Arctos: taxonomy relationships

[dustymc]

Splitting this out from https://github.com/ArctosDB/arctos/issues/1094 in hopes of quick resolution.

Should we update taxon relations using https://docs.google.com/spreadsheets/d/1S9tRAtgJQjCTTYKanxdTTSBouWj3CAZTrBdBh6HwUnE/edit#gid=894404859 ?

Note that there are two tabs on the spreadsheet: terms and definitions, and a proposed migration pathway.

[DerekSikes]

Do we have a field to indicate a taxonomic name's status? (eg valid, invalid, unavailable)? I ask because this would be a non-relationship field but not completely independent... it would be a useful field to hold information like 'nomen nudum' or 'nomen dubium' and although usually the older name of two synonyms (the senior synonym) is the valid name, this cannot be assumed. Sometimes priority is reversed in favor of stability (when a younger name has been in use and the older name forgotten). Thus you could have the valid name being the junior synonym. Thus we need a field to keep track of this separately from the name-relationship data.

[dustymc]

status

http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_STATUS

but see https://github.com/ArctosDB/arctos/issues/1126 (some of the stuff in taxon status doesn't make sense to me) and https://github.com/ArctosDB/arctos/issues/1137 (can we merge/simplify some term types?)

[sharpphyl]

Once we get Taxon Status updated, will be move forward on this proposal for Taxon Relationship - which I think everyone said OK to or does it need more discussion?

[Jegelewicz]

Why are we not using the standard relationship terms of synonym, etc instead of creating some new "Arctos version" (versions of "variant") that only we understand?

I think we just need to get good definitions of the appropriate terms in use in the community (junior synonym, senior synonym, etc.) and use them as intended.

I also believe that nomem dubium had been discussed in #1806 and can stay in the Taxon_status table but go from relationships.

[dustymc]

standard relationship

They're ambiguous, Code-dependent, and they require "experts."

Given "junior synonym" I can't know what you're talking about - I need to know the Code as well. (That is, one term means at least two things.)

I often discover that names have some sort of overlap, I might even know which one is "better," but that's about as far as I'm willing to venture into those waters. For scale, there are currently 291226 relationships and 217121 (~75%) of them are "mine" - they use a relationship I created to mean "has something to do with each other," and I created most of them. Moving to Code terminology would probably mean deleting those.

https://github.com/ArctosDB/arctos/issues/1079#issuecomment-291884374

https://github.com/ArctosDB/arctos/issues/1094

[dustymc]

I added this Issue to the AWG agenda for 20181213.

The lack of stable relationships is preventing pulling relationship data from WoRMS. The folks using WoRMS (and probably everyone else) want these data.

Best case, WoRMS just provides an "accepted" pointer - http://www.marinespecies.org/aphia.php?p=taxdetails&id=302594

I think we have three alternatives being proposed:

1) Use "Code" terms.

• There seem to be some terminology conflicts ("senior synonym" means different things in different contexts, I think). Ambiguous terms are evil, so my only (bad!) idea is something like "senior synonym according to CODE [and maybe some revision or something]" instead of "senior synonym."
• I think these things may require "experts" - I certainly can't get to Code terms from WoRMS data, for example.
• reciprocals aren't clear; these may need human intervention in order to lead both ways.

2) Carefully avoid "Code" terminology - see above including the link to a spreadsheet.

3) Something else - use Code terms in non-code ways or something - see https://github.com/ArctosDB/arctos/issues/1826#issuecomment-444312385 https://github.com/ArctosDB/arctos/issues/1079#issuecomment-291912330 etc.

@campmlc @sharpphyl @Jegelewicz @DerekSikes please help summarize this!

[Jegelewicz]

WoRMS says this:

In WoRMS invalid (unaccepted) synonyms are linked to valid (accepted) taxa. This requirement is not needed for cases like:
nomen nudum: i.e. 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
nomen dubium: i.e. 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: e.g. to create higher rank taxa to accommodate child taxa for which the classification is not sorted yet
species inquirenda: i.e. an incompletely defined species that requires further characterization, it is impossible to identify the species
incertae sedis: of an uncertain seat; i.e. of uncertain taxonomic position; or when the original material has not been studied or the description is insufficient. Usually applied to family and generic names

So terms that don't need an "accepted name" can go in TAXON_STATUS

After going back, I like what is proposed in https://github.com/ArctosDB/arctos/issues/1079#issuecomment-291901627 for TAXON_RELATION with a bit of modification that would leave us with just 4 terms:

1. accepted/valid synonym of: defined from the Hawksworth paper as accepted name: (1) the designation adopted by an author as the correct name for a taxon under consideration. (2) (bio.) the acceptable name (q.v.) that must be adopted under the rules of the Code. (3) (cult. pl.) the earliest name for a cultivar, group, or intergeneric graft-chimaera that must be adopted except in specified circumstances. (4) (phyl.) the name that must be adopted for a taxon under the Code. (5) (vir.) a name recorded as approved by the ICTV (q.v.). valid name: (1) (zool.) of an available name, one acceptable under the provisions of the Code and which is the correct name for a taxon in an author’s taxonomic judgement. (2) (bot.) a validly published name, i.e. one published according to criteria for valid publication according to the Code; an effectively published name fulfilling certain requirements, and before considerations of legitimacy are entertained; only designations that are validly published are names in the sense of the Code; see also publication. (3) (vir.) a name conforming to the Code and pertaining to established taxa; _see also accepted name_. Reciprocates with unaccepted/invalid synonym of.

2. unaccepted/invalid synonym of - I can't write the opposite of above right now, but I am sure we can manage.

3. objective synonym of: Also homotypic or nomenclatural synonym. A synonym based on the same type as that of another name in the same rank (e.g. different combinations with the same basionym). Reciprocates with auto generated objective synonym of

4. subjective synonym of: Also heterotypic synonym or taxonomic synonym. One of two or more names whose synonymy is only a matter of individual opinion, i.e. it is not objective. Reciprocates with auto generated subjective synonym of

All definitions derived from the Hawksworth paper.

More information about name statuses can be found at _Hawksworth, D.L. 2010. Terms Used in Bionomenclature. The naming of organisms (and plant communities)._ Copenhagen: Global Biodiversity Information Facility, 216 pp

[dustymc]

@Jegelewicz I think I could live with that. WoRMS data (which includes "preference") fits in (1,2), (4) is my "these names seem to have something to do with each other" option, I'll save (3) for the "experts."

Here's the paper you mentioned.

gbif_terms_nomenclature_guide_en_v1.pdf

[DerekSikes]

That list of 4 terms in Teresa's email is problematic.

Items 1 & 2 are redundant with items 3 & 4. That is one can have an
accepted/valid synonym that is also an objective synonym or a subjective
synonym.

That is, items 3 & 4 are qualifiers of items 1 & 2.

-Derek

On Mon, Dec 10, 2018 at 2:14 PM dustymc [e-mail] wrote:

@Jegelewicz https://github.com/Jegelewicz I think I could live with
that. WoRMS data (which includes "preference") fits in (1,2), (4) is my
"these names seem to have something to do with each other" option, I'll
save (3) for the "experts."

Here's the paper you mentioned.

gbif_terms_nomenclature_guide_en_v1.pdf
https://github.com/ArctosDB/arctos/files/2665306/gbif_terms_nomenclature_guide_en_v1.pdf

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[dustymc]

@DerekSikes that's why I prefer to completely avoid anything that might be considered "official" terminology, as I've suggested in my spreadsheet above. I'm trying to keep Arctos in sync with WoRMS. They provide a thing called "accepted name." If this discussion fails, I'll either ignore that or use "synonym of" in both directions, which serves to get users to specimens. If we can come up with something directional and appropriate then I'll use that, which will get users to specimens, maybe provide some context, and perhaps even be useful for things like data entry. I'm not going to know or have means of discovering anything much beyond that. I think I create most taxonomy data in Arctos, and most of what I see has about this much information.

I don't think that conflicts with having more specific vocabulary, but I don't think I'd ever have enough information to use more specific terms either.

https://github.com/ArctosDB/arctos/issues/1826#issuecomment-444303622 contains some relationship discussion.

[Jegelewicz]

@DerekSikes Care to offer an alternative? Can we pick a pair (1&2 or 3&4)? WOuld the use of either pair, along with appropriate valid/accepted or invalid/unaccepted taxon status do the trick?

[dustymc]

along with appropriate ... taxon status

Those are a different kind of data and they carry different kinds of information. I would like to focus on relationships for now in the hope of resolving this old Issue.

Relationships are ideally backed by "publications" - {author} thinks we should all spell woodfrog as Lithobates instead of Rana.

Status is more local or curatorial. MVZ:Herp agrees with {author}, UAM:Herp does not (or agrees with other authors who assert different relationships).

"Publications" because I wouldn't necessarily limit the scope - eg, WoRMS or AmphibiaWeb are useful "publications" for things like this.

[DerekSikes]

I think items 1&2 cover our needs because the details of why a name is a
synonym (objective vs subjective) are pretty unimportant to us - they only
matter to the taxonomists who revise the taxonomy of the groups they work
on. They are of little interest to curators.

However, it sounds like Dusty wants to make the relationships 'synonym of'
with no indication in the relationship of which name is valid (of its taxon
status).

I agree that it seems like a bad idea to have this information in 2 fields
(taxon status and a relationship field) unless we can force them to agree
somehow. People could easily change one to disagree with the other unless
they are prevented somehow.

I think it's critical that we know whether a name is valid/accepted or not
but as long as that information is in the taxon status field we don't need
it in the relationship terminology.

However, we should DISPLAY both whenever showing that name X is a synonym
of name Y. For example:

Name X (valid/accepted) -> synonym of -> name Y (invalid/unaccepted)

Rather than the unhelpful: Name X -> synonym of -> Name Y

-Derek

On Tue, Dec 11, 2018 at 8:56 AM dustymc [e-mail] wrote:

along with appropriate ... taxon status

Those are a different kind of data and they carry different kinds of
information. I would like to focus on relationships for now in the hope of
resolving this old Issue.

Relationships are ideally backed by "publications" - {author} thinks we
should all spell woodfrog as Lithobates instead of Rana.

Status is more local or curatorial. MVZ:Herp agrees with {author},
UAM:Herp does not (or agrees with other authors who assert different
relationships).

"Publications" because I wouldn't necessarily limit the scope - eg, WoRMS
or AmphibiaWeb are useful "publications" for things like this.

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University of Alaska Museum
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[email protected]

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FAX: [phone]

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[dustymc]

sounds like Dusty wants to make the relationships 'synonym of' with no indication in the relationship of which name is valid

Sometimes that's all I have (and that relationship exists now, and I'm leaning towards using it if this discussion doesn't lead somewhere more useful). If I know more (and I do from WoRMS) and have a place for it, I'll use that. I'm hoping we can find a place for those data this Thursday so I'm not tossing out information and/or creating ambiguous relationships that everyone will hate forever.

critical that we know whether a name is valid/accepted or not

Again, there are two things there.

Author A say use Y, not Z.
Author B says use Z, not Y.
Author C says use Y, not Z.
Author D says use Z, not Y.
etc.

Those are relationships supported by publications, and they're not capable of getting to "this collection prefers Z"; we need taxon_status for that. https://github.com/ArctosDB/arctos/issues/1700

We can always talk about display, but we need to do so in the context of #1700. We need (or so ya'll have been telling me) in support of the flip-floppy relationship data above

Y: preferred by something-more-specific-than-everyone
Y: preferred by something-else-more-specific-than-everyone
Z: preferred by something-more-specific-than-everyone

Any or all of those may have something or nothing to do with any/all/no relationship(s).

I can easily display all of that, but maybe not in a nice compact string.

[Jegelewicz]

Status is more local or curatorial. MVZ:Herp agrees with {author}, UAM:Herp does not (or agrees with other authors who assert different relationships).

Those are relationships supported by publications, and they're not capable of getting to "this collection prefers Z"; we need taxon_status for that. #1700

I am not aware that any one is using taxon status in the way you describe. I am pretty sure that @sharpphyl is using it to indicate that someone, somewhere said it is valid or invalid and that WoRMS has indicated that, and she is accepting that, but we can't use it in the way you are describing, because if I disagree and we are both using Arctos as our taxonomy source, we will spend forever flipping it back and forth. That field just isn't useful in that way. If that is how it is intended to be used, then it needs to be accompanied by the "who" is considering it valid/invlaid....

[dustymc]

valid or invalid and that WoRMS has indicated that

"valid-or-whatever (WoRMS)" or something might make more sense then.

flipping it back and forth

https://github.com/ArctosDB/arctos/issues/1136#issuecomment-446338700

There can be any number of them, no reason to flip anything.

accompanied by the "who"

That's precisely what I'm suggesting (on behalf of the folks who've told me they need that).

[DerekSikes]

So Dusty,

How might we allow, within the Arctos classification, a way to indicate
differences of opinion on a taxon's status?

Taxon X - valid according to publication Y
Taxon X - invalid according to publication Z

and allow collection A to choose the one they want (and somehow make this
obvious to all the technicians at that collection so they know which name
to use)?

-D

On Tue, Dec 11, 2018 at 1:04 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

Those are relationships supported by publications, and they're not capable
of getting to "this collection prefers Z"; we need taxon_status for that.

1700 https://github.com/ArctosDB/arctos/issues/1700

I am not aware that any one is using taxon status in the way you describe.
I am pretty sure that @sharpphyl https://github.com/sharpphyl is using
it to indicate that someone, somewhere said it is valid or invalid and that
WoRMS has indicated that, and she is accepting that, but we can't use it in
the way you are describing, because if I disagree and we are both using
Arctos as our taxonomy source, we will spend forever flipping it back and
forth. That field just isn't useful in that way. If that is how it is
intended to be used, then it needs to be accompanied by the "who" is
considering it valid/invlaid....

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[email protected]

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[dustymc]

https://github.com/ArctosDB/arctos/issues/1700

I don't really care what the taxon_status values are, and you'd need to work out using them with your techs (or maybe I can set the pick to somehow help). "valid for UAM:Ento collected from Barrow Quad in February" or "valid" (I think there's a general agreement for the vast majority of taxa; no need to complicate this when we don't have to) or "valid for everyone except CollectionX" or WHATEVER works. "valid according to Frost et. al 2006" might deal with all the frog conflicts. "valid according to WoRMS" seems to be about what @sharpphyl uses and might make some sense. I'd certainly prefer something that makes sense to the world, but I don't think that's a requirement.

[DerekSikes]

but can a taxon have more than one taxon_status?

On Tue, Dec 11, 2018 at 4:05 PM dustymc [e-mail] wrote:

1700 https://github.com/ArctosDB/arctos/issues/1700

I don't really care what the taxon_status values are, and you'd need to
work out using them with your techs (or maybe I can set the pick to somehow
help). "valid for UAM:Ento collected from Barrow Quad in February" or
"valid" (I think there's a general agreement for the vast majority of taxa;
no need to complicate this when we don't have to) or "valid for everyone
except CollectionX" or WHATEVER works. "valid according to Frost et. al
2006" might deal with all the frog conflicts. "valid according to WoRMS"
seems to be about what @sharpphyl https://github.com/sharpphyl uses and
might make some sense. I'd certainly prefer something that makes sense to
the world, but I don't think that's a requirement.

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[email protected]

phone: [phone]
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University of Alaska Museum - search 400,276 digitized arthropod records
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[dustymc]

yes

[DerekSikes]

how, for example?

On Tue, Dec 11, 2018 at 4:07 PM dustymc [e-mail] wrote:

yes

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Professor of Entomology
University of Alaska Museum
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[email protected]

phone: [phone]
FAX: [phone]

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[dustymc]

[DerekSikes]

Ok, cool!

How now will we indicate taxon status 'according to'

-Derek

On Tue, Dec 11, 2018 at 4:15 PM dustymc [e-mail] wrote:

[image: screen shot 2018-12-11 at 5 11 19 pm]
https://user-images.githubusercontent.com/5720791/49840448-47ede800-fd68-11e8-89fa-82798e064988.png

[image: screen shot 2018-12-11 at 5 13 24 pm]
https://user-images.githubusercontent.com/5720791/49840426-386e9f00-fd68-11e8-98c0-340c6a3b24da.png

[image: screen shot 2018-12-11 at 5 13 31 pm]
https://user-images.githubusercontent.com/5720791/49840430-3a386280-fd68-11e8-8ba4-50593c0ceb87.png

[image: screen shot 2018-12-11 at 5 13 42 pm]
https://user-images.githubusercontent.com/5720791/49840434-3d335300-fd68-11e8-927a-e08752f3574b.png

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[email protected]

phone: [phone]
FAX: [phone]

University of Alaska Museum - search 400,276 digitized arthropod records
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[dustymc]

I think in the value - "valid (WoRMS)" or something.

[Jegelewicz]

From Taxonomy Committee:

We discussed just using “synonym” to indicate a relationship with status according to added.

AWG Agreed.

One relationship: “synonym of”

@dustymc let's move forward with this.

[dustymc]

UAM@ARCTOS> desc taxon_relations
 Name                                  Null?    Type
 ----------------------------------------------------------------- -------- --------------------------------------------
 TAXON_NAME_ID                             NOT NULL NUMBER(10)
 RELATED_TAXON_NAME_ID                         NOT NULL NUMBER(10)
 TAXON_RELATIONSHIP                        NOT NULL VARCHAR2(50)
 RELATION_AUTHORITY                             VARCHAR2(255)
 TAXON_RELATIONS_ID                        NOT NULL NUMBER

1) I see no functional difference between saying the same thing for every situation and saying nothing; instead of asserting "synonym" we could just alter table taxon_relations drop column taxon_relationship.

I'm not sure about keeping an authority with "these have something to do with each other" either; maybe we should reduce that table to a pair of keys and nothing else.

2) https://github.com/ArctosDB/arctos/issues/1851

2) To not lose the information currently in relationships, we need to

1) work out taxon_status terminology
2) map existing relationships to taxon_status
3) maybe do something with taxon_relations.RELATION_AUTHORITY

[Jegelewicz]

I see no functional difference between saying the same thing for every situation and saying nothing; instead of asserting "synonym" we could just alter table taxon_relations drop column taxon_relationship.

Makes sense, instead of RELATED_TAXON_NAME_ID and TAXON_RELATIONSHIP, we just have RELATED_TAXON_NAME_ID which could be displayed like this (Myodes as an example):

Synonyms
Clethrionomys (Authority: Wilson and Reeder, 3rd ed.)
Clethrionomys (Authority: Wilson and Reeder 2005)

instead of the way it looks now:

But it will need good documentation.

I'm not sure about keeping an authority with "these have something to do with each other" either; maybe we should reduce that table to a pair of keys and nothing else.

I think authority should now be REQUIRED so that multiple and/or conflicting synonyms will be documented and so that those unfamiliar with a taxon can go find what the actual relationship is.

[dustymc]

instead of RELATED_TAXON_NAME_ID and TAXON_RELATIONSHIP, we just have RELATED_TAXON_NAME_ID

I do not understand what you're suggesting; this doesn't seem structurally capable of doing what I thought we were proposing.

authority should now be REQUIRED

It seems strange to me to REQUIRE evidence for what is proposed to become very low-information data. I can completely see a need for authority when the relationship involves some technical minutia requiring different relationships to handle, and different relationships leading to different places. (Which was always our intent.) We are instead proposing to assert only that a name seems to have something to do with another. We are structurally incapable of acknowledging the details, and we are explicitly giving up any possibility of differential handling for certain relationships. (Which I see as mostly a change in intentions, not capability.)

[Jegelewicz]

Well, I guess I don't understand this then:

I see no functional difference between saying the same thing for every situation and saying nothing; instead of asserting "synonym" we could just alter table taxon_relations drop column taxon_relationship.

Can you explain?

As for the authority, that is what creates the relationship and I think it is super important, especially when a given name is synonymous with 3, 5 or 10 others.

[dustymc]

explain

Given...

One relationship: “synonym of”

the only possible assertion is "A synonym of B."

We'll define "synonym of" to mean something like "there's some sort of association between these names."

Without the relationship, the only possible assertion is "A and B" on a "row" in a table. We can also define that as "there's some sort of association between these names."

I don't think there's a functional difference, and simplifying when we can is generally good.

If we keep the explicit relationship it's a bit more data (don't think I care) and one more thing to select (you probably shouldn't care).

Simplifying would also eliminate the possibility of saying "A {something other than a synonym of} B." I suppose there's some chance that eventually some Curator will REALLY want that, and we can revive it from the current model with a code table change. Maybe that's enough reason to keep things as they are, at least for a while.

In any case this is REALLY low priority now - I've got what I need (use synonym of for everything) to proceed with worms, and we can use that to get rid of the funkiness we got from ITIS way back when and all that, and I don't think the baggage of carrying around a static term is going to bother anyone in any meaningful way.

I'm fine with keeping authority (and I'll use it for WoRMS). Just trying to cover all the bases....

[sharpphyl]

I think the issue of REQUIRING some non-classification fields be completed is elsewhere as well, but I'll address it here since it seems to pop up everywhere.

Some taxa have no author - not many - but a few. See http://marinespecies.org/aphia.php?p=taxdetails&id=51. We can encourage it strongly by the way we structure the page, feedback loops, etc. but I don't think we can demand that it be completed unless (like agents) we're ready to accept "unknown." If it's a homonym, then maybe we can require an author, but not for most taxa.

Source authority could be required (it's not a structured table) but sometimes the answer may be "none" - just a legacy ID that I can't figure out but I need to get the specimen into the database and it's the best I can do right now. That happened to us a lot when we first joined Arctos and slowly we're cleaning them out. That's not what any of us want to hear but it does happen. We just need collections to take responsibility for taxa like this that they add instead of leaving them incomplete and confusing. Again, we could require source authority for homonyms.

And sometimes I honestly don't know if the taxon is valid because all the sources disagree, so I leave it blank until an expert makes a choice - perhaps far in the future. I sometimes make a comment about why the taxon status is uncertain.

Still forcing me to delete the non-classification fields that I can't complete has a much better chance of getting the data we want than not having them there, so I like the idea of having them display upon entering the edit taxon screen and being required to delete them if there's no valid info.

[Jegelewicz]

I don't think we can demand that it be completed unless (like agents) we're ready to accept "unknown." If it's a homonym, then maybe we can require an author, but not for most taxa.

Agree and "unknown" would be a problem in the display name.

Source authority could be required (it's not a structured table) but sometimes the answer may be "none" [...] We just need collections to take responsibility for taxa like this that they add instead of leaving them incomplete and confusing. Again, we could require source authority for homonyms.

I think source authority should be required, just so we know the source of the information in the classification. It would be great to disallow "none" or "unknown" and require at least the name of the collection adding the classification. Of course, that isn't easily done since this is not a controlled vocabulary, but it could be encouraged via documentation. I don't think we can require this for some things and not for others (homonyms), I vote required for everything.

forcing me to delete the non-classification fields that I can't complete has a much better chance of getting the data we want than not having them there, so I like the idea of having them display upon entering the edit taxon screen and being required to delete them if there's no valid info.

Agree 100% and if this is the best solution we can get right now, I am for it.

[dustymc]

Followup on https://github.com/ArctosDB/arctos/issues/1136#issuecomment-447112445: are we good to merge everything in https://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_RELATION into "synonym of"? If so, should we keep the old relationships in a remark or something?

[DerekSikes]

We should only merge some of those terms into 'synonym of'.

Specifically:

accepted synonym of
junior synonym of
senior synonym of
subsequent name/combination
superfluous renaming (illegitimate)
synonym
synonym of
valid name for

The other terms are not appropriate to merge. Some other terms are not
relationship terms at all. Eg. nomen dubium

I don't think we should save the old terms in remarks because so many of
them are backwards and wrong. Perhaps saving them in some non-public
fashion might be wise though.

-Derek

On Thu, Jan 10, 2019 at 7:44 AM dustymc [e-mail] wrote:

Followup on #1136 (comment)
https://github.com/ArctosDB/arctos/issues/1136#issuecomment-447112445:
are we good to merge everything in
https://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_RELATION
into "synonym of"? If so, should we keep the old relationships in a remark
or something?

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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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[dustymc]

These are not used:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from cttaxon_relation where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from taxon_relations);

TAXON_RELATIONSHIP
------------------------------------------------------------------------------------------------------------------------
nomen nudum
junior homonym of
nomen protectum
ichnotaxon
senior homonym of

These are:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from taxon_relations;

TAXON_RELATIONSHIP
------------------------------------------------------------------------------------------------------------------------
junior synonym of
homonym & junior synonym
unavailable, suppressed by ruling
nomen oblitum
subsequent name/combination
unnecessary replacement
unavailable, other
child of
synonym
hybrid offspring of
synonym of
other, see comments
unavailable, database artifact
database artifact
original name/combination
valid name for
nomen dubium
pro parte
parent of
unavailable, nomen nudum
unavailable, incorrect orig. spelling
homonym (illegitimate)
junior homonym
senior synonym of
orthographic variant (misspelling)
unjustified emendation
misapplied
accepted synonym of
unavailable, literature misspelling
superfluous renaming (illegitimate)

This should probably go back to the taxonomy committee for discussion if we're changing direction.

[DerekSikes]

OK. Here's a more thorough breakdown. Only one term, 'valid name for,' will
need a case-by-case examination to clean up. What do others think?
-Derek

SYNONYM OF (DON'T SAVE IN REMARKS)
junior synonym of
accepted synonym of
senior synonym of
synonym
synonym of

SYNONYM OF (DO SAVE IN REMARKS)
superfluous renaming (illegitimate)
subsequent name/combination
unnecessary replacement
orthographic variant (misspelling)
unjustified emendation
unavailable, incorrect orig. spelling
unavailable, literature misspelling
original name/combination
homonym & junior synonym
nomen protectum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN OBLITUM)
nomen oblitum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN PROTECTUM)

DELETE SINCE THESE CAN BE FOUND BY COMPUTER (DON'T NEED PEOPLE TO SPECIFY
THAT TWO NAMES SPELLED THE SAME ARE HOMONYMS) BUT GOOD IDEA TO SAVE IN
REMARKS WITH RELATED NAME
homonym (illegitimate)
junior homonym

UNUSED, DELETE
nomen nudum
ichnotaxon
junior homonym of
senior homonym of

MOVE TO REMARKS (THESE AREN'T RELATIONSHIP TERMS)
unavailable, suppressed by ruling
unavailable, other
unavailable, database artifact
unavailable, nomen nudum
other, see comments
database artifact
nomen dubium
misapplied

THESE TERMS DON'T SEEM LIKE TAXON STATUS TERMS TO ME. MOVE TO REMARKS? BUT
FOR THOSE WITH 'OF' INCLUDE THE RELATED TAXON NAME
pro parte
child of
hybrid offspring of
parent of

PROBLEMATIC - EACH CASE NEEDS TO BE EXAMINED. THOSE THAT ARE SYNONYMS
MARKED AS SUCH, THOSE THAT ARE HOMONYMS, DELETE

valid name for

On Thu, Jan 10, 2019 at 8:27 AM dustymc [e-mail] wrote:

These are not used:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from cttaxon_relation where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from taxon_relations);

TAXON_RELATIONSHIP

nomen nudum
junior homonym of
nomen protectum
ichnotaxon
senior homonym of

These are:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from taxon_relations;

TAXON_RELATIONSHIP

junior synonym of
homonym & junior synonym
unavailable, suppressed by ruling
nomen oblitum
subsequent name/combination
unnecessary replacement
unavailable, other
child of
synonym
hybrid offspring of
synonym of
other, see comments
unavailable, database artifact
database artifact
original name/combination
valid name for
nomen dubium
pro parte
parent of
unavailable, nomen nudum
unavailable, incorrect orig. spelling
homonym (illegitimate)
junior homonym
senior synonym of
orthographic variant (misspelling)
unjustified emendation
misapplied
accepted synonym of
unavailable, literature misspelling
superfluous renaming (illegitimate)

This should probably go back to the taxonomy committee for discussion if
we're changing direction.

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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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
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[DerekSikes]

Regarding:

MOVE TO REMARKS (THESE AREN'T RELATIONSHIP TERMS)
unavailable, suppressed by ruling
unavailable, other
unavailable, database artifact
unavailable, nomen nudum
other, see comments
database artifact
nomen dubium
misapplied

If any of these terms are used in a relationship currently, presumably one
of the names is valid (accepted) and the other invalid (unaccepted). If
this is true then we should replace with SYNONYM OF, move the old term (eg
unavailable, other) to remarks and ensure the name that had this term is
given taxon status = invalid and the other name given taxon status = valid.

However, some (most?) of the above can be used for names without specifying
a relationship. For example, a nomen dubium is a name in which the species
it belongs to is unknown - thus it can't be in a relationship with another
name as a synonym by definition (because that would imply we know what the
species is and it would no longer be a nomen dubium).

-Derek

On Thu, Jan 10, 2019 at 10:30 AM Derek Sikes [e-mail] wrote:

OK. Here's a more thorough breakdown. Only one term, 'valid name for,'
will need a case-by-case examination to clean up. What do others think?
-Derek

SYNONYM OF (DON'T SAVE IN REMARKS)
junior synonym of
accepted synonym of
senior synonym of
synonym
synonym of

SYNONYM OF (DO SAVE IN REMARKS)
superfluous renaming (illegitimate)
subsequent name/combination
unnecessary replacement
orthographic variant (misspelling)
unjustified emendation
unavailable, incorrect orig. spelling
unavailable, literature misspelling
original name/combination
homonym & junior synonym
nomen protectum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN OBLITUM)
nomen oblitum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN PROTECTUM)

DELETE SINCE THESE CAN BE FOUND BY COMPUTER (DON'T NEED PEOPLE TO SPECIFY
THAT TWO NAMES SPELLED THE SAME ARE HOMONYMS) BUT GOOD IDEA TO SAVE IN
REMARKS WITH RELATED NAME
homonym (illegitimate)
junior homonym

UNUSED, DELETE
nomen nudum
ichnotaxon
junior homonym of
senior homonym of

MOVE TO REMARKS (THESE AREN'T RELATIONSHIP TERMS)
unavailable, suppressed by ruling
unavailable, other
unavailable, database artifact
unavailable, nomen nudum
other, see comments
database artifact
nomen dubium
misapplied

THESE TERMS DON'T SEEM LIKE TAXON STATUS TERMS TO ME. MOVE TO REMARKS? BUT
FOR THOSE WITH 'OF' INCLUDE THE RELATED TAXON NAME
pro parte
child of
hybrid offspring of
parent of

PROBLEMATIC - EACH CASE NEEDS TO BE EXAMINED. THOSE THAT ARE SYNONYMS
MARKED AS SUCH, THOSE THAT ARE HOMONYMS, DELETE

valid name for

On Thu, Jan 10, 2019 at 8:27 AM dustymc [e-mail] wrote:

These are not used:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from cttaxon_relation where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from taxon_relations);

TAXON_RELATIONSHIP

nomen nudum
junior homonym of
nomen protectum
ichnotaxon
senior homonym of

These are:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from taxon_relations;

TAXON_RELATIONSHIP

junior synonym of
homonym & junior synonym
unavailable, suppressed by ruling
nomen oblitum
subsequent name/combination
unnecessary replacement
unavailable, other
child of
synonym
hybrid offspring of
synonym of
other, see comments
unavailable, database artifact
database artifact
original name/combination
valid name for
nomen dubium
pro parte
parent of
unavailable, nomen nudum
unavailable, incorrect orig. spelling
homonym (illegitimate)
junior homonym
senior synonym of
orthographic variant (misspelling)
unjustified emendation
misapplied
accepted synonym of
unavailable, literature misspelling
superfluous renaming (illegitimate)

This should probably go back to the taxonomy committee for discussion if
we're changing direction.

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--

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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

--

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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

[campmlc]

I agree with Derek's suggestion to only merge those terms that relate to
synonym.

Non-relationship terms such as nomen dubium have now been moved to Taxon
Status. We should add orthrographic variant (mispelling) to that too. I
still feel like we need another field - we are trying to put too many
disparate things together. Taxon Status should be 'valid" or "invalid", or
maybe "valid" according to "MVZ" and "invalid" according to "MSB" or
"invalid" because of "orthorographic variant" according to
"author/publication XX". I know this has been brought up before - but can
someone explain why this is or isn't possible?

On Thu, Jan 10, 2019 at 4:20 PM DerekSikes [e-mail] wrote:

Regarding:

MOVE TO REMARKS (THESE AREN'T RELATIONSHIP TERMS)
unavailable, suppressed by ruling
unavailable, other
unavailable, database artifact
unavailable, nomen nudum
other, see comments
database artifact
nomen dubium
misapplied

If any of these terms are used in a relationship currently, presumably one
of the names is valid (accepted) and the other invalid (unaccepted). If
this is true then we should replace with SYNONYM OF, move the old term (eg
unavailable, other) to remarks and ensure the name that had this term is
given taxon status = invalid and the other name given taxon status = valid.

However, some (most?) of the above can be used for names without specifying
a relationship. For example, a nomen dubium is a name in which the species
it belongs to is unknown - thus it can't be in a relationship with another
name as a synonym by definition (because that would imply we know what the
species is and it would no longer be a nomen dubium).

-Derek

On Thu, Jan 10, 2019 at 10:30 AM Derek Sikes [e-mail] wrote:

OK. Here's a more thorough breakdown. Only one term, 'valid name for,'
will need a case-by-case examination to clean up. What do others think?
-Derek

SYNONYM OF (DON'T SAVE IN REMARKS)
junior synonym of
accepted synonym of
senior synonym of
synonym
synonym of

SYNONYM OF (DO SAVE IN REMARKS)
superfluous renaming (illegitimate)
subsequent name/combination
unnecessary replacement
orthographic variant (misspelling)
unjustified emendation
unavailable, incorrect orig. spelling
unavailable, literature misspelling
original name/combination
homonym & junior synonym
nomen protectum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN OBLITUM)
nomen oblitum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN PROTECTUM)

DELETE SINCE THESE CAN BE FOUND BY COMPUTER (DON'T NEED PEOPLE TO SPECIFY
THAT TWO NAMES SPELLED THE SAME ARE HOMONYMS) BUT GOOD IDEA TO SAVE IN
REMARKS WITH RELATED NAME
homonym (illegitimate)
junior homonym

UNUSED, DELETE
nomen nudum
ichnotaxon
junior homonym of
senior homonym of

MOVE TO REMARKS (THESE AREN'T RELATIONSHIP TERMS)
unavailable, suppressed by ruling
unavailable, other
unavailable, database artifact
unavailable, nomen nudum
other, see comments
database artifact
nomen dubium
misapplied

THESE TERMS DON'T SEEM LIKE TAXON STATUS TERMS TO ME. MOVE TO REMARKS?
BUT
FOR THOSE WITH 'OF' INCLUDE THE RELATED TAXON NAME
pro parte
child of
hybrid offspring of
parent of

PROBLEMATIC - EACH CASE NEEDS TO BE EXAMINED. THOSE THAT ARE SYNONYMS
MARKED AS SUCH, THOSE THAT ARE HOMONYMS, DELETE

valid name for

On Thu, Jan 10, 2019 at 8:27 AM dustymc [e-mail]
wrote:

These are not used:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from cttaxon_relation
where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from
taxon_relations);

TAXON_RELATIONSHIP

>>

nomen nudum
junior homonym of
nomen protectum
ichnotaxon
senior homonym of

These are:

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from taxon_relations;

TAXON_RELATIONSHIP

>>

junior synonym of
homonym & junior synonym
unavailable, suppressed by ruling
nomen oblitum
subsequent name/combination
unnecessary replacement
unavailable, other
child of
synonym
hybrid offspring of
synonym of
other, see comments
unavailable, database artifact
database artifact
original name/combination
valid name for
nomen dubium
pro parte
parent of
unavailable, nomen nudum
unavailable, incorrect orig. spelling
homonym (illegitimate)
junior homonym
senior synonym of
orthographic variant (misspelling)
unjustified emendation
misapplied
accepted synonym of
unavailable, literature misspelling
superfluous renaming (illegitimate)

This should probably go back to the taxonomy committee for discussion if
we're changing direction.

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--

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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

--

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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

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[dustymc]

nomen dubium have now been moved to Taxon Status.

Nope

https://github.com/ArctosDB/arctos/issues/1136#issuecomment-453182079

UAM@ARCTOS> select a.scientific_name,b.scientific_name from taxon_name a, taxon_name b, taxon_relations where a.taxon_name_id=taxon_relations.taxon_name_id and b.taxon_name_id=taxon_relations.related_taxon_name_id and taxon_relationship in ('nomen dubium');


SCIENTIFIC_NAME
------------------------------------------------------------------------------------------------------------------------
SCIENTIFIC_NAME
------------------------------------------------------------------------------------------------------------------------
Etrumeus teres
Etrumeus sadina

Tenualosa reevesii
Clupea sinensis

Motacilla tschutschensis alascensis
Motacilla flava alascensis

Maccaffertium flaveolum
Stenacron flaveolum

Microprius rufulus
Eudesmula californica

Pteragogus flagellifer
Labrus ramentosus

Bufo spinulosus
Bufo nigricans

Polymerurus macrurus
Ichthydium macrurum

Peripatopsis capensis
Peripatus brevis

Eremomela scotops pulelira
Eremomela scotops pulchra

Prinia jacksoni
Apalis jacksoni

Pycnophyes
Pycnophyes denticulatus

Pycnophyes
Pycnophyes echinoderoides

Desmognathus fuscus
Desmognathus fuscus fuscus

Desmognathus fuscus
Salamandra fusca

Carangoides ciliarius
Caranx armatus

Motacilla flava alascensis
Motacilla tschutschensis

Reguliidae
Regulidae


18 rows selected.

We should add ... to that too.

Maybe we should do both, but those are functionally different fields. Taxon status (and other terms) provide information about a single name (and metadata). Relationships lead to other names. Someone searching for "Reguliidae" (status=nomen dubium) just doesn't find anything. Someone searching for Reguliidae (some_relationship of Regulidae) finds specimens identified as Regulidae.

trying to put too many disparate things together

Not much argument from me.

explain why this is or isn't possible?

UAM@ARCTOS> UAM@ARCTOS> desc taxon_term;
 Name                                  Null?    Type
 ----------------------------------------------------------------- -------- --------------------------------------------
 TAXON_TERM_ID                             NOT NULL NUMBER -- primary key; doesn't do anything
 TAXON_NAME_ID                             NOT NULL NUMBER -- foreign key
 CLASSIFICATION_ID                              VARCHAR2(4000) -- groups terms into classification
 TERM                                  NOT NULL VARCHAR2(4000) -- the one single value in a record
 TERM_TYPE                                  VARCHAR2(255) -- the one single key in a record
 SOURCE                                NOT NULL VARCHAR2(255) -- FKEY taxon_source
 GN_SCORE                                   NUMBER -- GN's magic as an integer
 POSITION_IN_CLASSIFICATION                         NUMBER -- orders stuff
 LASTDATE                              NOT NULL DATE -- housekeeping
 MATCH_TYPE                                 VARCHAR2(255) -- GN stuff

There's no third field. We could add something, but not in our model (and maybe not with our computational power).

whatever - controlled-value - free-text details

and

whatever - free-text details

look functionally identical (ish) given the use case to me, but whatever...

[campmlc]

The code table for Taxon Status has nomen dubium . . . ?
http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_STATUS

[dustymc]

and so does http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_RELATION

[Jegelewicz]

we need another field - we are trying to put too many disparate things together. Taxon Status should be 'valid" or "invalid", or maybe "valid" according to "MVZ" and "invalid" according to "MSB" or "invalid" because of "orthorographic variant" according to "author/publication XX". I know this has been brought up before - but can someone explain why this is or isn't possible?

I suggest we add the field PREFERRED BY COLLECTION which would be a controlled vocabulary including all collection GUID prefixes and could be used any number of times. This would fulfill the "valid according to" need.

Perhaps instead of TAXON STATUS (valid/invalid) we need two fields:

VALID ACCORDING TO - which could hold a publication, author text, or other source info (web page)
INVALID ACCORDING TO - ditto

If these could be used without limit, then we could display all possible opinions.

[dustymc]

Given the current structure, there are two possibilities here:

• paired terms (simple vocabulary, basically no way of enforcing anything, complicates everything)
• a single term with less-simple vocabulary (much more usable, slightly less searchable)

We don't search this, ever. A user is cataloging a woodfrog and gets Rana and Lithobates in the pick. They need to pick one if they're working in a particular collection. That is, as far as I know, the entirety of the use case.

I know of perhaps a dozen taxa for which this is a problem (and I'm not entirely sure it's a real problem for them). I think we're over-complicating this.

[dustymc]

I think the "preferred" stuff is addressed in https://github.com/ArctosDB/arctos/issues/1851. That leave relationships.

Here's the code table before I did anything.

cttaxon_relation.csv.zip

I deleted unused relationships.

UAM@ARCTOS> select distinct TAXON_RELATIONSHIP from cttaxon_relation where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from taxon_relations);

TAXON_RELATIONSHIP
------------------------------------------------------------------------------------------------------------------------
nomen nudum
junior homonym of
nomen protectum
ichnotaxon
senior homonym of

5 rows selected.

Elapsed: 00:00:01.06
UAM@ARCTOS> delete from cttaxon_relation where TAXON_RELATIONSHIP not in (select TAXON_RELATIONSHIP from taxon_relations);

5 rows deleted.

That leaves this

UAM@ARCTOS> select TAXON_RELATIONSHIP from cttaxon_relation order by TAXON_RELATIONSHIP;

TAXON_RELATIONSHIP
------------------------------------------------------------------------------------------------------------------------
accepted synonym of
child of
database artifact
homonym & junior synonym
homonym (illegitimate)
hybrid offspring of
junior homonym
junior synonym of
misapplied
nomen dubium
nomen oblitum
original name/combination
orthographic variant (misspelling)
other, see comments
parent of
pro parte
senior synonym of
subsequent name/combination
superfluous renaming (illegitimate)
synonym
synonym of
unavailable, database artifact
unavailable, incorrect orig. spelling
unavailable, literature misspelling
unavailable, nomen nudum
unavailable, other
unavailable, suppressed by ruling
unjustified emendation
unnecessary replacement
valid name for

30 rows selected.

Low-hanging fruit

-- bah, bunch had both
UAM@ARCTOS>  update taxon_relations set TAXON_RELATIONSHIP='synonym of' where TAXON_RELATIONSHIP='synonym';

21453 rows updated.

Elapsed: 00:00:10.49
UAM@ARCTOS> delete from cttaxon_relation where TAXON_RELATIONSHIP='synonym';

1 row deleted.

Here are relationships (as strings) - might help with some of the discussion.

create table temp_tax_reln as select
 a.scientific_name onename,
 b.scientific_name othername,
 TAXON_RELATIONSHIP,
 RELATION_AUTHORITY
from 
taxon_name a,
taxon_name b,
taxon_relations
where
taxon_relations.TAXON_NAME_ID=a.TAXON_NAME_ID and
taxon_relations.RELATED_TAXON_NAME_ID=b.TAXON_NAME_ID and
TAXON_RELATIONSHIP != 'synonym of';

temp_tax_reln.csv.zip

From Derek's comments https://github.com/ArctosDB/arctos/issues/1136#issuecomment-453223615:

junior synonym of accepted synonym of senior synonym of synonym synonym of

Do I have final approval to switch these to "synonym of"?

superfluous renaming (illegitimate) subsequent name/combination unnecessary replacement orthographic variant (misspelling) unjustified emendation unavailable, incorrect orig. spelling unavailable, literature misspelling original name/combination homonym & junior synonym nomen protectum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN OBLITUM) nomen oblitum (SHOULD HAVE A SYNONYMOUS RELATED NOMEN PROTECTUM)

Do I have final approval to switch these to "synonym of" with the original relationship in remarks?

DELETE SINCE THESE CAN BE FOUND BY COMPUTER (DON'T NEED PEOPLE TO SPECIFY THAT TWO NAMES SPELLED THE SAME ARE HOMONYMS) BUT GOOD IDEA TO SAVE IN REMARKS WITH RELATED NAME homonym (illegitimate) junior homonym

IDK what these are (plant-thing?), but it's not that kind of homonym - it's things like

Bactrocera xanthodes
Tephrites xanthodes
homonym & junior synonym
ITIS

Can I make them synonym + remarks as well?

can we work through that much and then deal with whatever's left?

[Jegelewicz]

I am OK with this.

[campmlc]

Me too.

On Mon, Jan 28, 2019 at 3:32 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

I am OK with this.

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[DerekSikes]

me too

On Mon, Jan 28, 2019 at 2:01 PM Mariel Campbell [e-mail]
wrote:

Me too.

On Mon, Jan 28, 2019 at 3:32 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

I am OK with this.

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Professor of Entomology
University of Alaska Museum
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[email protected]

phone: [phone]
FAX: [phone]

University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
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[sharpphyl]

If you eliminate
junior synonym of
accepted synonym of
senior synonym of

and just use synonym of

will you change the taxon status from valid to invalid on everything that was a junior synonym or was not the accepted or senior synonym?? That's the only way we will now know which taxon is the preferred synonym.

[dustymc]

A bunch of those are wrong - apparently mangled from ITIS or something.

Relationships are linked to names. Status (and friends) is an attribute of classifications. It's not a clear path across.

I could maybe stuff something in somewhere random anyway...

Should I just add a remark eg "former relationship: {taxonA} {original relationship} {taxonB}" or something for everything, and then delete those if/as we find they're not useful??

[dustymc]

Much of this is done. Here's what's left:

UAM@ARCTOS>  select TAXON_RELATIONSHIP || ' @ ' || count(*) from taxon_relations group by TAXON_RELATIONSHIP;

TAXON_RELATIONSHIP||'@'||COUNT(*)
------------------------------------------------------------------------------------------------------------------------
unavailable, suppressed by ruling @ 41
unavailable, other @ 36
child of @ 5
hybrid offspring of @ 9
synonym of @ 916612
other, see comments @ 713
unavailable, database artifact @ 679
database artifact @ 36
valid name for @ 396
nomen dubium @ 18
parent of @ 2
pro parte @ 2
unavailable, nomen nudum @ 176
homonym (illegitimate) @ 2
junior homonym @ 561
misapplied @ 7

16 rows selected.

I did not keep the original for some, as suggested by Derek. (It's in the CSV above if we really want it back.) I think "I don't think we should save the old terms in remarks because so many of them are backwards and wrong." is more true than anyone could have known; these terms were used in every imaginable combination, and look a lot more like random things happening randomly over time than any sort of data-based pattern. From that, I suspect the "original" data we did save is just garbage and should be deleted to prevent confusion, and I suggest we simply merge the remainder into "synonym" without comment.

[DerekSikes]

Nomen dubium is not a relationship term. It's statement that the name can't
be properly associated with a species. Thus, if we knew what the name was a
synonym of we'd know what species it belonged to and it wouldn't be a nomen
dubium (unless it was a synonym of another nomen dubium!)

This remainder list I think we should definitely save in remarks.

-D

On Tue, Jan 29, 2019 at 7:24 AM dustymc [e-mail] wrote:

Much of this is done. Here's what's left:

UAM@ARCTOS> select TAXON_RELATIONSHIP || ' @ ' || count(*) from taxon_relations group by TAXON_RELATIONSHIP;

TAXON_RELATIONSHIP||'@'||COUNT(*)

unavailable, suppressed by ruling @ 41
unavailable, other @ 36
child of @ 5
hybrid offspring of @ 9
synonym of @ 916612
other, see comments @ 713
unavailable, database artifact @ 679
database artifact @ 36
valid name for @ 396
nomen dubium @ 18
parent of @ 2
pro parte @ 2
unavailable, nomen nudum @ 176
homonym (illegitimate) @ 2
junior homonym @ 561
misapplied @ 7

16 rows selected.

I did not keep the original for some, as suggested by Derek. (It's in the
CSV above if we really want it back.) I think "I don't think we should save
the old terms in remarks because so many of them are backwards and wrong."
is more true than anyone could have known; these terms were used in every
imaginable combination, and look a lot more like random things happening
randomly over time than any sort of data-based pattern. From that, I
suspect the "original" data we did save is just garbage and should be
deleted to prevent confusion, and I suggest we simply merge the remainder
into "synonym" without comment.

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--

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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]

Nomen dubium is not a relationship term.

https://github.com/ArctosDB/arctos/issues/1136#issuecomment-453364662

I have no idea what the intent was, but there's the result....

Unless someone has better ideas in the next couple hours, I'll update those and keep the original. We can use nomen dubium to practice getting rid of that if necessary!

[dustymc]

UAM@ARCTOS>  select TAXON_RELATIONSHIP from cttaxon_relation order by TAXON_RELATIONSHIP;

TAXON_RELATIONSHIP
------------------------------------------------------------------------------------------------------------------------
synonym of