taxon_status code table cleanup

[Jegelewicz]

We have not clearly defined the purpose of https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_status

Before I move on to suggestions for deleting/modifying terms, I'd like to get an agreement on what this code table and related taxon classification metadata attribute are intended to accomplish.

I suggest this definition

Taxon status is available for use as an attribute of taxon classifications as metadata. The taxon status table holds the controlled vocabulary terms available for use in this attribute. These terms are used to indicate the fitness of a name for use in identifications.

[sharpphyl]

I looked at ITIS and WoRMS etc. for some ideas.

Taxon status is classification metadata for a taxon name. It is selected from a controlled vocabulary. Preferably, the status is the taxonomic judgment of published literature and indicates its fitness for use in specimen identifications.

[dustymc]

extant/extinct have never made any sense to me, it's confounding taxa and taxon concepts and detectability and probably some other stuff.

MAYBE "ichnotaxon" is useful, but we need to pick one of it or the issue that's requesting ichnospecies etc., and it has nothing to do with "fitness for use"

It's not clear to me what purpose nomen dubium , nomen nudum , nomen oblitum could have in a specimen database.

species for count - what?!?

So that leaves valid/invalid, which are only "[don't] use this" and could be replaced by preferred_name, which is the same information plus what's actually needed.

Can we just drop this?

[Jegelewicz]

See also #2591 and #2594

[Jegelewicz]

Can we just drop this?

Nope.

This table is meant to help those doing data entry select appropriate names or know when to ask questions. Also it may help collection managers determine when they are continuing to use outdated names. So the table definition suggested is:

The taxon status table holds the controlled vocabulary terms available for use as taxon status in classification metadata. The terms included should convey the taxonomic judgment of published literature and indicate the fitness for use of a name in specimen identifications. These terms are meant to help those doing data entry or review of collection taxonomy select appropriate names or know when to ask questions.

We want the terms in this table to match what taxonomists use and the best case we have for that right now is WoRMS. @sharpphyl would like WoRMS (via Arctos) to reflect the actual data in WoRMS, adding the terms as requested in #2591 will make that happen. Once that is done, we will move extant/extinct - see #2594 which will leave the following:

ichnotaxon - I am probably going to suggest a new taxonomy source for ichnotaxa and that all classifications in that source use the "ichno" term types which will automatically demonstrate that they are ichnotaxa, so we shouldn't need this term at that point anyway.

species for count - I don't know who requested this or who uses it, but we need to find some other way for them to do whatever they are doing with it. I say it needs to be removed from the table.

DELETE - I don't think we need this either. Any reason we do?

I believe this will leave us with the WoRMS terminology (except that we are weirdly using valid instead of accepted and invalid instead of unaccepted - can we change that?).

[dustymc]

this will leave us with the WoRMS

https://github.com/ArctosDB/arctos/issues/2591#issuecomment-730028593

Sounds like an argument for drop to me....

[Jegelewicz]

For reference, WoRMS status list

[sharpphyl]

I believe this will leave us with the WoRMS terminology (except that we are weirdly using valid instead of accepted and invalid instead of unaccepted - can we change that?).

Someone in our committee ages ago (Derek?) advised against using "accepted" and "unaccepted" because of its meaning for plants or some other group of names. Does anyone else remember exactly why we didn't go with the WoRMS terms?

[Jegelewicz]

As I have been working on the TPT taxonomy, I think we should be using DarwinCore as a guide and as such, I suggest changing the taxon_status table to include terms as suggested in DwC:

taxon_status = dwc:taxonomicStatus

The status of the use of the scientificName as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept.

Bold is by me and is a project for another day.

controlled vocabulary from https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/ and https://www.iapt-taxon.org/nomen/pages/main/glossary.html (Thanks to the plant people for providing a linkable glossary...)

• homonym [ICZN] (1) In the family group: each of two or more available names having the same spelling, or differing only in suffix, and denoting different nominal taxa. (2) In the genus group: each of two or more available names having the same spelling, and denoting different nominal taxa. (3) In the species group: each of two or more available specific or subspecific names having the same spelling, or spellings deemed under Article 58 to be the same, and established for different nominal taxa, and either originally (primary homonymy) or subsequently (secondary homonymy) combined with the same generic name [Art. 53.3]. For examples, see Article 53.1 for family-group names, Article 53.2 for genus-group names, and Article 53.3 for species-group names. [IAPT] A name spelled exactly like another name published for a taxon at the same rank based on a different type (Art. 53.1). Note: names of subdivisions of the same genus or of infraspecific taxa within the same species that are based on different types and have the same final epithet are homonyms, even if they differ in rank (Art. 53.3), because the rank-denoting term is not part of the name (Art. 21 Note 1 and Art. 24 Note 2) https://www.iapt-taxon.org/nomen/pages/main/glossary.html#homonym
• invalid (illegitimate name) [ICZN] An available name which either (1) is objectively invalid (i.e. it is a junior homonym or a junior objective synonym of a potentially valid name, or must be rejected under the provisions of the Code, or has been suppressed by the Commission), or (2) is subjectively invalid (because it is considered subjectively to be a junior synonym or to be inapplicable to a particular taxonomic taxon). [IAPT] A validly published name that is not in accordance with specified rules (Art. 6.4), principally those on superfluity (Art. 52) and homonymy (Art. 53 and 54). https://www.iapt-taxon.org/nomen/pages/main/glossary.html#illegitimate%20name
• valid (accepted, legitimate name) [ICZN] Of an available name one that is acceptable under the provisions of the Code and, in the case of a name, which is the correct name of a taxon in an author's taxonomic judgment. [IAPT] A validly published name that is in accordance with the rules, i.e. one that is not illegitimate (Art. 6.5) https://www.iapt-taxon.org/nomen/pages/main/glossary.html#legitimate%20name
• synonym [ICZN] Each of two or more names of the same rank used to denote the same taxonomic taxon (subjective synonym, objective synonym). [IAPT] One of two or more names that apply to the same taxon (heterotypic synonym, homotypic synonym) should we just split these and include the two types of "synonym"?

I suggest that some terms currently in taxon_status be moved to a new code table:

nomenclatural_status = dwc:nomenclaturalStatus

The status related to the original publication of the name and its conformance to the relevant rules of nomenclature. It is based essentially on an algorithm according to the business rules of the applicable code. It requires no taxonomic opinion.

controlled vocabulary from https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/ and https://www.iapt-taxon.org/nomen/pages/main/glossary.html

• doubtful (nomen dubium) a name of unknown or doubtful application.
• replacement (nomen novum) A new name published as an explicit substitute (avowed substitute) for a legitimate or illegitimate, previously published name, which is its replaced synonym and which, when legitimate, does not provide the final epithet, name, or stem of the replacement name (Art. 6.11 and 7.4; for names not explicitly proposed as substitutes see Art. 6.12 and 6.13). https://www.iapt-taxon.org/nomen/pages/main/glossary.html#replacement%20name
• nonconforming (nomen nudum) A Latin term referring to a name that, if published before 1931, fails to conform to Article 12; or, if published after 1930, fails to conform to Article 13. A nomen nudum is not an available name, and therefore the same name may be made available later for the same or a different concept; in such a case it would take authorship and date [Arts. 50, 21] from that act of establishment, not from any earlier publication as a nomen nudum. https://www.iapt-taxon.org/nomen/pages/main/glossary.html#nomen nudum%20(nom.%20nud.)
• forgotten (nomen oblitum) applied after 1 January 2000 to a name, unused since 1899, which as a result of an action taken under Article 23.9.2 does not take precedence over a younger synonym or homonym in prevailing usage; the younger name which takes precedence over the nomen oblitum may be called a nomen protectum. Nomina oblita remain available names; see Articles 23.9 and 23.12 for conditions controlling their use as valid names.
• protected (nomen protectum) applied to a name which has been given precedence over its unused senior synonym or senior homonym relegated to the status of nomen oblitum (q.v., and see Article 23.9.2).
• illegitimate (nomen illegitimum) A validly published name that is not in accordance with specified rules (Art. 6.4), principally those on superfluity (Art. 52) and homonymy (Art. 53 and 54).
• misspelling (orthographical variant) An incorrect spelling, such as a lapsus calami, or a copyist's or a printer's error, not intended by the original author. Various spelling, compounding, and inflectional forms of a name or its final epithet when only one nomenclatural type is involved (Art. 61.2). https://www.iapt-taxon.org/nomen/pages/main/glossary.html#orthographical%20variants
• misapplication An application, deliberately or otherwise, of a name in a sense which is not correct under the provisions of the Code (e.g. in a manner not in accord with the name-bearing type).
• conserved name (nomen conservandum). (1) A name of a family, genus, or species, or in certain cases a name of a subdivision of a genus or of an infraspecific taxon, declared legitimate, even though it may have been illegitimate when published, and taking precedence over other specified names even if it lacks priority. (2) A name for which the type, orthography, or gender has been fixed by the conservation process. https://www.iapt-taxon.org/nomen/pages/main/glossary.html#conserved name (nomen%20conservandum)

other terms currently in taxon status - these don't fit in either of the DarwinCore terms, but I think they are useful for Arctos users? Where should we put them? All definitions come from https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/ glossary

• extant Of a taxon: having living representatives.
• extinct Of a taxon: having no living representatives. fossil-taxon.
• ichnotaxon A taxon based on the fossilized work of an organism, including fossilized trails, tracks or burrows (trace fossils) made by an animal.

This is a taxon_term that we currently use, that might end up being more useful in the future and might benefit from the DarwinCore definition

preferred name = dwc:acceptedNameUsage

The full name, with authorship and date information if known, of the currently valid (zoological) or accepted (botanical) taxon.

Ideally this would link to the accepted name, but just putting in the accepted name (as we do now) is probably OK. We might consider adding the following:

preferred name ID = dwc:acceptedNameUsageID

An identifier for the name usage (documented meaning of the name according to a source) of the currently valid (zoological) or accepted (botanical) taxon.

This could provide the link to the classification of the accepted name? But maybe isn't necessary. Just throwing it out here...

Sorry for the long-winded comment. I am sure this is not perfect and maybe needs to be parsed into separate issues, but I wanted to put it down somewhere while it is in my mind.

[sharpphyl]

Taxon status table:

extant Of a taxon: having living representatives. extinct Of a taxon: having no living representatives. fossil-taxon. ichnotaxon A taxon based on the fossilized work of an organism, including fossilized trails, tracks or burrows (trace fossils) made by an animal.

Would it make any sense to add "trace fossil specimen" to the catalog item type since "fossil specimen" and "specimen" are already there? Would we need to have these three taxon types if the catalog item type conveys the same information? Would GBIF know what to do with it?

If #3579 defines the genus/species as ichno taxa, that could align with "trace fossil" as the catalog item type and avoid need for another table.

[campmlc]

Sounds reasonable?

On Mon, Apr 26, 2021 at 9:03 AM Phyllis Sharp @.***> wrote:

• [EXTERNAL]*

Taxon status table:

extant Of a taxon: having living representatives. extinct Of a taxon: having no living representatives. fossil-taxon. ichnotaxon A taxon based on the fossilized work of an organism, including fossilized trails, tracks or burrows (trace fossils) made by an animal.

Would it make any sense to add "trace fossil specimen" to the catalog item type since "fossil specimen" and "specimen" are already there? Would we need to have these three taxon types if the catalog item type conveys the same information? Would GBIF know what to do with it?

[image: Screen Shot 2021-04-26 at 8 46 55 AM] https://user-images.githubusercontent.com/15368365/116102801-3de48f80-a66c-11eb-9d7f-cc6e9350c22d.png

If #3579 https://github.com/ArctosDB/arctos/issues/3579 defines the genus/species as ichno taxa, that could align with "trace fossil" as the catalog item type and avoid need for another table.

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[Jegelewicz]

Probably, but maybe needs it's own issue - this one is out of control.

[dustymc]

https://dwc.tdwg.org/terms/#dwc:basisOfRecord - adding values to https://arctos.database.museum/info/ctDocumentation.cfm?table=ctcataloged_item_type without changing the mapping and rebuilding the DWC cache will result in SOMETHING weird - probably GBIF rejecting the record (or dataset, IDK).

My only "objection" is extinct etc., but even that's not really an objection - I don't think we have the attention span or data resolution to pull that off in a useful fashion, but as long as that's documented and it's useful for some curatorial reason then whatever.

It requires no taxonomic opinion.

That's a bit optimistic, careers are built around those! https://github.com/ArctosDB/arctos/issues/3548 has been cooking since at least 1958.

Big-picture, this is definitely a better organization, I just wonder what benefit we would get out of the work required to create the data or deal with the complexity of having more authorities? How much of this conversation is a legacy of trying to make one(ish) giant blurb of taxonomy work for everyone? I think/hope we're moving towards things like https://github.com/ArctosDB/arctos/issues/3544, where these things are likely to be much less important (eg, just don't put the things you want to avoid in "your" classification, no need to add them and then flag them so you can avoid ever seeing them again). That leads to https://github.com/ArctosDB/arctos/issues/3525 - eg can we find a way to usefully integrate whatever comes in from things like WoRMS (however it comes in) with catalog records, or do we still need to "translate"?

Maybe we should only proceed when/if there's some compelling reason to do so, when having those data would DO SOMETHING for us.

From the technical side of things, controlling "local" taxon terms while also accepting whatever comes from GlobalNames needs a revisit - I think it's hard-coded, if we're going to fire up a bunch of new CTs then we need some more complexity (maybe something like we do for various Attributes) to hook them in.

[Jegelewicz]

WoRMS Terms

Possible statuses for a name:

Accepted: the used name is accepted in the present literature

Unaccepted: The used name is NOT accepted in the present literature

Nomen nudum: a name that does not comply with the name requirements of the codes, such as lack of a description or diagnoses or reference to a description or diagnosis or a type specimen is lacking for publications after 1999

Alternate representation: to link species that are represented twice: once with and once without subgenus. Alternate representation can also be used for a species and its nominal subspecies (note: you can only add a subspecies if the species is present in the database). See example in the box below

Nomen dubium: a name of uncertain application, because it is not possible to establish the taxon to which it should be referred. A good example is the "Ascothoracida" genus Laocoon. There is a debate whether this is based on a parasite or on a detached piece of the host. It is clearly a dubious name

Temporary name: to create higher rank taxa to accommodate child taxa for which the classification is not sorted yet

Taxon inquirendum: an incompletely defined taxon that requires further characterization, it is impossible to identify the taxon

Interim unpublished: an as yet unavailable name (until in a print issue) which has been published online only, in a work that does not show evidence of ZooBank registration (ICZN Article 8.5)

[Jegelewicz]

Discussion in code table committee - do we really need so much control? Could we lose all of this to some sort of free text taxon attributes that would let people use what they want to indicate validity or usefulnees?

For things like WoRMS (via Arctos) this means we could pull in and use whatever the heck they have instead of translating from their terms to ours.

Dusty also suggested removing all these terms except nomenclatural_code, display_name, scientific_name, and aphiaid because they are the only ones that DO anything:

Term	Has Code Table?
aphiaid	no
author_text	no
chemical_formula	no
dana_number_8	no
display_name	no
heys_cim	no
infraspecific_author	no
managed_by	no
nickel-strunz_10	no
nomenclatural_code	yes
nomenclature_4.0_identifier	no
preferred_name	no
remark	no
scientific_name	no
source_authority	no
taxon_status	yes

I think they could be useful, but does anyone actually use them?

If we left this table as is, but just removed the constraints of the taxon_status code table for taxon_status would that make that term less useful?

[Jegelewicz]

Added to January AWG issues agenda.

[dustymc]

removing all these terms except

Clarification: I'm asking if we can relax control, not remove any existing terms or values.

Background: All "classification stuff" is in one table, I have to accept everything that comes from GlobalNames, so the checks are all by trigger - if the source is in https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxonomy_source then I only allow terms from https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_term, and the term type is in my controlled list (also in the trigger), I go check if the value is in the appropriate code table (eg https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_term#nomenclatural_code requires a term from https://arctos.database.museum/info/ctDocumentation.cfm?table=ctnomenclatural_code)

Only local sources are allowed in identifications (https://github.com/ArctosDB/arctos/issues/3311) , so I have to "translate" things that come from eg WoRMS (destined for https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxonomy_source#worms__via_arctos_). I'd rather not; that requires maintenance, information may be lost in the translation, and it's different in Arctos than on WoRMS which is probably confusing to users.

Option Zero: Change no functionality, maybe do stuff requested above.

Option One: Relax the value controls. Continue translating status to taxon_status but just accept accepted from WoRMS instead of translating it to valid. This will keep the types of things consistent, but provide less control over values.

Option Two: Relax term and value controls. Just take 'status=valid' from WoRMS and use it. This may result in less-predictable data from locally-managed sources, which would matter if searching on specific types was important, but I don't think we have the data to support that no matter how we structure it - some arbitrary smattering of taxa have things like extinct/extant, it's useful when the name has been found, but it's not very useful in finding because we don't have consistent data.

I think I like Option Two. That would allow someone to download some relevant checklist-or-whatever, make a new Source, upload, and use with their untranslated terminology with very little work, in addition to things like making the WoRMS pull smoother and more as expected. It would provide more possibility for locally-managed data to get weird terms and values, but that can be mitigated to some extent (eg by suggesting existing values) and I don't think that has much of a functional implication in these data anyway. Hopefully we're all moving towards things like importing checklists rather than managing locally anyway.

[Jegelewicz]

I think I like Option Two. That would allow someone to download some relevant checklist-or-whatever, make a new Source, upload, and use with their untranslated terminology with very little work, in addition to things like making the WoRMS pull smoother and more as expected. It would provide more possibility for locally-managed data to get weird terms and values, but that can be mitigated to some extent (eg by suggesting existing values) and I don't think that has much of a functional implication in these data anyway. Hopefully we're all moving towards things like importing checklists rather than managing locally anyway.

@dustymc thanks for the clarification and I agree with the above.

[Jegelewicz]

Go with option two!

[mkoo]

AWG loves Option 2!

[Jegelewicz]

@dustymc what do we need to do from our end?

[dustymc]

Next release will have relaxed constraints, and the edit classification UI has been much simplified to accommodate.

• https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_term is now used to suggest term types in the UI, but they are only suggestions. (And so maybe some of the weird rock-things don't need to exist at all now?)
• https://arctos.database.museum/info/ctDocumentation.cfm?table=ctnomenclatural_code is used to suggest values for term type "nomencaltural_code."
• https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_status is used to suggest values for term type taxon_status.

Adding other kinds of suggestions involves changing code, but should be pretty simple to do if necessary.

The above code tables should not be connected to anything at this point - used terms can be removed or changed without consequence (beyond the suggestions changing).

Testing greatly appreciated.

http://test.arctos.database.museum/name/Conus%20abbas%20abbas#ArctosCulture is my poor tortured test mule, if that's somehow useful.

[Jegelewicz]

I like this

BUT when creating a classification from scratch - http://test.arctos.database.museum/editTaxonomy.cfm?action=editClassification&classification_id=65CDE689-8FDC-466A-ACB4B0F3A29ED41A&taxon_name_id=12117355

Nomenclatural code did not offer up the code table options

Taxon Status did not offer up the code table options

[Jegelewicz]

Adding other kinds of suggestions involves changing code, but should be pretty simple to do if necessary.

Could we offer suggestions for term already in use in the field? So if I type "A" into kingdom, "Animalia" would be a choice? Asking too much?

Then to ask even more, offer choices limited by previous fields in the classification. So, I have Animalia in kingdom, then choices for Phylum would pick only phylum names associated with "Animalia" BUT still let me type whatever if I in fact am using a new Phylum?

[Jegelewicz]

Finally, how about limiting the offered terms in the form based upon the name type? This way when creating a classification for a Linnean name I wouldn't be automatically offered all of the mineral and cultural stuff (but I could add them if I want for the weird oar things)?

[dustymc]

did not offer up

Show me, please.

"Animalia" would be a choice? Asking too much?

I don't think we have the resources for that.

offered terms in the form based upon the name type

That's probably possible, but would take some different structure of the authority data.

We should have a focused conversation (not here) before deciding to invest too much in this thing. I can't see much reason for anyone to use this form for any purpose - yet they do, and IDK if that's me not understanding what these data are used for, or users not understanding just how inconsistent this thing leaves data, or ?????