taxon name, formatting, and uniqueness

[dustymc]

https://arctos.database.museum/taxonomy.cfm?taxon_name=Liopistha

contains

Liopistha concentrica

and

Liopistha (Psilomya) concentrica

(and Liopistha (Psilomya) concentricia)

That feels WRONG to me - I don't think the inclusion of the subgenus changes the "taxon concept" enough to warrant a new name in Arctos. I doubt I can reliably prevent that behavior either.

• is this something we want to encourage/accept/tolerate?
• if not, what should we do about it?
• if so, can someone please document whatever it is that we're doing here?

(For whatever it's worth, I'd probably get rid of "traditional subgenus formatting" altogether. The inconsistent formatting makes creating hierarchies difficult, makes users guess what we've done to find specimens, and is indistinguishable from other "traditional" uses of that format.)

[campmlc]

In many cases, subgenera are eventually raised to genera. It is useful to be able to find records entered as either the subgeneric or generic status, as they may end up not being the same taxa.

…

On Fri, Sep 21, 2018 at 11:36 AM dustymc ***@***.***> wrote: https://arctos.database.museum/taxonomy.cfm?taxon_name=Liopistha contains Liopistha concentrica and Liopistha (Psilomya) concentrica (and Liopistha (Psilomya) concentricia) That feels WRONG to me - I don't think the inclusion of the subgenus changes the "taxon concept" enough to warrant a new name in Arctos. I doubt I can reliably prevent that behavior either. - is this something we want to encourage/accept/tolerate? - if not, what should we do about it? - if so, can someone please document whatever it is that we're doing here? (For whatever it's worth, I'd probably get rid of "traditional subgenus formatting" altogether. The inconsistent formatting makes creating hierarchies difficult, makes users guess what we've done to find specimens, and is indistinguishable from other "traditional" uses of that format.) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1704>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOH0hIQEbbHnVJnO7WqiEccueJg1Ndb2ks5udSN9gaJpZM4W0lg7> .

[DerekSikes]

Of course, if consistency was enforced somehow in our taxonomy table this would not be possible: Liopistha concentrica and Liopistha (Psilomya) concentrica Since the former is the same species as the latter. The only difference is the latter has more information. I think this is something we should discourage or if possible, prevent, if our goal was to curate the names in Arctos taxonomy to become a consistent single classification. However, I have no good ideas on how to prevent/discourage this under our current system. And I can see at least some advantages to allowing it - some collections might want to enforce subgenera for all their names and others might not want them at all. The Arctos taxonomy table is not, and likely will never be, a consistent single taxonomy - we've already made the point that flagging a name as valid /invalid should be collection specific so one collection can call a name invalid while another calls it valid. Not sure how this will be implemented but I think folks want that flexibility. Perhaps an automated relationship crawl that finds all names with identical spelling of genus & epithet (regardless of subgenus) and relates them somehow?

…

-Derek

On Fri, Sep 21, 2018 at 9:35 AM dustymc ***@***.***> wrote: https://arctos.database.museum/taxonomy.cfm?taxon_name=Liopistha contains Liopistha concentrica and Liopistha (Psilomya) concentrica (and Liopistha (Psilomya) concentricia) That feels WRONG to me - I don't think the inclusion of the subgenus changes the "taxon concept" enough to warrant a new name in Arctos. I doubt I can reliably prevent that behavior either. - is this something we want to encourage/accept/tolerate? - if not, what should we do about it? - if so, can someone please document whatever it is that we're doing here? (For whatever it's worth, I'd probably get rid of "traditional subgenus formatting" altogether. The inconsistent formatting makes creating hierarchies difficult, makes users guess what we've done to find specimens, and is indistinguishable from other "traditional" uses of that format.) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1704>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIraMwVTosUUn-aFr03tWIKWCwxdCQH0ks5udSN9gaJpZM4W0lg7> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 [email protected] 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/> +++++++++++++++++++++++++++++++++++ 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 <http://www.akentsoc.org/contact.php>

[dustymc]

@campmlc most all taxa are eventually changed, it's good to be able to find related things, this actively prevents that by ~doubling the number of records that have to be tracked down and linked up (or I don't understand something). No relationships were added with the recently-created names.

It's only necessary to find records entered by one of the variants if we allow the variants. Minimally, I'd like documentation here. "When encountering {situation that's preventing users from finding specimens at this very moment}, do {something that might somehow minimize that}." Ideally I'd like rules - "disallow parentheses in taxon_name.scientific_name" is absolutely where I'd go, but that's from the perspective of a data-shuffler and not a taxonomist. I'm asking ya'll where we can or should go with this.

Note also that display_name is automagically generated and what's generally displayed. Given taxon name=Bla bla+genus=Bla + subgenus=Bla + species=Bla bla I can show most users "Bla (Bla) bla" by slightly altering the code which generates display name.

former is the same species as the latter.

I guess that's the root of my question - is there some difference in something that we care about between the two, or is this entirely "tradition"? Eg, given two specimens, if there a defensible reason for someone to catalog one of them as "Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica"?

There's more discussion of string-variants and automation and "preferred" in #757.

[campmlc]

I may not be following completely, but if this is possible: "It's only necessary to find records entered by one of the variants if we allow the variants " Then that seems like a reasonable approach, e.g. similar to what we do with alternate agent names. We could have one taxon name, with "accepted/unaccepted" or "valid/invalid" variant names, which could include a subgeneric string? Then different collections could enter and display their version of choice?

…

On Fri, Sep 28, 2018 at 8:54 AM dustymc ***@***.***> wrote: @campmlc <https://github.com/campmlc> most all taxa are eventually changed, it's good to be able to find related things, this actively prevents that by ~doubling the number of records that have to be tracked down and linked up (or I don't understand something). No relationships were added with the recently-created names. It's only necessary to find records entered by one of the variants if we allow the variants. Minimally, I'd like documentation here. "When encountering {situation that's preventing users from finding specimens at this very moment}, do {something that might somehow minimize that}." Ideally I'd like rules - "disallow parentheses in taxon_name.scientific_name" is absolutely where I'd go, but that's from the perspective of a data-shuffler and not a taxonomist. I'm asking ya'll where we can or should go with this. Note also that display_name is automagically generated and what's generally displayed. Given taxon name=Bla bla+genus=Bla + subgenus=Bla + species=Bla bla I can show most users "Bla (Bla) bla" by slightly altering the code which generates display name. former is the same species as the latter. I guess that's the root of my question - is there some difference in something that we care about between the two, or is this entirely "tradition"? Eg, given two specimens, if there a defensible reason for someone to catalog one of them as "Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica"? There's more discussion of string-variants and automation and "preferred" in #757 <#757>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1704 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOH0hAPOX0AbDfVIIq0cshWo0-iZS1r7ks5ufjg5gaJpZM4W0lg7> .

[dustymc]

I think you may be mixing up names and classifications, but I'm not really sure of that either.

Agents are NOT analogous. I can name my poor kid 𓀉 𓃡 * aB1한글⌛ (Unicode is fun!) and you just have to deal with it. I very fortunately can't do that with taxonomy - we should (theoretically, anyway) be able to definitively say "that string does not appear as anything which might be considered a name in any publication which anyone might consider to be part of the taxonomic literature, so we won't accept it as a taxon name."

There are a couple million species-names in Arctos, and 97 of them have subgenus. Those are incredibly difficult to integrate with everything else. I see a few possibilities:

1. Do nothing, except maybe document that subgenera are weird and it's likely nobody will find your specimens if you use them.
2. Do something as names - allow subgenera, try to magic-link them to the "normal" format or add documentation or whatever.
3. So something in classifications and ban parentheses from taxon names. This could be fully automated (through display_name), or we could add some sort of "alternative namestring" concept, or whatever.

I think the best answer comes from the answer to

given two specimens, if there a defensible reason for someone to catalog one of them as "Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica"

and if that works the way I think/hope then (3) above is probably the best approach (which still doesn't mean it's what we have to do - maybe tradition wins??).

[campmlc]

From my perspective, the subgenus is not an essential part of the classification and could be part of display name or an alternate namestring. I deal with taxa with subgeneric identifications that will eventually need to be raised to genus level. As long as I can search on and find the all specimens assigned a particular name and its variants, it is not essential to me that the subgenus be included in the classification, and I would want any specimens cataloged as Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica" to be considered the same taxon in the same hierarchy. Not sure if that completely answers the question.

…

On Fri, Sep 28, 2018 at 9:52 AM dustymc ***@***.***> wrote: I think you may be mixing up names and classifications, but I'm not really sure of that either. Agents are NOT analogous. I can name my poor kid 𓀉 𓃡 * aB1한글⌛ (Unicode is fun!) and you just have to deal with it. I very fortunately can't do that with taxonomy - we should (theoretically, anyway) be able to definitively say "that string does not appear as anything which might be considered a name in any publication which anyone might consider to be part of the taxonomic literature, so we won't accept it as a taxon name." There are a couple million species-names in Arctos, and 97 of them have subgenus. Those are incredibly difficult to integrate with everything else. I see a few possibilities: 1. Do nothing, except maybe document that subgenera are weird and it's likely nobody will find your specimens if you use them. 2. Do something as names - allow subgenera, try to magic-link them to the "normal" format or add documentation or whatever. 3. So something in classifications and ban parentheses from taxon names. This could be fully automated (through display_name), or we could add some sort of "alternative namestring" concept, or whatever. I think the best answer comes from the answer to given two specimens, if there a defensible reason for someone to catalog one of them as "Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica" and if that works the way I think/hope then (3) above is probably the best approach (which still doesn't mean it's what we have to do - maybe tradition wins??). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1704 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOH0hP8Y_NZn3N_g-igv6nUfMKZf__0kks5ufkWpgaJpZM4W0lg7> .

[DerekSikes]

Perhaps this is too soon but I understand Arctos will eventually institute a formal way to manage Taxon Concepts. This might solve a lot of these problems. Basically, Liopistha concentrica, is a name but it can have many different concepts (different authors will define this name in different ways) - even if the higher classification is identical. I think in many cases we won't know which concept a name was applied under, although we could make some logical deductions based on dates (a concept published in 2006 couldn't have been the one used for a specimen identified to that name in 1980). Personally I don't want to use subgenera but I wouldn't want a system that prevents others from using them if they so choose. I also think we have to be careful about excluding parentheses (if this affects the parentheses around author names because those parentheses are very important - their presence means the species was described in a different genus than it is in currently). Arctos is very flexible and allows alternate classifications but we all want a way to (as easily as possible) make the classifications we use consistent.

…

-Derek On Fri, Sep 28, 2018 at 8:06 AM Mariel Campbell <[email protected]> wrote:

From my perspective, the subgenus is not an essential part of the classification and could be part of display name or an alternate namestring. I deal with taxa with subgeneric identifications that will eventually need to be raised to genus level. As long as I can search on and find the all specimens assigned a particular name and its variants, it is not essential to me that the subgenus be included in the classification, and I would want any specimens cataloged as Liopistha (Psilomya) concentrica" and the other as "Liopistha concentrica" to be considered the same taxon in the same hierarchy. Not sure if that completely answers the question. On Fri, Sep 28, 2018 at 9:52 AM dustymc ***@***.***> wrote: > I think you may be mixing up names and classifications, but I'm not really > sure of that either. > > Agents are NOT analogous. I can name my poor kid 𓀉 𓃡 * aB1한글⌛ > (Unicode is fun!) and you just have to deal with it. I very fortunately > can't do that with taxonomy - we should (theoretically, anyway) be able to > definitively say "that string does not appear as anything which might be > considered a name in any publication which anyone might consider to be part > of the taxonomic literature, so we won't accept it as a taxon name." > > There are a couple million species-names in Arctos, and 97 of them have > subgenus. Those are incredibly difficult to integrate with everything else. > I see a few possibilities: > > 1. Do nothing, except maybe document that subgenera are weird and it's > likely nobody will find your specimens if you use them. > 2. Do something as names - allow subgenera, try to magic-link them to > the "normal" format or add documentation or whatever. > 3. So something in classifications and ban parentheses from taxon > names. This could be fully automated (through display_name), or we could > add some sort of "alternative namestring" concept, or whatever. > > I think the best answer comes from the answer to > > given two specimens, if there a defensible reason for someone to catalog > one of them as "Liopistha (Psilomya) concentrica" and the other as > "Liopistha concentrica" > > and if that works the way I think/hope then (3) above is probably the best > approach (which still doesn't mean it's what we have to do - maybe > tradition wins??). > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#1704 (comment)>, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AOH0hP8Y_NZn3N_g-igv6nUfMKZf__0kks5ufkWpgaJpZM4W0lg7 > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1704 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIraM-EfKYT5KiJhv_W9x_z_TNkUTOn0ks5ufkkagaJpZM4W0lg7> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 [email protected] 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/> +++++++++++++++++++++++++++++++++++ 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 <http://www.akentsoc.org/contact.php>

[dustymc]

too soon

Na. I might not be able to implement something, but I can probably avoid painting myself into that particular corner if I know what ya'll are thinking.

use subgenera

I'm not proposing to eliminate subgenera from the model, just wondering if we can avoid the funky formatting - eg, move them from the name into the classification, like we've done with all other similar data.

parentheses around author names

Those are classification data. "Echidna" is the name, "Echidna Forster, 1788" is metadata of the name (eg, classification data).

consistent

A model which allows nothing else will do it!

Taxon Concepts

I've never quite figured out how that could be usably implemented from the taxonomy side. I think the botanists have this one correct: it's "identification concepts" and not taxonomy at all. That is, to the extent I understand the concept of taxon concepts, the same sort of THING, at least from a specimen/collection perspective: "this critter is a member of that group-of-critters according to how this publication circumscribes said group-of-critters" - but it does it without making the mess that is taxonomy into a messier mess. This has been implemented in Arctos for quite some time.

[dustymc]

Lacking further feedback, I'll move forward with this.

Ursus (Euarctos) will be deleted, and parentheses will be disallowed in taxon_name.scientific_name.

Nothing will change when subgenus is not included.

UAM@ARCTOSTE>  select generateDisplayName('1076622') from dual;

GENERATEDISPLAYNAME('1076622')
------------------------------------------------------------------------------------------------------------------------
<i>Ursus</i>

Euarctos will be created as a name. The classification for a subgenus-term should include genus.

Display name will be formatted in the traditional way:

UAM@ARCTOSTE>  select generateDisplayName('1ADFAF35-B80C-E3B7-29DF47F8A5FA241C') from dual;

GENERATEDISPLAYNAME('1ADFAF35-B80C-E3B7-29DF47F8A5FA241C')
------------------------------------------------------------------------------------------------------------------------
<i>Ursus (Euarctos)</i> Some Dude, Probably

Subgeneric terms will also generate "traditional" display name when subgenus is included.

 UAM@ARCTOSTE>  select generateDisplayName('97') from dual;

GENERATEDISPLAYNAME('97')
------------------------------------------------------------------------------------------------------------------------
<i>Ursus (Euarctos) americanus</i> Pallas 1780

UAM@ARCTOSTE> 
GENERATEDISPLAYNAME('1076623')
------------------------------------------------------------------------------------------------------------------------
<i>Ursus (Euarctos) americanus amblyceps</i>

If there are no objections or better ideas in ~a week, I'll move this to production.

Here are current subgenus-like names:

select scientific_name from taxon_name where scientific_name like '%(%';

SCIENTIFIC_NAME
------------------------------------------------------------------------------------------------------------------------
Anodontia (Anodontia) alba
Cassis (Echinophoria)
Chiton (Rhyssoplax) olivaceus
Galba (Galba) palustris
Lepidochitona (Lepidochitona) cinerea
Liopistha (Psilomya) concentrica
Liopistha (Psilomya) concentricia
Liopistha (Psilomya) elongata
Marginella (Prunum)
Neoechinorhynchus (Neoechinorhynchus)
Odostomia (Boonea) bisuturalis
Oxytropidoceras (Adkinsites) belknapi
Oxytropidoceras (Adkinsites) imlayi
Oxytropidoceras (Manuaniceras)
Oxytropidoceras (Manuaniceras) elaboratum
Oxytropidoceras (Oxytropidoceras) bravoensis
Paludina (Vivipara)
Pecten (Camptonectes) bubonis
Pecten (Pallium)
Potamides (Pirenella)
Sigaretus (Eunaticina) textilis
Symphynota (Lasmigona) costata
Ursus (Euarctos)
Vexillum (Costellaria)
Serpula (Cycloserpula) cragini
Fossarus (Gottoina) bella
Physa (Gyrina)
Alaria (Paralaria)
Alasmidonta (Pressodonta) calceola
Aporrhais (Perissoptera) prolabiata
Anchura (Drepanocheilus) mudgeana
Anchura (Drepanochilus) calcaris
Cardium (Granocardium) tippanum
Cardium (Trachycardium) longstreeti
Fulvia (Fulvia) laevigata
Mangilia (Pleurotomella) blakeana
Cucullaea (Idonearca) capax
Pedetontus (Verhoeffilis)
Fasciolaria (Piestochilus) galpiniana
Meretrix (Flaventia) belviderensis
Ostrea (Lopha) subovata
Diplopoma (Troschelvindex)
Clava (Clava) fasciata
Plagiola (Amygdalonaias) donaciformis
Plagiola (Amygdalonaias) elegans
Labiostomum (Eugenuris)
Astraea (Fissicella) denticulata
Turritella (Haustator) whitei
Turritella (Itaustator) whitei
Pachydiscus (Pachydiscus) kamishakensis
Plagiorchis (Plagiorchis)
Catostomus (Pantosteus) clarkii
Catostomus (Pantosteus) discobolus
Catostomus (Pantosteus) plebeius
Hexaplex (Trunculariopsis) princeps
Xenophora (Onustus) exuta
Lampsilis (Eurynia) iris
Lampsilis (Lampsilis) multiradiatus
Lampsilis (Proptera) alata
Lampsilis (Proptera) alatus
Lampsilis (Proptera) amphichaenus
Lampsilis (Proptera) inflata
Lampsilis (Proptera) purpuratus
Calliostoma (Jujubinus) exasperatum
Lymnaea (Galba)
Quadrula (Fusconaia) rubiginosa
Quadrula (Fusconaia) solida
Quadrula (Theliderma) asper
Quadrula (Theliderma) lachrymosa
Quadrula (Theliderma) sphaerica
Pterotrigonia (Scabrotrigonia) thoracica
Ischnochiton (Stenoradsia) conspicuus
Mortoniceras (Angolaites) wintoni
Aleochara (Calochara)
Nassa (Amycla) corniculum
Nassarius (Plicarcularia) jonasi
Hybodus (Leiacanthus)
Gryphaea (Texigryphaea)
Gryphaea (Texigryphaea) belviderensis
Gryphaea (Texigryphaea) navia
Gryphaea (Texigryphaea) pitcheri
Gryphaea (Texigryphaea) tucumcarii
Gryphaea (Texigryphaea) washitaensis
Alabastrina (Alabastrina)
Alabastrina (Alabastrina) subvanvincquiae
Alabastrina (Atlasica)
Alabastrina (Atlasica) aguergourensis
Alabastrina (Atlasica) interica
Alabastrina (Atlasica) tamanarensis
Alabastrina (Atlasica) tildiana
Alabastrina (Siretia)
Alabastrina (Siretia) pallaryi
Pleuriocardia (Dochmocardia) pauperculum
Pleurobema (Pleurobema) raveneliana
Elliptio (Elliptio) gibbosus
Amphidonte (Ceratostreon)
Amphidonte (Ceratostreon) texanum

97 rows selected.

and names which contain subgenus-bearing local classifications:

select scientific_name from taxon_name, taxon_term where taxon_name.taxon_name_id=taxon_term.taxon_name_id and
source in ('Arctos','Arctos Plants') and term_type='subgenus';

are https://docs.google.com/spreadsheets/d/144cwe4pPmcVduFye9ikn_J6Hty7OUtcAS8idNpgaAeM/edit?usp=sharing

[DerekSikes]

looks good to me,

…

-D

On Tue, Oct 2, 2018 at 10:33 AM dustymc ***@***.***> wrote: Lacking further feedback, I'll move forward with this. Ursus (Euarctos) will be deleted, and parentheses will be disallowed in taxon_name.scientific_name. Nothing will change when subgenus is not included. [image: screen shot 2018-10-02 at 11 18 57 am] <https://user-images.githubusercontent.com/5720791/46368403-fcff7800-c634-11e8-80f1-6d57918380f2.png> ***@***.***> select generateDisplayName('1076622') from dual; GENERATEDISPLAYNAME('1076622') ------------------------------------------------------------------------------------------------------------------------ <i>Ursus</i> Euarctos will be created as a name. The classification for a subgenus-term should include genus. [image: screen shot 2018-10-02 at 11 14 41 am] <https://user-images.githubusercontent.com/5720791/46368189-6af76f80-c634-11e8-8603-65e55160a593.png> Display name will be formatted in the traditional way: ***@***.***> select generateDisplayName('1ADFAF35-B80C-E3B7-29DF47F8A5FA241C') from dual; GENERATEDISPLAYNAME('1ADFAF35-B80C-E3B7-29DF47F8A5FA241C') ------------------------------------------------------------------------------------------------------------------------ <i>Ursus (Euarctos)</i> Some Dude, Probably Subgeneric terms will also generate "traditional" display name when subgenus is included. [image: screen shot 2018-10-02 at 11 21 42 am] <https://user-images.githubusercontent.com/5720791/46368557-5ff10f00-c635-11e8-8738-98ee03ccab4c.png> ***@***.***> select generateDisplayName('97') from dual; GENERATEDISPLAYNAME('97') ------------------------------------------------------------------------------------------------------------------------ <i>Ursus (Euarctos) americanus</i> Pallas 1780 [image: screen shot 2018-10-02 at 11 22 20 am] <https://user-images.githubusercontent.com/5720791/46368591-739c7580-c635-11e8-87ff-392c5036674b.png> ***@***.***> GENERATEDISPLAYNAME('1076623') ------------------------------------------------------------------------------------------------------------------------ <i>Ursus (Euarctos) americanus amblyceps</i> If there are no objections or better ideas in ~a week, I'll move this to production. Here are current subgenus-like names: select scientific_name from taxon_name where scientific_name like '%(%'; SCIENTIFIC_NAME ------------------------------------------------------------------------------------------------------------------------ Anodontia (Anodontia) alba Cassis (Echinophoria) Chiton (Rhyssoplax) olivaceus Galba (Galba) palustris Lepidochitona (Lepidochitona) cinerea Liopistha (Psilomya) concentrica Liopistha (Psilomya) concentricia Liopistha (Psilomya) elongata Marginella (Prunum) Neoechinorhynchus (Neoechinorhynchus) Odostomia (Boonea) bisuturalis Oxytropidoceras (Adkinsites) belknapi Oxytropidoceras (Adkinsites) imlayi Oxytropidoceras (Manuaniceras) Oxytropidoceras (Manuaniceras) elaboratum Oxytropidoceras (Oxytropidoceras) bravoensis Paludina (Vivipara) Pecten (Camptonectes) bubonis Pecten (Pallium) Potamides (Pirenella) Sigaretus (Eunaticina) textilis Symphynota (Lasmigona) costata Ursus (Euarctos) Vexillum (Costellaria) Serpula (Cycloserpula) cragini Fossarus (Gottoina) bella Physa (Gyrina) Alaria (Paralaria) Alasmidonta (Pressodonta) calceola Aporrhais (Perissoptera) prolabiata Anchura (Drepanocheilus) mudgeana Anchura (Drepanochilus) calcaris Cardium (Granocardium) tippanum Cardium (Trachycardium) longstreeti Fulvia (Fulvia) laevigata Mangilia (Pleurotomella) blakeana Cucullaea (Idonearca) capax Pedetontus (Verhoeffilis) Fasciolaria (Piestochilus) galpiniana Meretrix (Flaventia) belviderensis Ostrea (Lopha) subovata Diplopoma (Troschelvindex) Clava (Clava) fasciata Plagiola (Amygdalonaias) donaciformis Plagiola (Amygdalonaias) elegans Labiostomum (Eugenuris) Astraea (Fissicella) denticulata Turritella (Haustator) whitei Turritella (Itaustator) whitei Pachydiscus (Pachydiscus) kamishakensis Plagiorchis (Plagiorchis) Catostomus (Pantosteus) clarkii Catostomus (Pantosteus) discobolus Catostomus (Pantosteus) plebeius Hexaplex (Trunculariopsis) princeps Xenophora (Onustus) exuta Lampsilis (Eurynia) iris Lampsilis (Lampsilis) multiradiatus Lampsilis (Proptera) alata Lampsilis (Proptera) alatus Lampsilis (Proptera) amphichaenus Lampsilis (Proptera) inflata Lampsilis (Proptera) purpuratus Calliostoma (Jujubinus) exasperatum Lymnaea (Galba) Quadrula (Fusconaia) rubiginosa Quadrula (Fusconaia) solida Quadrula (Theliderma) asper Quadrula (Theliderma) lachrymosa Quadrula (Theliderma) sphaerica Pterotrigonia (Scabrotrigonia) thoracica Ischnochiton (Stenoradsia) conspicuus Mortoniceras (Angolaites) wintoni Aleochara (Calochara) Nassa (Amycla) corniculum Nassarius (Plicarcularia) jonasi Hybodus (Leiacanthus) Gryphaea (Texigryphaea) Gryphaea (Texigryphaea) belviderensis Gryphaea (Texigryphaea) navia Gryphaea (Texigryphaea) pitcheri Gryphaea (Texigryphaea) tucumcarii Gryphaea (Texigryphaea) washitaensis Alabastrina (Alabastrina) Alabastrina (Alabastrina) subvanvincquiae Alabastrina (Atlasica) Alabastrina (Atlasica) aguergourensis Alabastrina (Atlasica) interica Alabastrina (Atlasica) tamanarensis Alabastrina (Atlasica) tildiana Alabastrina (Siretia) Alabastrina (Siretia) pallaryi Pleuriocardia (Dochmocardia) pauperculum Pleurobema (Pleurobema) raveneliana Elliptio (Elliptio) gibbosus Amphidonte (Ceratostreon) Amphidonte (Ceratostreon) texanum 97 rows selected. and names which contain subgenus-bearing local classifications: select scientific_name from taxon_name, taxon_term where taxon_name.taxon_name_id=taxon_term.taxon_name_id and source in ('Arctos','Arctos Plants') and term_type='subgenus'; are https://docs.google.com/spreadsheets/d/144cwe4pPmcVduFye9ikn_J6Hty7OUtcAS8idNpgaAeM/edit?usp=sharing — You are receiving this because you commented. 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[dustymc]

Attached are the intended identification -->taxon name targets.

temp_former_subgenus_ids.csv.zip

Affected collections are:

select
substr(guid,1,instr(guid,':',1,2)) || ' @ ' ||count(*) 
from 
temp_former_subgenus_ids
group by
substr(guid,1,instr(guid,':',1,2))
  7  ;

SUBSTR(GUID,1,INSTR(GUID,':',1,2))||'@'||COUNT(*)
------------------------------------------------------------------------------------------------------------------------
MSB:Para: @ 49
MSB:Host: @ 2
UNR:Fish: @ 2
USNPC:Para: @ 3
MSB:Fish: @ 4648
UNM:ES: @ 137
KNWR:Ento: @ 1
UAM:ES: @ 1
CHAS:Inv: @ 138
UAM:Ento: @ 3

10 rows selected.

That should happen today; I plan to leave the ID strings and just switch the pointers to taxa.

Here's one of the newly-created names (http://arctos.database.museum/name/Gryphaea%20pitcheri)

I clicked "seed hierarchy" for the Genus - note that this solves the "subgenera break the editor" thing (which has always really been a "inconsistent data cannot be hierarchical, and the editor can be nothing else" problem).

And can we add a point or two to #1698? There are something like 6 fractured hierarchies for 7 species here; it would be difficult to design a system better at hiding specimens from users.

[dustymc]

done

[sharpphyl]

How do I get a new taxon name to include the subgenus in parentheses?

Specifically, WoRMS (in their "match taxa tool") refers me to Cancellaria (Pyruclia) solida aphiaID 464689 as an "exact subgenus match" for Cancellaria solida which it doesn't recognize.

I was able to clone the WoRMS classification into the WoRMS (via Arctos) classification but now the Taxon Name is Cancellaria solida and the species in the WoRMS (via Arctos) classification is Cancellaria (Pyruclia) solida.

Somehow this didn't get into our tables through the normal WoRMS (via Arctos) refreshes.

[dustymc]

How do I get a new taxon name to include the subgenus in parentheses?

You can't; that's the point! Cancellaria solida and Cancellaria (Pyruclia) solida are the same THING, if we allow them both then people can't find what they're looking for. The information is retained in the classification - that's what classifications do, this one is no different. If you want to use something other than the bare name as the identification the A {string} formula is available, same as any other case of not wanting to use the verbatim name as the identification.

[sharpphyl]

Got it!

[Jegelewicz]

From #988

I am not seeing the inclusion of the subgenus in the display name. The example given above https://arctos.database.museum/name/Gryphaea%20pitcheri does not include the subgenus in the display name anywhere that I can find.

In fact, on the catalog record pages, what the display name does is put the subgenus where the genus should be.

I would expect this identification to be Gryphaea (Texigryphaea) pitcheri as shown on the classification.

Texigryphaea pitcheri is a thing, but apparently so is Gryphaea (Texigryphaea) pitcheri and now we have them muddled together? Or am I missing something?

With regard to #1704 (comment)

If someone wants to identify something as Gryphaea (Texigryphaea) our current position in Arctos is that they must use Gryphaea {Gryphaea (Texigryphaea)} correct? But we allow the use of this subgenus in the classification, so we will end up with competing classifications for Gryphaea, one that includes the subgenus and one that doesn't? None of this feels good to me and I'm sure we are eventually going to have a conversation about a better way to handle it.

[dustymc]

I am not seeing the inclusion of the subgenus in the display name

You're just not seeing display_name.

is identification.scientific_name.

I could do WHATEVER with display_name (I don't think we currently do anything at all), almost certainly needs discussed in a dedicated Issue.

what the display name does is put the subgenus where the genus should be.

If you mean the little gray bits....

... that's full_taxon_name (which is autogenerated by https://github.com/ArctosDB/PG_DDL/blob/master/function/getFlatTaxonomy.sql and could be changed)

expect this identification to be

I'd expect it to be whatever was specified, and it is.

apparently so is Gryphaea (Texigryphaea) pitcheri

That cannot be a THING in Arctos - that's what this Issue (wisely!) prevents. https://arctos.database.museum/name/Gryphaea%20pitcheri is a THING, if it has something to do with https://arctos.database.museum/name/Texigryphaea%20pitcheri then that should be documented via Relationships. I do not think that's something that can safely be derived from strings - a taxonomic assertion is needed.

f someone wants to identify something as Gryphaea (Texigryphaea) our current position in Arctos is that they must use Gryphaea {Gryphaea (Texigryphaea)} correct?

Correct.

But we allow the use of this subgenus in the classification, so we will end up with competing classifications for Gryphaea, one that includes the subgenus and one that doesn't?

Potentially yes, and your collection could prefer the "same as WHATEVER, but with subgenus" in front of the WHATEVER classifications. That's what classifications DO - allow various assertions of metadata for a name.

[Jegelewicz]

BUT you could easily have both classifications used in a single collection - Some things ID'd to the subgenus and some not.

[dustymc]

I'm lost.

Classification preference is by collection - there's some consistency in how things happen within a collection, but not necessarily between collections. So CollectionA might prefer my "same as WHATEVER, but with subgenus" classification while CollectionB ignores it, but everything in CollectionA would encounter the preferred classifications in the same order and end up with the same data.

If you mean they'll only sometimes-maybe use the A {string} IDs then yes, probably, that's up to them and their procedures (and it's why we've separated classifications and taxonomy, and why I'm insistent that we don't denormalize taxonomy).

[Jegelewicz]

I mean, that Derek could say "This one is Gryphaea {Gryphaea (Texigryphaea)} and that one is Gryphaea, but he can only choose ONE taxonomic source for his classifications, so all of his Gryphaea will either include the subgenus (Texigryphaea) or they won't.

[dustymc]

Ah - correct, both of those would use the first-encountered preferred classification for "Gryphaea." Perhaps that's a place where we could do more with taxon concepts - presumably asserting concepts is the goal if those are planned assertions and not just gappy procedures.

[Jegelewicz]

With regard to TPT Taxonomy, I plan to enter classifications that include a subgenera like this one.

Dennyus carljonesi carljonesi

Note that the name does not include the subgenus, but the classification does....

So far, I have not run into the problem discussed above, so I think this should work. @campmlc thoughts? Also, @sharpphyl what do you think?

[Jegelewicz]

Of course, this makes the display name look weird...

[dustymc]

makes the display name look weird...

The formatter expects "Collodennyus" as subgenus.

[Jegelewicz]

makes the display name look weird...

The formatter expects "Collodennyus" as subgenus.

Yep, but that doesn't seem to be how subgenera are displayed in a classification?

[Jegelewicz]

This is probably why there are issues with WoRMS classifications?

[Jegelewicz]

But it looks good on the catalog record

[Jegelewicz]

I think we just need to change the way display name formats when a subgenus is involved. BUT is display name USED for anything?

[Jegelewicz]

Also, I think we need a way for people to SEARCH Cancellaria (Pyruclia) solida and get all of the Cancellaria solida because there will be people who do that....

[campmlc]

So can the display name be in line with convention, e.g Worms (genus (subgenus) species or genus species), even if we do something weird with the classification? I agree we need to make it possible to find all instances of records with and without subgenus added.

…

On Wed, Jan 27, 2021 at 9:49 AM Teresa Mayfield-Meyer < ***@***.***> wrote: * [EXTERNAL]* Also, I think we need a way for people to SEARCH *Cancellaria (Pyruclia) solida* and get all of the *Cancellaria solida* because there will be people who do that.... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1704 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADQ7JBH2MRG2W7STWME6RYLS4A7YBANCNFSM4FWSLA5Q> .

[sharpphyl]

This is probably why there are issues with WoRMS classifications?

YES

And until I linked Cancellaria solida to the WoRMS aphiaID 464689 for Cancellaria (Pyruclia) solida I was using a taxon name without a WoRMS aphiaID so it didn't automatically update. I catch them one by one but, as you noted, the name that shows on our catalog record is not the same as in the WoRMS (via Arctos) classification.

[dustymc]

even if we do something weird with the classification?

https://en.wikipedia.org/wiki/gigo, but that does raise an interesting point for #3311 - I get the sense that we want to do more with display name, but that relies on various things (predictable format, the existence of nomenclatural_code, the existence of ranks, etc.) that can't be expected to exist in "external" classifications (nor apparently in "internalized" classifications).