entire WoRMS database to incorporate into
> Arctos. Thx Derek.
>
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
dssikes@alaska.edu
phone: 907-474-6278
FAX: 907-474-5469
University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
<http://www.uaf.edu/museum/collections/ento/>
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Closing for issue consolidation. |
I am working to add appropriate definitions to the Taxon Status code table.
Is anyone opposed to changing "invalid" to "invalid/unaccepted" and "valid" to "valid/accepted"?
I propose this because WoRMS uses the terms accepted and unaccepted and ITIS defines taxon status as:
In this way, the status will reflect both possible versions of "accepted".
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