nature of ID

[dustymc]

http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID is a mess.

Ideally I think we should say something about the evidence used for the ID, but that doesn't seem possible. Minimally we can not say the same thing a bunch of different ways?

NATURE_OF_ID	Documentation	Hu?
ID of kin	An identification based upon the identification of another related individual, often the mother of an embryo. Such a specimen should have at least one individual relationship.	spiffy
ID to species group	Within a genus, some groups of closely related species are referred to by the species name of one widespread or well known species within the group.	Hu? This (and much more) can be done with eg, Sorex {Sorex cinereus complex}, I don't think we need multiple ways of doing that.
curatorial	An identification determined by qualified personnel assisting with collection management including collection managers, curators, trained students, staff and others who may not be experts in the group in question but have some knowledge of relevant taxonomy.	this looks functionally identical to student
erroneous citation	The specimen has been cited in refereed scientific literature by this name but this name is clearly wrong. This situation arises mostly from typographical errors in catalog numbers.	spiffy - or not, but it happens
expert	The determiner is a person recognized by other experts working with the taxa in question, or the regional biota.	this looks functionally identical to student, or at least heavily overused. One agent is an expert on 7112 different taxa! Users have the tools to decide who they consider experts and act on that.
field	A determination made without access to specialized equipment or references.	"Looks like a moose" may be necessary, but I'm still not sure how it's not yet another version of 'student.'
geographic distribution	Specimen is assumed, on the basis of known geographic ranges, to be the species or subspecies expected at the collecting locality. The specimen has not been identified to species or subspecies by comparing it to other subspecies within the genus or species. "It's probably that species because that species lives there and we know what species lives there because we're museums and telling people where stuff lives is what we do....."	still looks circular to me
legacy	The identification has been transposed from an earlier version of data that did not include identification metadata. In this case the date of the determination is the date that the data were transposed, and the determiner is unknown.	I think we're stuck with the concept, but maybe "unknown" is a better label
molecular data	An identification made by a laboratory analysis comparing the specimen to related taxa by molecular criteria, generally DNA sequences.	yay us!
photograph	"Field ID" or perhaps "morphology" is probably always more important than this.	"student" version 5
published referral	The specimen has been specifically determined to be of a particular taxon in a publication that describes or re-describes that taxon, but the specimen has no type status. Such a specimen record should include a citation, and the determiner(s) of record should be among the authors of the publication. (This means nothing.)	I still have no idea what this means
revised taxonomy	This designation is appropriate only in the presence of an earlier identification. It implies that the specimen has not been reexamined, and only that a different taxonomic name is being applied. In most cases this results from taxonomic synonymization of names.	we're stuck with this
student	Specimen has been identified by a person using appropriate references, knowledge, and/or and tools, but not by an expert. This is a broad use of the term student.	I think maybe everyone hates the label, but the concept seems accurate for the vast majority of our identifications
type specimen	This particular specimen has been described in the literature by this name. The specimen record should contain a citation of the appropriate literature,and the determiner(s) of record should be among the authors of the publication.	yay us!

@ccicero

[ccicero]

I'm ok with the confidence score.

Are we settled on the vocabulary? I'm still strugging with 'fine features' and 'coarse features' - I like the contrast, but it just sounds funny to me when applied to birds and isn't really clear without reading the definition. Can we think of something better that works for cultural as well as natural history specimens? Can we use 'fine traits' and 'coarse traits' instead? We use trait-based data all the time, and I think (?) that is clearer for natural history phenotypic information but does it work for cultural collections @AJLinn ?

We need to work on the migration path.

[dustymc]

fine features' and 'coarse features'

It's not COMPLETELY painless, but changing vocabulary, as long as we're not altering the concept/meaning, isn't too difficult. I'm not thrilled with the current vocab either, but I think it sufficiently says what we're trying to get across.

I think "trait" may in some communities be tainted with the implication of precise measurements, but otherwise I like it....

I've made some minor updates to the migration tab on the spreadsheet. Again this will be a "it's been X time and nobody's contacted me" fallback; I will work with anyone who wants to to bring their data across in non-default ways, and the path I've laid out above doesn't require us to do that before moving to the new vocabulary/structure. I can also retain the old values in remarks, so we can revisit anything that didn't get migrated as it should have.

FWIW in looking for "ID of kin" I scrolled by "relationship" about 8 times - perhaps that term could still use some help (or maybe it's just me...).

[campmlc]

For ID of kin, there may not be an explicitly stated relationship to another individual. The relationship may be to others in a captive breeding population, and we only have some of those individuals cataloged in Arctos, and we don't have all the familiar relationships tracked.

[dustymc]

I can't readily enforce such things (and don't really want to), but without a relationship the 'relationship' identification is less than useless. We are asserting that this is the same as something else, but you can't have any of that because we're not going to tell you what it is. I very strongly recommend we add the caution regarding relationships back to the documentation.

I don't think any of the reasons given are barriers - nests and eggs can be cataloged and referenced, sightings can be cataloged as observations, reference material in other collections can be linked (or at least given IDs, which will presumably become links when the other collection gets better technology), etc.

In the case @campmlc mentioned, I'd probably use 'unknown' and elaborate in remarks: "This specimen was not examined, but it is the sibling of ABCXYZ which was examined using......"

[AJLinn]

Can we use 'fine traits' and 'coarse traits' instead? We use trait-based data all the time, and I think (?) that is clearer for natural history phenotypic information but does it work for cultural collections @AJLinn ?

"Traits" instead of "features" should be fine for us. Any of these new changes will require some re-training, but that's just fine with me if it gives us more clear explanations! Just curious... if we go thru and make changes/updates to the nature of ID based on these new categories, does Arctos retain a history of those changes so we can see "it used to be IDed as a toggle but someone with a high confidence changed it to be a belt fastener on this date"? I assume so, but I don't know how to get at that info.

[dustymc]

@AJLinn ID history is preserved, but the old terminology will only be preserved in remarks.

http://arctos.database.museum/guid/MSB:Mamm:55245 has a bunch of IDs, all in agreement with each other.

I can certainly 'unaccept' the current ID and add one as part of the migration process if that's somehow useful to you.

[AJLinn]

@AJLinn ID history is preserved, but the old terminology will only be preserved in remarks.

http://arctos.database.museum/guid/MSB:Mamm:55245 has a bunch of IDs, all in agreement with each other.

In that example, those additional IDs were inserted by "Add Determination", right? Is there a best practice for making changes, by "Edit an Existing Determination" vs. "Add Determination"? Will the most current & highest confidence be privileged over the later, lower confidence ID if they're just added vs. editing? If we use edit to change, we would manually enter the change history in remarks?

[dustymc]

inserted by "Add Determination", right?

Yes, same pathway/structure anyway - they were likely created with the citation bulkloader.

"Edit an Existing Determination" vs. "Add Determination"

If you're not changing anything fundamental, edit is probably OK. If you're changing something fundamental, or adding new opinions (including those that agree with current opinions), add is better. I don't think adding can ever be "wrong."

You can choose "accept" (or not) when creating an ID. A new accepted will push everything else to unaccepted; nothing manual is required.

You can explicitly choose which ID is accepted - eg, keeping an older or lower-confidence ID as accepted is fine, that's 100% a curatorial call.

[dustymc]

I'm going to next task and implement per https://github.com/ArctosDB/arctos/issues/2170#issuecomment-514784485 unless someone stops me soonish, lest this falls through the cracks again.

[dustymc]

The table structure is in place and the single-record form can access identification_confidence. I'll get the other Arctos forms next.

After that I'll add https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899 to the code table, and then I intend to disallow usage of existing terms - I can't just get rid of them until we've migrated everything. That's probably going to be a bit disruptive for things currently in the bulkloader - please let me know if I can help update anything.

Can we NOT implement identification_confidence in the bulkloader for the time being? It should be there, but if there is not an immediate need I would like to delay that until we get to a new system so I don't have to rebuild a huge amount of complex code in two languages. If there is an immediate need I'll just deal with it.

[dustymc]

"legacy terms" are now blocked from new ~usage~ insert; they can still be used for update (necessary to allow adding identifications, which implicitly updates all existing IDs). I'm increasing priority of this; the longer we put off finalizing migration, the more chances that will have to cause problems.

/remind me, check back in two weeks

I am taking migration requests. I'll do something hopefully-not-too-random (and leave verbose remarks) with the legacy data if I don't receive specific instructions in the next two weeks.

Here's a very tentative plan. Please let me know if I can make any of these updates globally (for all identifications in all collections) now; some seem straightforward, but perhaps I'm missing something.

ID of kin --> relationship ID to species group --> unknown curatorial --> unknown erroneous citation --> unknown expert --> unknown field --> unknown legacy --> unknown - CAN I DO THIS NOW? molecular data--> molecular - CAN I DO THIS NOW? photograph --> unknown published referral --> unknown ~revised taxonomy --> taxonomic revision - CAN I DO THIS NOW?~ student --> unknown type specimen --> unknown

[DerekSikes]

Dusty,

I need all the IDs in my collections with nature of id 'expert' -> confidence = 'high'

& why are you planning on changing 'revised taxonomy' back to 'taxonomic revision'????? We changed 'taxonomic revision' to 'revised taxonomy' for very good reasons!! They should stay 'revised taxonomy'!!

Re: molecular data-> molecular.... sure, why not

re: legacy-> unknown .... I suppose so.

I also want all my nature of id 'student' to have confidence = medium

& nature of ID 'type specimen' should not become 'unknown' !! those are the HIGHEST confidence IDs we can possibly have, since the name they are given is correct, by definition.

-Derek

On Wed, Oct 2, 2019 at 10:55 AM dustymc notifications@github.com wrote:

"legacy terms" are now blocked from new usage insert; they can still be used for update (necessary to allow adding identifications, which implicitly updates all existing IDs). I'm increasing priority of this; the longer we put off finalizing migration, the more chances that will have to cause problems.

!remind me, check back in two weeks

I am taking migration requests. I'll do something hopefully-not-too-random (and leave verbose remarks) with the legacy data if I don't receive specific instructions in the next two weeks.

Here's a very tentative plan. Please let me know if I can make any of these updates globally (for all identifications in all collections) now; some seem straightforward, but perhaps I'm missing something.

ID of kin --> relationship ID to species group --> unknown curatorial --> unknown erroneous citation --> unknown expert --> unknown field --> unknown legacy --> unknown - CAN I DO THIS NOW? molecular data--> molecular - CAN I DO THIS NOW? photograph --> unknown published referral --> unknown revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? student --> unknown type specimen --> unknown

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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]

nature of id 'expert' ->confidence = 'high'

I need a new value for nature - that's not a change, it's an addition.

nature of id 'student' to have confidence = medium

ditto

hanging 'revised taxonomy' back to 'taxonomic revision'?????

That's what's in the spreadsheet: https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

'type specimen' should not become 'unknown' !!

What should they become then? I certainly don't know how they were made!

HIGHEST confidence

That's a separate issue. "We don't know where this came from (nature_of_id=unknown), but it can't possibly be wrong (confidence=high)" fits in the new model.

[DerekSikes]

D,

I just don't want to lose nature of ID = expert BEFORE we set confidence for those IDs to High, otherwise, how would we do so??

& ditto for nature of ID = student

Re: revised taxonomy.... what argument was made to change this back to taxonomic revision?? I'm sure there's a record of all the discussion on this but in a nutshell, 'revised taxonomy' is better because the term 'revision' has a specific meaning in taxonomy and not all taxonomic changes come from taxonomic revisions. Thus it is confusing and misleading to use 'taxonomic revision'. Change the table.

re: type specimens - if we don't want to keep this in nature of ID then it should be in the confidence field. It would represent a step above 'high', at least for primary types... My concern is there must be specimens with nature of ID = type specimen that are not linked to publications via a citation as 'types' & thus we'll loose this information. Perhaps it should be added to ID remarks to ensure it's not lost?

-Derek

On Wed, Oct 2, 2019 at 11:07 AM dustymc notifications@github.com wrote:

nature of id 'expert' ->confidence = 'high'

I need a new value for nature - that's not a change, it's an addition.

nature of id 'student' to have confidence = medium

ditto

hanging 'revised taxonomy' back to 'taxonomic revision'?????

That's what's in the spreadsheet: https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

'type specimen' should not become 'unknown' !!

What should they become then? I certainly don't know how they were made!

HIGHEST confidence

That's a separate issue. "We don't know where this came from (nature_of_id=unknown), but it can't possibly be wrong (confidence=high)" fits in the new model.

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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]

D - I'd prefer to set them all at once so they don't have an opportunity to get mixed up with any 'legacy' values.

UPDATE identification SET nature=newthing, confidence=whatever WHERE {anything I can get from existing data - collection, agent, nature, dates, publications, whatever}

is my strong preference.

revised taxonomy.... what argument

I have none - I'm just copying from the spreadsheet!

My concern is there must be specimens with nature of ID = type specimen that are not linked to publications via a citation as 'types'

Very possible, and I'd interpret that the other way - there's no publication, this therefore can't be a type, someone used the wrong nature.

added to ID remarks

Perhaps instead of by-request I should just add the original to remarks for everything that gets updated from this. It's no problem to do so.

[dustymc]

/remind me to finalize this in 2 weeks

[reminders[bot]]

@dustymc set a reminder for Oct 16th 2019

[DerekSikes]

Perhaps instead of by-request I should just add the original to remarks

for everything that gets updated from this. It's no problem to do so.

yes - sounds good

 there's no publication, this therefore can't be a type, someone used

the wrong nature.

Illogical. Nothing prevents people from failing to enter publications for real types.

& re: revised taxonomy. Just fix the spreadsheet

-D

On Wed, Oct 2, 2019 at 11:25 AM dustymc notifications@github.com wrote:

D - I'd prefer to set them all at once so they don't have an opportunity to get mixed up with any 'legacy' values.

UPDATE identification SET nature=newthing, confidence=whatever WHERE {anything I can get from existing data - collection, agent, nature, dates, publications, whatever}

is my strong preference.

revised taxonomy.... what argument

I have none - I'm just copying from the spreadsheet!

My concern is there must be specimens with nature of ID = type specimen that are not linked to publications via a citation as 'types'

Very possible, and I'd interpret that the other way - there's no publication, this therefore can't be a type, someone used the wrong nature.

added to ID remarks

Perhaps instead of by-request I should just add the original to remarks for everything that gets updated from this. It's no problem to do so.

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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]

Unless someone explicitly directs me otherwise, all updates will include...

AND id_remarks+=Original Nature_of_ID: {oldvalue}

fix the spreadsheet

I don't think that's my call - those values (which have already been implemented) got there by consensus (maybe...). I don't know if someone feels that the current term is better for some reason, or it's just arbitrary. I think @jldunnum had something to say at some point?? @ccicero @campmlc you edited the spreadsheet??

I have no opinion - I think they're saying the same THING, I think it's a straight update (won't require changing confidence), should be easy to update when I figure out how we got here.

[DerekSikes]

Just to reiterate what I wrote previously:

Re: revised taxonomy.... what argument was made to change this back to taxonomic revision?? I'm sure there's a record of all the discussion on this but in a nutshell, 'revised taxonomy' is better because the term 'revision' has a specific meaning in taxonomy and not all taxonomic changes come from taxonomic revisions. Thus it is confusing and misleading to use 'taxonomic revision'. Change the table.

& the history was that this value had been 'taxonomic revision' since forever... and I argued, and others agreed, to change it to 'revised taxonomy' so it's baffling to me that people want to change it back & I'd like to hear what reasoning was behind that?

-Derek

On Wed, Oct 2, 2019 at 11:36 AM dustymc notifications@github.com wrote:

Unless someone explicitly directs me otherwise, all updates will include...

AND id_remarks+=Original Nature_of_ID: {oldvalue}

fix the spreadsheet

I don't think that's my call - those values (which have already been implemented) got there by consensus (maybe...). I don't know if someone feels that the current term is better for some reason, or it's just arbitrary. I think @jldunnum https://github.com/jldunnum had something to say at some point?? @ccicero https://github.com/ccicero @campmlc https://github.com/campmlc you edited the spreadsheet??

I have no opinion - I think they're saying the same THING, I think it's a straight update (won't require changing confidence), should be easy to update when I figure out how we got here.

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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 finally found that thread

https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

• change all taxonomic revision to revised taxonomy
• allow revised taxonomy for new IDs
• remove taxonomic revision from the code table

Bueno?

[jldunnum]

Is this why I'm getting this error right now when reiding as Revised taxonomy? Legacy nature_of_id terms are disallowed; see https://github.com/ArctosDB/arctos/issues/2170 [Macromedia][Oracle JDBC Driver][Oracle]ORA-20001: Legacy nature_of_id terms are disallowed; see https://github.com/ArctosDB/arctos/issues/2170 ORA-06512: at "UAM.TEMP_TR_ID_BIU", line 4 ORA-04088: error during execution of trigger 'UAM.TEMP_TR_ID_BIU' Error Executing Database Query. Check the Arctos Handbookhttp://handbook.arctosdb.org/documentation/understanding-errors.html for more information on errors.

---

Jonathan L. Dunnum Ph.D. Senior Collection Manager Division of Mammals, Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351

MSB Mammals website: http://www.msb.unm.edu/mammals/index.html Facebook: http://www.facebook.com/MSBDivisionofMammals

Shipping Address: Museum of Southwestern Biology Division of Mammals University of New Mexico CERIA Bldg 83, Room 204 Albuquerque, NM 87131

---

From: dustymc notifications@github.com Sent: Wednesday, October 2, 2019 2:45 PM To: ArctosDB/arctos arctos@noreply.github.com Cc: Jonathan Dunnum jldunnum@unm.edu; Mention mention@noreply.github.com Subject: Re: [ArctosDB/arctos] nature of ID (#2170)

I finally found that thread

1093https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

• change all taxonomic revision to revised taxonomy
• allow revised taxonomy for new IDs
• remove taxonomic revision from the code table

Bueno?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=AED2PA6F5VEMBO4CIDWH4N3QMUB7LA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGD2FY#issuecomment-537672983, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AED2PA32OON6JQFZK2QEZPLQMUB7LANCNFSM4IEIGLOA.

[DerekSikes]

Bueno!!

-Derek

On Wed, Oct 2, 2019 at 12:45 PM dustymc notifications@github.com wrote:

I finally found that thread

1093 https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

• change all taxonomic revision to revised taxonomy
• allow revised taxonomy for new IDs
• remove taxonomic revision from the code table

Bueno?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=ACFNUM5NZIBEDXJE5D2QXH3QMUB7JA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGD2FY#issuecomment-537672983, or mute the thread https://github.com/notifications/unsubscribe-auth/ACFNUM5YP7XCYVZRQTYCTFDQMUB7JANCNFSM4IEIGLOA .

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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]

The rule is flipped - you can use "revised taxonomy" now. I'll update the documentation, flip the values (plus remark), and delete taxonomic revision ~now-ish.

[dustymc]

taxonomic revision is no more

[DerekSikes]

awesome

On Wed, Oct 2, 2019 at 1:31 PM dustymc notifications@github.com wrote:

taxonomic revision is no more

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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/ +++++++++++++++++++++++++++++++++++

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[atrox10]

I am getting that same error for Expert as Nature of ID and High confidence. Can we not change identifications right now?

On Wed, Oct 2, 2019 at 1:45 PM dustymc notifications@github.com wrote:

I finally found that thread

1093 https://github.com/ArctosDB/arctos/issues/1093

Looks like we were all agreed on "revised taxonomy" at some point - not a clue what happened in the meantime.

Unless someone stops me in the very near future I will

• change all taxonomic revision to revised taxonomy
• allow revised taxonomy for new IDs
• remove taxonomic revision from the code table

Bueno?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=ABCJF4KWYIPBQBICEFXBCL3QMUB7JA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGD2FY#issuecomment-537672983, or mute the thread https://github.com/notifications/unsubscribe-auth/ABCJF4MR5MK2NLEKZ7YT5KLQMUB7JANCNFSM4IEIGLOA .

-- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 atrox10@gmail.com or atrox@berkeley.edu 510-643-5778 http://mvz.berkeley.edu/

[dustymc]

You can change IDs, but you can't use the terms which are going away very soon. http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID is currently the best source of information.

Let me if I can help update any of your data with a little more finesse than https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840

[atrox10]

Thanks Dusty!!!

On Wed, Oct 2, 2019 at 5:13 PM dustymc notifications@github.com wrote:

You can change IDs, but you can't use the terms which are going away very soon. http://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID is currently the best source of information.

Let me if I can help update any of your data with a little more finesse than #2170 (comment) https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=ABCJF4N4OEO2MXU6KDOSWTDQMU2MNA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAGSI3Y#issuecomment-537732207, or mute the thread https://github.com/notifications/unsubscribe-auth/ABCJF4N37YRZE2PFFCA3KVDQMU2MNANCNFSM4IEIGLOA .

-- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 atrox10@gmail.com or atrox@berkeley.edu 510-643-5778 http://mvz.berkeley.edu/

[mkoo]

here's the crosswalk: ID of kin --> relationship ID to species group --> unknown curatorial --> unknown erroneous citation --> unknown expert --> FINE FEATURES field --> COARSE FEATURES legacy --> unknown - CAN I DO THIS NOW? yes molecular data--> molecular - CAN I DO THIS NOW? yes photograph --> COARSE FEATURES? published referral --> unknown revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? student --> unknown type specimen --> unknown

[campmlc]

ID of kin --> relationship ID to species group --> unknown curatorial --> FINE FEATURES erroneous citation --> unknown expert -->FINE FEATURES field --> COARSE FEATURES legacy --> unknown - CAN I DO THIS NOW? yes molecular data--> molecular - CAN I DO THIS NOW? yes photograph --> COARSE FEATURES published referral --> unknown revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? yes student --> COARSE FEATURES type specimen --> FINE FEATURES

[dustymc]

select guid_prefix,nature_of_id, count(*) c from collection,cataloged_item,identification where collection.collection_id=cataloged_item.collection_id and cataloged_item.collection_object_id=identification.collection_object_id group by guid_prefix,nature_of_id order by guid_prefix,nature_of_id;

GUID_PREFIX      NATURE_OF_ID                C
-------------------- ------------------------------ ----------
ALMNH:ES         expert                 19
ALMNH:ES         legacy              10351
ALMNH:ES         published referral              3
ALMNH:ES         revised taxonomy                2
ALMNH:ES         type specimen              16
APSU:Herp        legacy               7010
ASNHC:Mamm       field                   1
ASNHC:Mamm       legacy                135
BYU:Herp         field                1281
BYU:Herp         legacy                177
BYU:Herp         photograph                  8
CHAS:Bird        ID to species group             1
CHAS:Bird        expert                139
CHAS:Bird        field                   1
CHAS:Bird        legacy              21858
CHAS:Bird        revised taxonomy                1
CHAS:Bird        student                   230
CHAS:EH          curatorial                  4
CHAS:EH          expert                119
CHAS:EH          legacy                620
CHAS:EH          student                   281
CHAS:Egg         ID of kin                 679
CHAS:Egg         geographic distribution             3
CHAS:Egg         legacy               3337
CHAS:Egg         revised taxonomy                1
CHAS:Egg         student                     1
CHAS:Ento        ID of kin                   1
CHAS:Ento        curatorial                  1
CHAS:Ento        expert                 16
CHAS:Ento        legacy              32137
CHAS:Ento        revised taxonomy               15
CHAS:Ento        student                   564
CHAS:Fish        expert                  1
CHAS:Fish        legacy                 29
CHAS:Herb        expert                 52
CHAS:Herb        field                   9
CHAS:Herb        legacy                 99
CHAS:Herp        expert                  1
CHAS:Herp        legacy                  1
CHAS:Herp        student                     1
CHAS:Inv         curatorial                 34
CHAS:Inv         expert               1971
CHAS:Inv         legacy              25050
CHAS:Inv         published referral              1
CHAS:Inv         revised taxonomy              927
CHAS:Inv         student                    72
CHAS:Inv         type specimen             124
CHAS:Mamm        expert                 37
CHAS:Mamm        field                   2
CHAS:Mamm        geographic distribution             1
CHAS:Mamm        legacy               9912
CHAS:Mamm        revised taxonomy                8
CHAS:Mamm        student                    33
CHAS:Mamm        type specimen              17
CHAS:Teach       ID of kin                   1
CHAS:Teach       expert                 71
CHAS:Teach       field                   1
CHAS:Teach       legacy                954
CHAS:Teach       published referral              1
CHAS:Teach       student                   966
COA:Bird         legacy                878
COA:Egg          legacy                119
COA:Ento         legacy                 37
COA:Herp         legacy                 61
COA:Mamm         legacy                187
DGR:Bird         erroneous citation              1
DGR:Bird         expert                 22
DGR:Bird         field                 351
DGR:Bird         geographic distribution             1
DGR:Bird         legacy               2149
DGR:Bird         molecular data              1
DGR:Bird         revised taxonomy                1
DGR:Bird         type specimen               6
DGR:Ento         legacy                 35
DGR:Mamm         expert                131
DGR:Mamm         field                   2
DGR:Mamm         geographic distribution             3
DGR:Mamm         legacy                664
DGR:Mamm         molecular data             18
DGR:Mamm         revised taxonomy                3
DGR:Mamm         student                     1
DGR:Mamm         type specimen               1
DMNS:Bird        ID of kin                  23
DMNS:Bird        curatorial                 37
DMNS:Bird        erroneous citation             15
DMNS:Bird        expert               1938
DMNS:Bird        field                9106
DMNS:Bird        geographic distribution            42
DMNS:Bird        legacy              42312
DMNS:Bird        molecular data             26
DMNS:Bird        published referral              5
DMNS:Bird        revised taxonomy             3198
DMNS:Bird        student                     5
DMNS:Bird        type specimen              21
DMNS:Egg         field                 182
DMNS:Egg         legacy               6958
DMNS:Egg         published referral              1
DMNS:Egg         revised taxonomy              135
DMNS:Herp        curatorial                  2
DMNS:Herp        expert                 97
DMNS:Herp        field                  13
DMNS:Herp        geographic distribution             7
DMNS:Inv         ID of kin                  12
DMNS:Inv         erroneous citation              2
DMNS:Inv         expert                524
DMNS:Inv         geographic distribution             6
DMNS:Inv         legacy              13118
DMNS:Inv         published referral              3
DMNS:Inv         revised taxonomy             8415
DMNS:Inv         student                 10609
DMNS:Mamm        ID of kin                 185
DMNS:Mamm        ID to species group             5
DMNS:Mamm        curatorial                  4
DMNS:Mamm        expert               3764
DMNS:Mamm        field               15057
DMNS:Mamm        geographic distribution           102
DMNS:Mamm        legacy                544
DMNS:Mamm        molecular data            132
DMNS:Mamm        published referral             21
DMNS:Mamm        revised taxonomy             1108
DMNS:Mamm        student                    29
DMNS:Mamm        type specimen              48
DMNS:Para        expert                771
DMNS:Para        field                  11
DMNS:Para        molecular data              6
DMNS:Para        student                   123
HWML:Para        expert                  4
HWML:Para        legacy              24396
HWML:Para        type specimen            1711
KNWR:Ento        ID of kin                  14
KNWR:Ento        ID to species group             1
KNWR:Ento        erroneous citation              1
KNWR:Ento        expert               3432
KNWR:Ento        field                 223
KNWR:Ento        geographic distribution             3
KNWR:Ento        legacy                 59
KNWR:Ento        molecular data            565
KNWR:Ento        photograph                 59
KNWR:Ento        published referral              9
KNWR:Ento        revised taxonomy              282
KNWR:Ento        student                  8057
KNWR:Ento        type specimen              15
KNWR:Herb        ID of kin                   3
KNWR:Herb        expert               1087
KNWR:Herb        field                  93
KNWR:Herb        legacy                621
KNWR:Herb        molecular data              5
KNWR:Herb        photograph                  2
KNWR:Herb        revised taxonomy               25
KNWR:Herb        student                   721
KNWR:Inv         expert                 25
KNWR:Inv         field                   8
KNWR:Inv         molecular data              6
KNWR:Inv         revised taxonomy                4
KNWR:Inv         student                    26
KNWRObs:Fish         expert                 11
KNWRObs:Herb         field                 830
KWP:Ento         ID to species group           465
KWP:Ento         erroneous citation              2
KWP:Ento         expert              77860
KWP:Ento         geographic distribution           235
KWP:Ento         molecular data              7
KWP:Ento         photograph                259
KWP:Ento         revised taxonomy            34601
KWP:Ento         student                  9520
KWP:Ento         type specimen               1
MLZ:Bird         ID of kin                  21
MLZ:Bird         expert               7046
MLZ:Bird         geographic distribution           245
MLZ:Bird         legacy              62310
MLZ:Bird         published referral           1032
MLZ:Bird         revised taxonomy             2704
MLZ:Bird         type specimen             193
MLZ:Egg          ID of kin                   3
MLZ:Egg          expert                  7
MLZ:Egg          field                   7
MLZ:Egg          legacy                 21
MLZ:Herb         expert                 16
MLZ:Mamm         ID of kin                  10
MLZ:Mamm         expert                  7
MLZ:Mamm         geographic distribution            12
MLZ:Mamm         legacy               2157
MLZ:Mamm         revised taxonomy               25
MSB:Bird         ID of kin                   7
MSB:Bird         expert              13823
MSB:Bird         field                  83
MSB:Bird         legacy              24770
MSB:Bird         molecular data              4
MSB:Bird         revised taxonomy               30
MSB:Bird         student                  6165
MSB:Bird         type specimen              10
MSB:Fish         ID to species group          4648
MSB:Fish         expert              60797
MSB:Fish         field               31708
MSB:Fish         legacy               3122
MSB:Fish         molecular data              1
MSB:Fish         published referral              1
MSB:Fish         revised taxonomy               30
MSB:Fish         student                  3441
MSB:Fish         type specimen               8
MSB:Herp         ID of kin                  20
MSB:Herp         ID to species group             1
MSB:Herp         expert                165
MSB:Herp         field               18873
MSB:Herp         geographic distribution             1
MSB:Herp         legacy              13176
MSB:Herp         revised taxonomy                2
MSB:Herp         student                   102
MSB:Host         ID of kin                  17
MSB:Host         ID to species group             5
MSB:Host         curatorial                  6
MSB:Host         expert                207
MSB:Host         field                3225
MSB:Host         geographic distribution           216
MSB:Host         legacy              22510
MSB:Host         molecular data            247
MSB:Host         published referral              4
MSB:Host         revised taxonomy              753
MSB:Host         student                   168
MSB:Host         type specimen               1
MSB:Mamm         ID of kin                 691
MSB:Mamm         ID to species group             2
MSB:Mamm         curatorial              11815
MSB:Mamm         erroneous citation             45
MSB:Mamm         expert              11063
MSB:Mamm         field               72188
MSB:Mamm         geographic distribution           429
MSB:Mamm         legacy             223114
MSB:Mamm         molecular data           6079
MSB:Mamm         photograph                  7
MSB:Mamm         published referral             15
MSB:Mamm         revised taxonomy            18268
MSB:Mamm         student                 22218
MSB:Mamm         type specimen            4780
MSB:Para         ID of kin                  64
MSB:Para         ID to species group             6
MSB:Para         curatorial                 45
MSB:Para         expert               2494
MSB:Para         field                3492
MSB:Para         legacy              21186
MSB:Para         molecular data            415
MSB:Para         published referral              5
MSB:Para         revised taxonomy               13
MSB:Para         student                  2438
MSB:Para         type specimen              68
MSBObs:Mamm      ID of kin                   3
MVZ:Bird         ID of kin                   4
MVZ:Bird         ID to species group          4019
MVZ:Bird         coarse features                 9
MVZ:Bird         expert               1327
MVZ:Bird         field                3807
MVZ:Bird         geographic distribution         11466
MVZ:Bird         legacy             180916
MVZ:Bird         molecular data             56
MVZ:Bird         published referral             11
MVZ:Bird         revised taxonomy            54185
MVZ:Bird         student                     2
MVZ:Bird         type specimen             482
MVZ:Egg          ID of kin                   1
MVZ:Egg          ID to species group           247
MVZ:Egg          expert                 24
MVZ:Egg          field                 407
MVZ:Egg          geographic distribution          1010
MVZ:Egg          legacy              14386
MVZ:Egg          published referral             10
MVZ:Egg          revised taxonomy             3315
MVZ:Fish         field                   1
MVZ:Herp         ID of kin                  11
MVZ:Herp         ID to species group           182
MVZ:Herp         curatorial                  1
MVZ:Herp         erroneous citation              5
MVZ:Herp         expert              15964
MVZ:Herp         field               51074
MVZ:Herp         fine features               4
MVZ:Herp         geographic distribution          3045
MVZ:Herp         legacy             228836
MVZ:Herp         molecular data            227
MVZ:Herp         photograph                  4
MVZ:Herp         published referral            699
MVZ:Herp         revised taxonomy            35319
MVZ:Herp         student                    18
MVZ:Herp         type specimen            4389
MVZ:Hild         expert                  3
MVZ:Hild         field                  72
MVZ:Hild         legacy                585
MVZ:Hild         revised taxonomy                6
MVZ:Mamm         ID of kin                1466
MVZ:Mamm         ID to species group             1
MVZ:Mamm         curatorial                  3
MVZ:Mamm         erroneous citation              1
MVZ:Mamm         expert              40893
MVZ:Mamm         field               15624
MVZ:Mamm         geographic distribution          3713
MVZ:Mamm         legacy             193130
MVZ:Mamm         molecular data            530
MVZ:Mamm         published referral             89
MVZ:Mamm         revised taxonomy            20240
MVZ:Mamm         student                   858
MVZ:Mamm         type specimen            1844
MVZObs:Bird      ID to species group             3
MVZObs:Bird      expert                  3
MVZObs:Bird      field                4621
MVZObs:Bird      geographic distribution          1565
MVZObs:Bird      legacy                238
MVZObs:Bird      revised taxonomy              524
MVZObs:Herp      expert                  3
MVZObs:Herp      field                  19
MVZObs:Herp      photograph                  6
MVZObs:Herp      type specimen               1
MVZObs:Mamm      field                 101
NBSB:Bird        field                 321
NMU:Bird         ID of kin                   3
NMU:Bird         field                 308
NMU:Bird         legacy                  9
NMU:Mamm         ID of kin                  58
NMU:Mamm         expert                 70
NMU:Mamm         field                1203
NMU:Mamm         geographic distribution            95
NMU:Mamm         legacy               1026
NMU:Mamm         molecular data             87
NMU:Mamm         student                     2
NMU:Para         field                   7
OWU:Bird         curatorial                  2
OWU:Bird         student                    26
OWU:ES           curatorial                  3
OWU:ES           expert                 52
OWU:ES           field                   4
OWU:ES           legacy                297
OWU:ES           revised taxonomy               25
OWU:Fish         curatorial                 16
OWU:Fish         field                   1
OWU:Fish         student                     5
OWU:Mamm         ID of kin                   7
OWU:Mamm         curatorial                  7
OWU:Mamm         field                   1
OWU:Mamm         legacy                153
OWU:Mamm         student                     2
OWU:Para         curatorial                  2
OWU:Para         expert                  3
OWU:Rept         curatorial                  7
OWU:Rept         field                  81
OWU:Rept         legacy                137
UAM:Alg          legacy               4639
UAM:Arc          ID of kin               22859
UAM:Arc          expert               8502
UAM:Arc          field                 301
UAM:Arc          legacy             615096
UAM:Arc          student                   558
UAM:Art          expert                422
UAM:Art          legacy               3873
UAM:Bird         expert               1135
UAM:Bird         field               29489
UAM:Bird         legacy               7055
UAM:Bird         revised taxonomy                2
UAM:Bird         type specimen             156
UAM:EH           ID of kin                 890
UAM:EH           curatorial                 85
UAM:EH           expert                144
UAM:EH           field                   1
UAM:EH           legacy              14653
UAM:EH           photograph                  1
UAM:EH           student                   175
UAM:ES           ID of kin                  39
UAM:ES           erroneous citation              1
UAM:ES           expert              27465
UAM:ES           field               20062
UAM:ES           molecular data             14
UAM:ES           photograph                  1
UAM:ES           published referral              2
UAM:ES           revised taxonomy              292
UAM:ES           student                  7916
UAM:ES           type specimen               7
UAM:Ento         ID of kin                 447
UAM:Ento         ID to species group             1
UAM:Ento         coarse features                13
UAM:Ento         curatorial                753
UAM:Ento         erroneous citation             45
UAM:Ento         expert             279626
UAM:Ento         field                3018
UAM:Ento         geographic distribution           783
UAM:Ento         legacy              10861
UAM:Ento         molecular                   2
UAM:Ento         molecular data           1241
UAM:Ento         photograph                 47
UAM:Ento         published referral             38
UAM:Ento         revised taxonomy            21669
UAM:Ento         student                236131
UAM:Ento         type specimen             103
UAM:Env          student                   334
UAM:Fish         ID of kin                  25
UAM:Fish         expert               1980
UAM:Fish         field                1422
UAM:Fish         geographic distribution             4
UAM:Fish         legacy               6841
UAM:Fish         molecular data             20
UAM:Fish         revised taxonomy              472
UAM:Fish         student                    40
UAM:Fish         type specimen               3
UAM:Herb         ID of kin                 146
UAM:Herb         curatorial                  1
UAM:Herb         erroneous citation             10
UAM:Herb         expert              15290
UAM:Herb         field                2173
UAM:Herb         geographic distribution             3
UAM:Herb         legacy             201740
UAM:Herb         molecular data             24
UAM:Herb         revised taxonomy             2267
UAM:Herb         student                  9338
UAM:Herb         type specimen             515
UAM:Herp         ID of kin                   1
UAM:Herp         expert                 21
UAM:Herp         field                 383
UAM:Herp         geographic distribution             2
UAM:Herp         legacy                 35
UAM:Herp         molecular data              2
UAM:Herp         revised taxonomy              183
UAM:Herp         student                    44
UAM:Herp         type specimen               2
UAM:Inv          ID of kin                   9
UAM:Inv          expert                 89
UAM:Inv          field                 306
UAM:Inv          geographic distribution             4
UAM:Inv          legacy              19832
UAM:Inv          revised taxonomy                8
UAM:Inv          student                    56
UAM:Inv          type specimen              21
UAM:Mamm         ID of kin                 396
UAM:Mamm         curatorial                219
UAM:Mamm         erroneous citation              1
UAM:Mamm         expert               2867
UAM:Mamm         field               46898
UAM:Mamm         geographic distribution           655
UAM:Mamm         legacy              62850
UAM:Mamm         molecular data            654
UAM:Mamm         published referral              3
UAM:Mamm         revised taxonomy            20784
UAM:Mamm         student                 29046
UAM:Mamm         type specimen            6710
UAMObs:Bird      field                 164
UAMObs:Ento      ID of kin                  12
UAMObs:Ento      ID to species group             1
UAMObs:Ento      erroneous citation             22
UAMObs:Ento      expert              14216
UAMObs:Ento      field                  14
UAMObs:Ento      geographic distribution           129
UAMObs:Ento      legacy              18638
UAMObs:Ento      molecular                   1
UAMObs:Ento      molecular data           3168
UAMObs:Ento      photograph                 30
UAMObs:Ento      published referral           1981
UAMObs:Ento      revised taxonomy             1982
UAMObs:Ento      student                  1768
UAMObs:Ento      type specimen            1353
UAMObs:Fish      field                   6
UAMObs:Fish      photograph                  7
UAMObs:Mamm      ID of kin                   1
UAMObs:Mamm      curatorial                  1
UAMObs:Mamm      field                 212
UAMObs:Mamm      photograph                 20
UAMObs:Mamm      student                    20
UAMObs:Mamm      type specimen               7
UAMb:Herb        expert              11160
UAMb:Herb        field                   9
UAMb:Herb        geographic distribution             1
UAMb:Herb        legacy              52444
UAMb:Herb        photograph                  1
UAMb:Herb        student                   208
UCM:Bird         ID of kin                   1
UCM:Bird         curatorial                  3
UCM:Bird         erroneous citation              1
UCM:Bird         expert               1073
UCM:Bird         field                   2
UCM:Bird         legacy              11122
UCM:Bird         revised taxonomy               35
UCM:Bird         student                     1
UCM:Bird         type specimen               8
UCM:Egg          ID of kin                   1
UCM:Egg          expert                760
UCM:Egg          legacy               2436
UCM:Egg          revised taxonomy               18
UCM:Egg          student                   153
UCM:Fish         ID of kin                   5
UCM:Fish         ID to species group             1
UCM:Fish         expert                294
UCM:Fish         field                   1
UCM:Fish         legacy               2107
UCM:Fish         revised taxonomy               23
UCM:Fish         student                    11
UCM:Fish         type specimen              25
UCM:Herp         curatorial                 80
UCM:Herp         expert               3349
UCM:Herp         field                   1
UCM:Herp         geographic distribution           413
UCM:Herp         legacy              63160
UCM:Herp         photograph                  1
UCM:Herp         published referral             15
UCM:Herp         revised taxonomy            25751
UCM:Herp         student                     1
UCM:Herp         type specimen             510
UCM:Mamm         expert               1476
UCM:Mamm         field                  13
UCM:Mamm         geographic distribution            11
UCM:Mamm         legacy              19077
UCM:Mamm         molecular data            106
UCM:Mamm         published referral              3
UCM:Mamm         revised taxonomy              223
UCM:Mamm         student                    11
UCM:Mamm         type specimen              28
UCM:Obs          expert                 26
UCM:Obs          field                 205
UCM:Obs          photograph                 20
UCM:Obs          revised taxonomy               36
UCSC:Bird        legacy                175
UCSC:Herp        legacy                  1
UCSC:Mamm        field                 173
UCSC:Mamm        legacy                 24
UMNH:Bird        curatorial                 46
UMNH:Bird        expert                  5
UMNH:Bird        field                  41
UMNH:Bird        legacy              20741
UMNH:Bird        revised taxonomy                3
UMNH:Herp        field                   4
UMNH:Herp        legacy              22431
UMNH:Mamm        ID of kin                  52
UMNH:Mamm        curatorial                354
UMNH:Mamm        expert                 71
UMNH:Mamm        field                3055
UMNH:Mamm        geographic distribution            35
UMNH:Mamm        legacy              40169
UMNH:Mamm        published referral              1
UMNH:Mamm        revised taxonomy              133
UMNH:Mamm        student                     6
UMNH:Mamm        type specimen              18
UMZM:Bird        legacy               6161
UMZM:Mamm        legacy              15830
UNM:ES           ID of kin                   2
UNM:ES           expert                603
UNM:ES           legacy                205
UNM:ES           revised taxonomy               72
UNM:ES           student                   768
UNR:Bird         field                 198
UNR:Fish         ID of kin                  32
UNR:Fish         expert                 66
UNR:Fish         field                3028
UNR:Fish         legacy                205
UNR:Fish         student                   484
UNR:Herp         ID of kin                   3
UNR:Herp         expert                  7
UNR:Herp         field                3589
UNR:Herp         student                     1
UNR:Mamm         ID of kin                   1
UNR:Mamm         field                2016
USNPC:Para       expert                809
USNPC:Para       legacy                  1
USNPC:Para       type specimen               1
UTEP:Arc         expert                451
UTEP:Bird        expert                631
UTEP:Bird        legacy               2426
UTEP:Bird        student                    22
UTEP:ES          ID of kin                 604
UTEP:ES          erroneous citation              3
UTEP:ES          expert              23715
UTEP:ES          legacy                276
UTEP:ES          molecular data              1
UTEP:ES          revised taxonomy              138
UTEP:ES          student                    35
UTEP:ES          type specimen              18
UTEP:Ento        curatorial                  5
UTEP:Ento        expert                530
UTEP:Ento        legacy               7828
UTEP:Ento        student                    32
UTEP:Ento        type specimen              40
UTEP:Fish        expert                 93
UTEP:Fish        field                   4
UTEP:Fish        legacy                  1
UTEP:Fish        student                   147
UTEP:Herb        curatorial                 44
UTEP:Herb        erroneous citation              1
UTEP:Herb        expert              49407
UTEP:Herb        field                 104
UTEP:Herb        legacy              34787
UTEP:Herb        molecular data             47
UTEP:Herb        student                    36
UTEP:Herb        type specimen              15
UTEP:Herp        ID of kin                   4
UTEP:Herp        curatorial                613
UTEP:Herp        expert              10223
UTEP:Herp        field                 113
UTEP:Herp        geographic distribution            37
UTEP:Herp        legacy              11595
UTEP:Herp        molecular data            145
UTEP:Herp        revised taxonomy               24
UTEP:Herp        student                    11
UTEP:Herp        type specimen             336
UTEP:HerpOS      expert                572
UTEP:HerpOS      geographic distribution             2
UTEP:HerpOS      legacy               1166
UTEP:HerpOS      type specimen               1
UTEP:Inv         expert              10207
UTEP:Inv         legacy               1697
UTEP:Inv         type specimen              21
UTEP:Mamm        ID of kin                  20
UTEP:Mamm        expert               8517
UTEP:Mamm        geographic distribution            39
UTEP:Mamm        revised taxonomy                2
UTEP:Teach       expert                 62
UTEP:Teach       field                   1
UTEP:Teach       legacy                180
UTEP:Teach       revised taxonomy                2
UTEP:Teach       student                     2
UTEP:Zoo         expert                 17
UTEP:Zoo         student                   107
UTEP:Zoo         type specimen              27
UTEPObs:Ento         expert                  2
UTEPObs:Herp         ID of kin                   1
UTEPObs:Herp         expert                 75
UTEPObs:Herp         field                  20
UTEPObs:Herp         legacy                 73
UTEPObs:Herp         photograph                 22
UWBM:Herp        ID of kin                 897
UWBM:Herp        expert                568
UWBM:Herp        field                1141
UWBM:Herp        geographic distribution             2
UWBM:Herp        legacy               7754
UWBM:Herp        revised taxonomy               89
UWBM:Herp        student                   164
UWBM:Herp        type specimen               2
UWBM:Mamm        ID of kin                   3
UWBM:Mamm        ID to species group             2
UWBM:Mamm        expert                 14
UWBM:Mamm        field                   4
UWBM:Mamm        legacy              55660
UWYMV:Bird       ID of kin                   1
UWYMV:Bird       curatorial                 12
UWYMV:Bird       expert               2217
UWYMV:Bird       field                  52
UWYMV:Bird       geographic distribution           122
UWYMV:Bird       legacy                  3
UWYMV:Bird       student                    30
UWYMV:Egg        geographic distribution             1
UWYMV:Egg        student                     1
UWYMV:Fish       expert                539
UWYMV:Herp       curatorial                  2
UWYMV:Herp       expert                346
UWYMV:Herp       field                   1
UWYMV:Herp       legacy                  3
UWYMV:Mamm       curatorial                 19
UWYMV:Mamm       expert                  1
UWYMV:Mamm       field                   4
UWYMV:Mamm       geographic distribution          1112
UWYMV:Mamm       legacy               5222
WNMU:Bird        legacy               1339
WNMU:Fish        expert                 55
WNMU:Fish        legacy                324
WNMU:Mamm        expert                 16
WNMU:Mamm        legacy               6542
WNMU:Mamm        revised taxonomy              332

[mkoo]

Find your types in USAGE!

Dusty will implement the migration outlined in Mariel's last comment in two weeks-- complain before then or make changes accordingly.

[DerekSikes]

Seems Mariel didn't catch the discussion on this:

revised taxonomy --> taxonomic revision - CAN I DO THIS NOW? yes

The conclusions was NO, this is not going to happen. All 'taxonomic revision' will become 'revised taxonomy', not the other way around.

-Derek

On Thu, Oct 3, 2019 at 11:07 AM Michelle Koo notifications@github.com wrote:

Find your types in USAGE!

Dusty will implement the migration outlined in Mariel's last comment in two weeks-- complain before then or make changes accordingly.

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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]

Revised taxonomy is done.

Current values will be preserved in remarks.

Relevant code tables are https://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID and https://arctos.database.museum/info/ctDocumentation.cfm?table=CTIDENTIFICATION_CONFIDENCE

These will happen ~today unless someone stops me:

• legacy --> unknown
• molecular data--> molecular

These will happen for anything that hasn't been handled about Oct 16th 2019. PLEASE comment here ASAP if you'd like a different migration path (eg, one that does something with 'confidence') for some or all of your collection.

• ID of kin --> relationship
• ID to species group --> unknown
• curatorial --> FINE FEATURES
• erroneous citation --> unknown
• expert -->FINE FEATURES
• field --> COARSE FEATURES
• photograph --> COARSE FEATURES
• published referral --> unknown
• student --> COARSE FEATURES
• type specimen --> FINE FEATURES

[DerekSikes]

Good.

For UAM:Ento, UAMObs:Ento, KWP:Ento, KNWR:Ento, and KNWR:Inv

I would like confidence set to 'high' for any identifications with nature of ID = expert & I would like confidence set to 'medium' for any identifications with nature of ID = student

I am not sure about this migration:

expert -->FINE FEATURES student --> COARSE FEATURES

I think this is incorrect - lots of student IDs are based on 'fine features'; similar problem with photograph... plenty of IDs based on photos are of fine features (eg SEM or any photos taken through microscopes...)

I'm a little worried that we'll be forced to make distinctions between FINE & COARSE that are over-precise and subjective. It would be good to have a 3rd option "PHENOTYPE" or "MORPHOLOGY" or perhaps "EXTERNAL FEATURES" for cases where we don't know if the ID was based on FINE or COARSE features. Sorry if this sets us back a bit.

-Derek

On Thu, Oct 3, 2019 at 11:54 AM dustymc notifications@github.com wrote:

Revised taxonomy is done.

Current values will be preserved in remarks.

Relevant code tables are https://arctos.database.museum/info/ctDocumentation.cfm?table=CTNATURE_OF_ID and https://arctos.database.museum/info/ctDocumentation.cfm?table=CTIDENTIFICATION_CONFIDENCE

These will happen ~today unless someone stops me:

• legacy --> unknown
• molecular data--> molecular

These will happen for anything that hasn't been handled about Oct 16th

2019. PLEASE comment here ASAP if you'd like a different migration path (eg, one that does something with 'confidence') for some or all of your collection.

      • ID of kin --> relationship
      • ID to species group --> unknown
      • curatorial --> FINE FEATURES
      • erroneous citation --> unknown
      • expert -->FINE FEATURES
      • field --> COARSE FEATURES
      • photograph --> COARSE FEATURES
      • published referral --> unknown
      • student --> COARSE FEATURES
      • type specimen --> FINE FEATURES

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2170?email_source=notifications&email_token=ACFNUM56XRULEPTPDMKYG7TQMZEYVA5CNFSM4IEIGLOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAJMUYY#issuecomment-538102371, or mute the thread https://github.com/notifications/unsubscribe-auth/ACFNUMYJ4ZD723C4IEQLQE3QMZEYVANCNFSM4IEIGLOA .

--

+++++++++++++++++++++++++++++++++++ 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 don't disagree; my "morphology" proposal died ^^ way up there ^^ somewhere.

I'm not sure anything like SEM is required to get at "fine" - think keying out blue vs. fin whale skulls.

I don't like "external" - think "this adult bear femur is obviously a grizzly because it looks like one."

Given the existing overlap, another hopefully-temporary morphology-or-whatever(==we don't know what "fine" and "course" mean so we don't know if this should be "fine" or "course") option would not bother me too much, particularly if it lets us proceed.

Alternatively, I still like "unknown" (https://github.com/ArctosDB/arctos/issues/2170#issuecomment-537631840) for these. I suppose it's a matter of how much we don't know before we admit we don't know....

[ccicero]

What about "external phenoype" (looks like moose") vs "anatomy" (internal morphology/structure) vs "microscopy"?

[dustymc]

external phenoype

I think I like it.

"anatomy" vs "microscopy"

Are these different or just taxon-specific things? Folks who look at grasshopper genitalia under a microscope are doing about the same things (probably, I think) as those who look at large mammal femurs, it's just that the latter don't require magnification.

I think there's a place for "took 600 detailed measurements of this sea lion skull from the CT scan" - maybe "microscopy" works for that and we just need to be careful in the definition?

[campmlc]

I think morphology fits all these. If I look at mouse teeth, is that external or internal?

On Thu, Oct 3, 2019 at 4:54 PM dustymc notifications@github.com wrote:

external phenoype

I think I like it.

"anatomy" vs "microscopy"

Are these different or just taxon-specific things? Folks who look at grasshopper genitalia under a microscope are doing about the same things (probably, I think) as those who look at large mammal femurs, it's just that the latter don't require magnification.

I think there's a place for "took 600 detailed measurements of this sea lion skull from the CT scan" - maybe "microscopy" works for that and we just need to be careful in the definition?

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[ccicero]

I think external phenotype is better for a general 'looks like a moose' or "looks like a certain subspecies of a bird" scenario. Morphology doesn't really cover looking at plumage characteristics, for example. Definition: "Identification based on a coarse examination of external features including size, shape, and color."

I think anatomy would cover things like looking at teeth, bones, appendages, etc. - whether under a scope or not. Definition: "Identification based on a detailed look at structure such as teeth, bones, appendages, etc. whether under a microscope or not."

I was trying to figure out another word for 'microscopy' that would cover things like CT scans or something that requires specialized equipment. "Microscopy" probably isn't the best term. What about "Advanced Imaging" - Definition: "Identification based on advanced imaging technology, including CT scanning, Scanning Electron Microscopy (SEM), etc."

So these three terms would cover progressively more advanced, detailed examination of features for identification.

[dustymc]

I'm still not quite seeing the split between anatomy and "microscopy." https://arctos.database.museum/guid/UAM:Mamm:11507 was done with calipers. There's a grant pending to do the same(ish) thing with CT/digital measuring. I don't think the results will be fundamentally different, so I don't think the equipment is a useful split.

Does "detailed measurements" (however we say it) work for the last category? So LOOKING (and maybe making some casual measurements), whether it's at a blue whale or a virus, is "anatomy," but carefully measuring characteristics is something else.

I think that works for more than morphology as well - quantitative colors, maybe some of the stuff that happens around bat detectors, testing artwork for caesium-137 (maybe that's molecular??), etc.

[ccicero]

What about "general phenotype" for field or "casual" IDs (could include casual measurements, scale counts). I like the term phenotype because most field ids are based on that.

I agree we need something for more careful analysis, could be scans or quantitative color analysis etc. Something more advanced that contrasts with "general"

[atrox10]

I like the wording of General Phenotype. But since we are really just trying to get back to how we ID things in the field (which are possibly by an expert but checked quickly with only some or no reference material available), why can't we keep "field" as one possibility? "general phenotype" can be another. It conveys a lot on how the animal or plant, etc was identified. Whereas all the others our more specific about tools used, etc.

On Fri, Oct 4, 2019 at 9:28 AM Carla Cicero notifications@github.com wrote:

What about "general phenotype" for field or "casual" IDs (could include casual measurements, scale counts). I like the term phenotype because most field ids are based on that.

I agree we need something for more careful analysis, could be scans or quantitative color analysis etc. Something more advanced that contrasts with "general"

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[DerekSikes]

Don't we have to consider cultural objects? Maybe this is why we settled on 'features' initially?

I think features is fine I just feel we need an alternative for when we don't know if the examination was of coarse or fine features...

maybe 'feature examination' ? pretty vague but works & is better than 'unknown'

-Derek

On Fri, Oct 4, 2019 at 8:28 AM Carla Cicero notifications@github.com wrote:

What about "general phenotype" for field or "casual" IDs (could include casual measurements, scale counts). I like the term phenotype because most field ids are based on that.

I agree we need something for more careful analysis, could be scans or quantitative color analysis etc. Something more advanced that contrasts with "general"

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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 don't think "phenotype" works for all of Arctos. "This looks like a Clovis point" and "the 800 measurements that fell out of the CT analysis support this being a Clovis point" should work alongside biological material.

The objections yesterday arose around the split between "general" and "detailed" (whatever we ultimately call them). It would be good if the terms themselves included/excluded "sorta-detailed" things like scale count, but that can probably be in the definition as well.

[dustymc]

field

I think that would fail to support what we're trying to do here. If we can get at HOW an ID was made, then people can search for cryptospecies (eg, things that look the same under some technique) and such. Saying where it was made (and I think "field" would be used for that, however it's defined) can't do that; people do drag microscopes to the field.

"Expertness" should be derived from the identifier's agent record and the new "confidence" field.

[dustymc]

'feature examination' ? pretty vague but works & is better than 'unknown'

I think this is confounding some stuff.

1. We should have clear terminology going forward; if you {whatever} then you need to use term {something}.
2. We need a migration path. I don't think there's a universal landing spot for the stuff currently in nature of ID (that's the problem we're trying to fix). Expert, student, curatorial, etc., all could have come from any technique. From here, at the scope of Arctos, I have absolutely no way to say more; I just don't know, and that's what "unknown" says. You may know more - 'experts' in your collection always use 'feature examination' or something. If you have that (or are willing to guess - the existing data will be preserved in remarks, I don't think this has to be perfect) PLEASE let me know so I can write custom migration scripts and move those records now, so they're not caught up in the default/fallback migration.

[AJLinn]

I don't think "phenotype" works for all of Arctos.

Please no biologically-specific terms. "Features" was a much more inclusive term for all collections held in Arctos.

[dustymc]

• I think we need a 'general features' term, and it should be easy to adjust the name as long as we don't significantly alter the concept.
• I think we need a 'fine features' term, and it should be easy to adjust the name as long as we don't significantly alter the concept.
• Do we also need a "features" term that encompasses both of the above? I think this is the current blocker.