Author of taxon name not visible in ID on catalog record

[DerekSikes]

Issue Documentation is http://handbook.arctosdb.org/how_to/How-to-Use-Issues-in-Arctos.html

Describe the bug A clear and concise description of what the bug is.

Previously the author_text of a taxon name would appear in the classification list but it no longer does:

eg https://arctos.database.museum/guid/UAM:Ento:335179 Identifications [ expand ] Edit Idolus debilis Animalia, Protostomia, Ecdysozoa, Arthropoda, Hexapoda, Insecta, Pterygota, Holometabola, Coleoptera, Polyphaga, Elateriformia, Elateroidea, Elateridae, Elaterinae, Pomachiliini, Idolus, Idolus debilis Identified by Hume Douglas on 2019-05-01 Nature of ID: features Confidence: high

It should look like: https://arctos.database.museum/guid/UAM:Ento:335179 Identifications [ expand ] Edit Idolus debilis Animalia, Protostomia, Ecdysozoa, Arthropoda, Hexapoda, Insecta, Pterygota, Holometabola, Coleoptera, Polyphaga, Elateriformia, Elateroidea, Elateridae, Elaterinae, Pomachiliini, Idolus, Idolus debilis (LeConte, 1884) Identified by Hume Douglas on 2019-05-01 Nature of ID: features Confidence: high

Priority medium

[dustymc]

I tacked display_name on and manually refreshed https://arctos.database.museum/guid/UAM:Ento:335179.

It would be useful if you could refresh a few more to make sure that's doing what you want.

I can set small chunks of records to refresh, if you want everything it should be scheduled - that would take several days of processing.

[DerekSikes]

What does

"It would be useful if you could refresh a few more to make sure that's doing what you want."

mean

https://arctos.database.museum/guid/UAM:Ento:335179.

looks fine now.

& please go ahead and schedule to do all.

thanks, Derek

On Tue, May 18, 2021 at 1:37 PM dustymc @.***> wrote:

I tacked display_name on and manually refreshed https://arctos.database.museum/guid/UAM:Ento:335179.

It would be useful if you could refresh a few more to make sure that's doing what you want.

I can set small chunks of records to refresh, if you want everything it should be scheduled - that would take several days of processing.

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+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

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[dustymc]

mean

Click this:

wait a minute (or check...

... status), refresh, confirm it's doing what it's supposed to be doing.

schedule

@ArctosDB/arctos-working-group-officers this will mean about a week of updates, including new records from the bulkloader, not being processed. I can kick the update off at any time. Help!

[ewommack]

@ArctosDB/arctos-working-group-officers this will mean about a week of updates, including new records from the bulkloader, not being processed. I can kick the update off at any time. Help!

Like no nothings comes up from the bulkloader to be added to any collection while this is processing?

[dustymc]

The bulkloader will still run, but things will take a while to be processed into FLAT and visible in the UI.

[ewommack]

The bulkloader will still run, but things will take a while to be processed into FLAT and visible in the UI.

Like I upload something, and come back after 15 minute coffee; or I upload something and come back after the weekend?

[dustymc]

From taxon committee meeting: we should do more with display_name.

Possibility:

1. un-do the 'tack display_name onto full_taxon_name' thing
2. Display display_name separately from (above, maybe) full_taxon_name (on specimendetail)

Yay everybody, no giant updates involved?

@DerekSikes @Jegelewicz @sharpphyl

[DerekSikes]

If this works to display author names without a need for giant updates, great!

-D

On Wed, May 19, 2021 at 12:33 PM dustymc @.***> wrote:

From taxon committee meeting: we should do more with display_name.

Possibility:

1. un-do the 'tack display_name onto full_taxon_name' thing
2. Display display_name separately from (above, maybe) full_taxon_name

Yay everybody, no giant updates involved?

@DerekSikes https://github.com/DerekSikes @Jegelewicz https://github.com/Jegelewicz @sharpphyl https://github.com/sharpphyl

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+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[dustymc]

For next release:

[Jegelewicz]

Reopening because the changes we have made to classification metadata may mean that "display name" is not always built correctly.

Because many classification (from WoRMS) place the author text in "authority", these do not get added to the "display name", which I believe is a concatenation of taxon name and "author_text".

[wellerjes]

Would love to have the author show up in the identification. I've had researchers give me their identifications that included the author with the taxon name, so it is standard in the research world. It gives an extra level of authority on the catalog record page, instead of having to click to the taxonomy page for more information.

[Jegelewicz]

I've had researchers give me their identifications that included the author with the taxon name

HMMMMM - a very specific identification. The way Arctos works, there is a distinct possibility that the author name you get with a classification may not match the one that shows up (if it shows up) in display name....

[campmlc]

I've been thinking for awhile we need a verbatim ID field. . . I've been putting this in Identification remarks.

On Thu, Jul 14, 2022, 3:46 PM Teresa Mayfield-Meyer < @.***> wrote:

• [EXTERNAL]*

I've had researchers give me their identifications that included the author with the taxon name

HMMMMM - a very specific identification. The way Arctos works, there is a distinct possibility that the author name you get with a classification may not match the one that shows up (if it shows up) in display name....

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[Jegelewicz]

BUT - that does not negate the need for what we are talking about here.

[dustymc]

"display name" is not always built correctly.

Almost certainly true, absolutely inevitable as we move towards https://github.com/ArctosDB/arctos/issues/3311 (which also seems inevitable despite our best efforts to ignore it!).

need a verbatim ID field. . . I've been putting this in Identification remarks.

IDs are verbatim taxonomy, sorta. You're not required to share any strings, although it's perhaps easier to do so (eg by just reusing the taxon name). Display_name was mostly an attempt to magic more than the bare name into the identification, but I think we've entirely outgrown the idea.

The easy solution seems to be just using A {string} IDs, spelled however you want (eg including authors, years, cryptic abbreviations, whatever). Requests for tools to simplify that are most welcome.

[sharpphyl]

Can we just make the display name look the same whether the taxon source is Arctos or WoRMS (via Arctos)?

Arctos Display Name

WoRMS (via Arctos) Display Name

[dustymc]

Can we just make the display name look the same

https://github.com/ArctosDB/arctos/issues/3609#issuecomment-1187696719, I don't think we can reliably build display_name for "local" classifications, less-local are even more unlikely.

I am grabbing display name (when available) and putting it into FORMATTED_SCIENTIFIC_NAME, which is what gets displayed as above, and I could add other term types to that list. BUT, WoRMs seems to be doing something "interesting" with 'name string' so that will end up as some random choice or a concatenation or something of the sort - I've got to stuff two (in your screenshot) into one somehow. I'll need further instructions.

That still seems fairly fragile, if you want the identification to read as something other than the default then you should just construct it that way.

[sharpphyl]

@dustymc I may not understand how you create the display name, but can we return to the original request to show the display name as the taxon name plus the "authority" for WoRMS (via Arctos) classifications instead of "author_text." For the collections using WoRMS (via Arctos) as the first source, the catalog records show no author in the display name. It makes it look like the taxon name is just repeated for no reason in light gray under the linked taxon name. Additionally the author doesn't show anywhere in the catalog record and, as pointed out by others, that can be helpful data.

[Jegelewicz]

@dustymc for WoRMS (via Arctos) use name string as the display_name. When there are two or more name_string values, just concatenate them separated by pipes.

Workable in some way?

[dustymc]

Workable in some way?

I really don't think so. Calculating taxa-stuff is already insanely complicated, we no longer require the stuff that's required to build display_name, etc., etc., etc. - I still think we've completely outgrown the idea that I can somehow know what you wished you could have said, and we now have the model under which you can just say whatever you want to.

I'm willing to try WHATEVER, I'm just relatively certain it's going to be a lot of work that ultimately makes your data worse (less consistent, less predictable), Arctos harder to understand (magic name comes from where?), etc.

I think we would be a lot better off investing in eg building A {string} identifications from stuff in taxonomy - something that YOU control, where you can see if it meets expectations, looks like other stuff, etc., etc.

I'm also not very interested in explaining to some potential collaborator that stringing a bunch of the wrong things together with pipes is some sort of default Arctos behavior.

I feel like maybe what I'm trying to say isn't coming across somehow, I've said it a few ways, maybe this needs to be resolved via zoom?

[sharpphyl]

I think we would be a lot better off investing in eg building A {string} identifications from stuff in taxonomy - something that YOU control, where you can see if it meets expectations, looks like other stuff, etc., etc.

Can you explain this step further? I'd build a string that says Conus marmoreus {Linnaeus, 1758}?

[dustymc]

I'd build a string that says Conus marmoreus {Linnaeus, 1758}

https://handbook.arctosdb.org/documentation/bulkloader.html#taxonomy

https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxa_formula

Yes, strings of whatever format which point to taxa have long been an option.

I'm suggesting tools to make that process easier, whatever those might look like, make more sense than trying to magic fancy stuff out of data which almost certainly don't support magicking fancy stuff after the fact.

[DerekSikes]

I don't like this A string idea. It's a path to even less consistency than we currently have.

If a record in taxonomy has data in the author field that should appear on the identification record after the name. What's the problem?

-Derek

On Thu, Aug 4, 2022 at 10:07 AM dustymc @.***> wrote:

I'd build a string that says Conus marmoreus {Linnaeus, 1758}

https://handbook.arctosdb.org/documentation/bulkloader.html#taxonomy

https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxa_formula

Yes, strings of whatever format which point to taxa have long been an option.

I'm suggesting tools to make that process easier, whatever those might look like, make more sense than trying to magic fancy stuff out of data which almost certainly don't support magicking fancy stuff after the fact.

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+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[Jegelewicz]

What's the problem?

The classification data pulled in from WoRMS doesn't have an "author_text", instead it includes a name string that is the whole taxon name - and sometimes as in the example above, there is more than one (this one is due to a subgenus). This complicates the building of "display_name".

[DerekSikes]

Ah, thanks Teresa,

Sounds like rather than have Dusty create weird scripts to magic these author names into identifications we need to get them into the correct author name field in taxonomy somehow. Perhaps a way for users to download worms data from arctos taxonomy, parse out the author names themselves, and re-upload the data so the arctos author name field is properly filled in?

But I don't really understand the whole worms-arctos data situation so this might not make any sense.

-Derek

On Thu, Aug 4, 2022 at 12:03 PM Teresa Mayfield-Meyer < @.***> wrote:

What's the problem?

The classification data pulled in from WoRMS doesn't have an "author_text", instead it includes a name string that is the whole taxon name - and sometimes as in the example above, there is more than one (this one is due to a subgenus). This complicates the building of "display_name".

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--

+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 @.*** phone: 907-474-6278 he/him/his University of Alaska Museum https://www.uaf.edu/museum/collections/ento/

• search 357,704 digitized arthropod records http://arctos.database.museum/uam_ento +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

[Jegelewicz]

Perhaps a way for users to download worms data from arctos taxonomy, parse out the author names themselves, and re-upload the data so the arctos author name field is properly filled in?

This would be thousands upon thousands of names - and every time there is a refresh from WoRMS - it would need to be re-done. It just isn't an option as far as I am concerned.

The thing is using the name_string as display name will work a lot of the time? Only in cases where there are more than one name_string does it be come an issue and @dustymc hates my solution for that, so here we are...

[sharpphyl]

I still think the issue how the "display name" is created. It appears that display_name is a concatenation of the "taxon name" and the "author_text." But the new (a few months ago) version of WoRMS (via Arctos) doesn't modify the WoRMS term "authority" to read "author_text," so the display name doesn't find the author. Here is another comparison showing the difference.

Can the code be modified to combine the "author_text" and/or "authority" so that the author will be included in the display name?

[dustymc]

I don't know how I'm being unclear, but it seems that I am. We literally accept any string from any source. There's nothing predictable in the data. I can't find order in chaos, because it does not exist. https://github.com/ArctosDB/arctos/issues/3311 seems inevitable and will be a huge multiplier of this type of thing.

Display_name also relies on nomenclatural_code and predictable ranks, neither of which can be expected to exist in data that I don't control.

MAYBE I could do something with some huge number of 'if ... then' statements, but that does not seem at all sustainable, even if it can be made to work now, which I doubt.

This is a (relatively minor, I think) component of https://github.com/ArctosDB/arctos/issues/3498. Can we look for a big-picture sustainable solution instead of chasing details?

[sharpphyl]

I promise this is my last attempt to explain - and yes, this is relatively minor compared to the other issues. All I want is for the display_name to look like it used to look before we went to a new format for WoRMS (via Arctos) metadata. (I'm not sure that's the same problem Derek had when he opened this issue.)

Example: This is the WoRMS (via Arctos) entry for Odobenus rosmarus before being refreshed. The display_name shows the scientific name and the author.

Here is the WoRMS (via Arctos) entry for Odobenus rosmarus after it's refreshed which modifies the metadata to the new format.

Can you make the display name look the way it used to look - that is show the scientific name and author which will then appear in the catalog record. Without the author it looks like the scientific name is being repeated in light gray under the blue link for no purpose.

[dustymc]

before being refreshed

Note the presence of author_text and nomenclatural_code

after it's refreshed

... and at which point it can contain anything, because we have grown way past the point where I have enough control over classifications to require the things I need to do ANYTHING predictable, including building display_name

Can you make the display name look the way it used to

I cannot, or at least I don't see a way to.

Without the author it looks like the scientific name is being repeated in light gray under the blue link for no purpose.

Yea, I seem to still be trying to build display name, failing (because I don't have the information needed), then falling back to something that probably just adds confusion. That should be removed. I'm hoping to find a useful alternative approach here.

not sure that's the same problem Derek had when he opened

Yes but not exactly - different problem (something was stuck), same root cause (there is no required data, trying to find predictable things to make fancy formats isn't going to work very often).

[sharpphyl]

I cannot, or at least I don't see a way to.

OK. @DerekSikes should decide whether or not to close this issue.

[Jegelewicz]

Can you make the display name look the way it used to

I cannot, or at least I don't see a way to.

We talked about this today in taxonomy committee and it is problematic that we are losing important information. So here is an idea.

• If you want the information on your records, you need to add authority to the metadata of your preferred taxonomy source.
• display_name will be built as taxon name authority

While this may not work forever, it will work for now. WoRMS (via Arctos) puts author text into "authority". If we match that, then most display names should build correctly. Not the ultimate solution, but a working one.

My alternative suggestion is that we need 2 different kinds of metadata associated with classifications: imported (no controlled vocaulary) and managed - with controlled vocabulary for terms that allows us to add author_text and whatever other things are needed by Arctos users.

[campmlc]

I support this. The need to add unambiguous author text citations to names is increasingly being recognized globally. Guidelines cetaf epublishing def.pdf

[dustymc]

If you want the information on your records, you need to add authority to the metadata of your preferred taxonomy source.

We need to have a blank-slate conversation regarding display_name; I'm about 99% sure that whatever you're suggesting won't do whatever you think it'll do.

[Jegelewicz]

Closing in favor of a new, focused issue.