taxon status

[dustymc]

http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_STATUS is insufficient. Some collections prefer Rana, some Lithobates, everyone agrees the names refer to the same sort of critters.

1) We need more specific vocabulary. "preferred by {collection}" (publication? author? curator? institution? all of the above??) or something 2) We need to clarify that the intent is only in how the taxon is applied in certain circumstances (eg, by a collection). There are no Code implications, even though the current terminology is used by various Codes in various ways. 3) This needs to be available in the taxonomy pick forms.

And can 'valid species' be merged into 'valid'?

[DerekSikes]

see below

On Wed, Sep 19, 2018 at 1:58 PM, dustymc notifications@github.com wrote:

http://arctos.database.museum/info/ctDocumentation.cfm? table=CTTAXON_STATUS is insufficient. Some collections prefer Rana, some Lithobates, everyone agrees the names refer to the same sort of critters.

1. We need more specific vocabulary. "preferred by {collection}" (publication? author? curator? institution? all of the above??) or something

agreed - I think institution would be the best but any institution would also want to cite a source (eg publication) but as a text field rather than a link to a publication record (although the latter would be a nice option, just not ideal to make required?)

1. We need to clarify that the intent is only in how the taxon is applied in certain circumstances (eg, by a collection). There are no Code implications, even though the current terminology is used by various Codes in various ways.

yes

1. This needs to be available in the taxonomy pick forms.

yes

And can 'valid species' be merged into 'valid'?

yes

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

dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

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 like the idea of including author whenever possible, and perhaps make it required entry via a pop-up if there is more than one classification in Arctos for the same name. Institution OK also.

On Wed, Sep 19, 2018 at 4:28 PM, DerekSikes notifications@github.com wrote:

see below

On Wed, Sep 19, 2018 at 1:58 PM, dustymc notifications@github.com wrote:

http://arctos.database.museum/info/ctDocumentation.cfm? table=CTTAXON_STATUS is insufficient. Some collections prefer Rana, some Lithobates, everyone agrees the names refer to the same sort of critters.

1. We need more specific vocabulary. "preferred by {collection}" (publication? author? curator? institution? all of the above??) or something

agreed - I think institution would be the best but any institution would also want to cite a source (eg publication) but as a text field rather than a link to a publication record (although the latter would be a nice option, just not ideal to make required?)

1. We need to clarify that the intent is only in how the taxon is applied in certain circumstances (eg, by a collection). There are no Code implications, even though the current terminology is used by various Codes in various ways.

yes

1. This needs to be available in the taxonomy pick forms.

yes

And can 'valid species' be merged into 'valid'?

yes

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+++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Professor of Entomology University of Alaska Museum 1962 Yukon Drive https://maps.google.com/?q=1962+Yukon+Drive+%0D%0AFairbanks,+AK+++99775&entry=gmail&source=g Fairbanks, AK 99775-6960

dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

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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[Jegelewicz]

See also #1079

[Jegelewicz]

See also #1126

[dustymc]

And can 'valid species' be merged into 'valid'? yes

done

including author whenever possible,

See display_name at http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXON_TERM - it's intended to be sprinkled around ("properly" formatting a name with author(s) can be non-trivial).

[dustymc]

available in the taxonomy pick forms.

Done.

also want to cite a source (eg publication) but as a text field rather than a link to a publication record (although the latter would be a nice option, just not ideal to make required?)

Text can't DO anything. If these data are important, they should be in the publication system (by DOI if at all possible - check out the "CrossRef Data" links in publications and projects for a small glimpse of what's possible there).

There's a place for publications (in the non-classification data) and lots of places for text. I'm happy to talk about the structure of that, but that almost certainly deserves it's own issue.

Relationships will get someone searching "Lithobates" to specimens identified using "Rana," and publications supporting those relationships will tell them WHY they searched Lithobates and found a bunch of Rana. Those data are certainly critical, but I don't think they belong here. I think the role of taxon_status is limited to "[don't] click here" - eg, "this collection wants you to use Rana instead of Lithobates for some sort of internal/curatorial/random reason."

Please let me know if I'm not understanding something.

[Jegelewicz]

It seems like we need a good definition of TAXON_STATUS

My confusion comes from the ITIS definition:

Taxonomic Status:

Current Standing (but see Data Quality Indicators, below) The status of a name for a taxon in the taxonomic judgment of an author and/or an ITIS steward.

don't think we should be using this field for the purpose expressed in the first comment of this issue.

[Jegelewicz]

Taxonomy Committee:

Valid/accepted or invalid/unaccepted in TAXON_STATUS along with “according to” (a publication or other authoritative source) will indicate which is valid/accepted.

AWG agrees that Taxon Status needs an attached authority:

TAXON_STATUS = Valid/accepted or Invalid/unaccepted “Accepted” as used as “valid” for taxon status in other databases: http://www.marinespecies.org/aphia.php?p=taxdetails&id=125527 For plants? Valid/accepted or invalid/unaccepted in TAXON_STATUS along with “according to” (a publication or other authoritative source) will indicate which is valid/accepted.

@dustymc can we get paired status and authority?

[dustymc]

can we get paired status and authority?

Not without major structural changes. I suggest putting the status-authority in the value. "valid (WoRMS") and similar.

[Jegelewicz]

That is not what everyone was thinking and wouldn't it make it very hard to find "valid" with all that extra stuff in there (it's not normalized...)?

I'm pretty sure everyone was discussing status=valid, authority=WoRMS

[dustymc]

I agree it's not ideal, but it's what I can readily do with the tools I have available.

... and term like 'valid%'... finds things that start with or are "valid" - if we're consistent in the vocabulary, which shouldn't be hard to do under code table control, I'm not sure we're giving up anything here.

You can of course enter two terms

• status=valid
• authority=WoRMS

but you can also enter 4 terms

• status=valid
• status=something else
• authority=WoRMS
• authority=something else

which I assume is what you were getting at with "paired."

[Jegelewicz]

Yup because we need to know which authority goes with which status...

[DerekSikes]

Why not have it work like we do with multiple agents eg:

status1 = valid status2 = invalid authority1= WoRMS authority2 = Smith pers. comm. etc.

And require a paired authority for a status to save.

-Derek

On Thu, Dec 13, 2018 at 1:43 PM Teresa Mayfield-Meyer < notifications@github.com> wrote:

Yup because we need to know which authority goes with which status...

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

dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

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]

I certainly use the childthing{n} format for things that have to go through a spreadsheet-like environment, but data are never stored that way. That's essentially a local DarwinCore - it's a usable transport mechanism (until someone has an extra part/agent name/whatever), but it's not a suitable storage/management model.

Taxon_term is a large table (155058374 rows and growing rapidly) and we have somewhat limited resources so performance isn't something I can ignore.

Finding anything that anyone thinks might be "valid" is straightforward in either case - it's a LIKE match on one side or the other, to TERM in my proposal or TERM_TYPE in the other.

To find things that someone specific considers valid....

• In the denormalized model, I'd have to grab all of the relevant authorities, sort through them with a LIKE to find what I need, then requery to with two IS. I'd also need some sort of code to keep the terms paired, which is anything but trivial in a system designed to accept whatever comes out of WoRMS or GlobalNames. Given a new value, we'd need to add two values to one code table and one to another, and then see the two anytime we access the primary code table.

• In what I'm proposing, this is one LIKE query. Dependencies are normalized to the code table; there's no additional cost once the values are created. All of the extra code table values are in a secondary code table, where they're not visible until they're needed.

[DerekSikes]

Not sure I understand... but perhaps relevant: in the specimens search form at the bottom of the curatorial section we can now search specimens based on their taxon status (so I can in theory find any of my specimens that have invalid names as IDs).

However, when I was using this yesterday I could get no searches to complete. They all timed out.

-Derek

On Fri, Dec 14, 2018 at 7:38 AM dustymc notifications@github.com wrote:

I certainly use the childthing{n} format for things that have to go through a spreadsheet-like environment, but data are never stored that way. That's essentially a local DarwinCore - it's a usable transport mechanism (until someone has an extra part/agent name/whatever), but it's not a suitable storage/management model.

Taxon_term is a large table (155058374 rows and growing rapidly) and we have somewhat limited resources so performance isn't something I can ignore.

Finding anything that anyone thinks might be "valid" is straightforward in either case - it's a LIKE match on one side or the other, to TERM in my proposal or TERM_TYPE in the other.

To find things that someone specific considers valid....

-

In the denormalized model, I'd have to grab all of the relevant authorities, sort through them with a LIKE to find what I need, then requery to with two IS. I'd also need some sort of code to keep the terms paired, which is anything but trivial in a system designed to accept whatever comes out of WoRMS or GlobalNames. Given a new value, we'd need to add two values to one code table and one to another, and then see the two anytime we access the primary code table.

In what I'm proposing, this is one LIKE query. Dependencies are normalized to the code table; there's no additional cost once the values are created. All of the extra code table values are in a secondary code table, where they're not visible until they're needed.

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--

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

dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

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]

all timed out

Hence my performance concerns!

I'll see if I can tune that up a bit, but more processors certainly wouldn't hurt anything.

[dustymc]

Going with https://github.com/ArctosDB/arctos/issues/1851