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

[dustymc]

The attempted distinction is between "to the eye, it looks like a ..." and "we stuffed it under a microscope/CT scanner/etc., and there it looks like a ...."

The concept of "ID of kin" is safe, I just don't like the redundant wording - kin and relatives means about the same thing.

If single locus vs multilocus is something that users might want to search on, I have no problem adding it (now or later). If not, I think we should be as generic as possible. (I suspect 'multilocus' can only come usefully from id_sensu - a publication describing the details - and general terms are what's needed here, but ???) "Molecular" seems reasonable to me.

[AJLinn]

Sorry to be out of this - I muted the thread thinking it wasn't really relevant to us as it's a field we often don't spend a lot of time thinking about, but in looking thru the google doc, I'm not seeing a lot of usefulness for cultural collections.

gross features

That term doesn't have previous meaning for cultural collections... but it's infinitely better than 'gross phenotype', which I have no idea what it means! 🥴I think we can make it work. I don't know of a better way of indicating how the ID was made that would work for all.

As Carla referenced, cultural collections people can partially ID items based on materials, but also design elements, overall form, or overall perceived function. But we make ID judgements about a variety of things (materials, culture of origin/use, copyright applicability, or even maker at times if it's not signed but looks exactly like another piece in the collection).

For cultural collections the ID field is referencing the name of the item (is it an arrow head or a spear head, is it a basket or a hat, is it a meat platter or a cutting board, a tea pot or coffee pot, a man's parka or woman's parka), which is usually directly tied to it's function. It can be complicated with objects are re-used (e.g., a leg trap spring is reused as a scraper blade or a file is turned into a knife). We get at that complexity in our attribute "description."

Most of our IDs right now are "legacy". New nature of ID labels are either curatorial (me) or student (my students doing data entry). If we have an elder come thru and correct an ID, we change it to "expert". We have lots of accidental "ID of kin" because of its default position - but I also sometimes use it intentionally with the thought: "this object looks just like another item that is IDed as a fish spear prong, so it must be a fish spear prong".

I actually wouldn't mind having a slide-o-meter for some of those other areas (attributes mostly) where we're making "educated guesses" because I'm often surprised by how clearly not-correct some of the IDs are.

I think for archaeology collections (and likely paleo as well), this is even more difficult and more important because they're looking at fragments of things. Archaeologists at our museum often come look at full-sized modern pieces in the ethnology & history collection to decide if a fragment is part of a tobacco or coffee can, or a birch bark basket rim vs. birch bark canoe top plate.

Sorry to be jumping in late and missing most of the discussion. I'm not sure how to make the nature of ID more applicable for cultural collections given these complications, but I hope you consider us in your changes. Most of the terms in the google sheet right now are not very helpful for us honestly.

[ccicero]

---> I don't like 'trait-based' for the reasons Dusty gave. A fine count of scales or a wing measurement is also trait based, but that is different from an overall qualitative assessment based on what something looks like.

---> I've never really liked 'ID of kin' - sounds awkward to me. I do prefer 'kin relationship' even though there is slight redundancy, because I think it's clearer.

---> @AJLinn I added 'function' as a term to address your points, see definition in google doc to see if that makes sense.

Also, to address what Angela was saying about identifying cultural items based on others that look the same, I changed 'ID of kin' / 'kin relationship' to just 'relationship' so that it can apply more broadly to both cultural and natural history collections. This also makes the most sense for things like nests. Here is the definition I put in the google doc:

Identification based on the identification of a related individual (e.g., parent, sibling), a maker (e.g., for objects such as nests or cultural items), or of another object that has the same function and/or features (e.g., for cultural items).

[dustymc]

Should "fine morphology" become "fine features" (detailed features? something features...) to better contrast with "gross features"?

Maybe "general features" and "detailed features"? Qualitative features/quantitative features??

"It's obviously a teapot" is definitely what we're trying to get at with "gross features" (whatever the label ends up being).

"There are signs of percussive flaking under microscope/xray/etc., therefore it must be a Whatever Point" is "fine morphology" (again, whatever we're calling it).

"We found Camellia sinensis residue on this potsherd, so it was probably a teapot" is "genomics" - the concept, we'd probably need a new label if we get those data.

Note also that the "trust factor" built into Agents doesn't live in isolation - eg if a student identifies a bunch of things, then an "expert" (eg, an agent with a bunch of relevant publications) comes through and reidentifies them, you can use the correlation between those IDs to figure out that the student is generally right (or wrong...) and use that to weight their other IDs. That's also yet another reason to create IDs when you have them instead of eg, stuffing "confirmed by {cryptic initials}" in some remarks field or something.

I like it!

[ccicero]

I had the same thought and like the contrast between 'fine' and 'gross' features - see modified description. Fine-scale analysis may be qualitative (e.g., shape of hummingbird feathers) so that contrast doesn't work. I modified the description to reflect that.

[ccicero]

genomics vs molecular: I think molecular is better. DNA sequence of cytochrome b isn't genomic, but it is molecular.

[ccicero]

minor detail - should we be consistent in adjective versus noun. e.g., 'molecules' vs 'molecular' ??? I think that would look better so changed made that change in the doc.

[ccicero]

btw, I increased the priority of this related issue to high.

[campmlc]

I don't like "molecules" - it may be semantically consistent, but it is not in any usage in the sense of "molecular" genetics. I would advocate for using terminology consistent with usage in the literature and in the rest of the research and collections community.

On Thu, Jul 18, 2019 at 6:18 PM dustymc notifications@github.com wrote:

https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899

There are two tabs - 'migration path' will remain very waffly until 'ctnature_of_id' is solidified, and will only come into play after we've dealt with whatever needs dealt with by itself (Derek's "all IDs by experts and students would be method = phenotype" and similar).

Are we agreed on "confidence" for the new field?

I'm fine with "[high|low] confidence" for the terminology, but I'm also fine with absolutely anything else that gets the idea across. Like all Arctos vocabulary, the term means precisely what we define it to mean, and using it in any way outside the definition we assign is objectively wrong.

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[ccicero]

ok, changed it back.

[campmlc]

I made a few more comments on the google doc. Please review.

On Sat, Jul 20, 2019 at 2:47 PM Carla Cicero notifications@github.com wrote:

ok, changed it back.

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[ccicero]

I'm not sure who changed it back to genomics, but I don't think that's accurate. What about just 'DNA' ?

'coarse features' - ok with me, nice (better) contrast with 'fine features'

'audio-visual' - yes, that's better!

[dustymc]

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to DNA from CC's suggestion, I'm not attached to that (or anything else, except the idea).

I'm not 100% attached to the idea, but I think there's a distinction between audio where you have only one kind of information and video where you potentially have much more. I suppose we can sort it out when we get some data...

[ccicero]

I think for the purposes of ID, audio-visual is sufficient. 'audio' could also include some behavioral aspect (observe a bird singing from the top of a juniper bush, and it sounds like an Oak Titmouse). Other information might go into 'habitat' or 'attributes' of some kind or another (and we could probably expand on attributes for behavioral data). As you said, can be sorted out later.

This brings up another point for the purposes of migration: basis of record will be important, because how data are migrated will depend on context (observation, preserved specimen, cultural item, etc.). For example, I would say that all bird observations with a 'field' nature of ID and an associated media would be changed to "audio-visual' - we should modify the migration tab to incorporate this somehow.

[ebraker]

I like where this is going and moving away from subjective expert vs. non-expert descriptors. I am ok with adding a slider but I propose we style it in a way that doesn't give false-precision to the confidence value (is 63% confidence significantly more meaningful than 65%? How do you determine this anyway?). Perhaps there can be intervals - enough so that we aren't degrading the data but not so many so as to drive ourselves nuts fretting over the minutia (e.g. 100%, >90%, >80% 70-50%,,<50% .... or something). When we have an expert redetermine or confirm ID for loans, do we unrealistically ask them to rate their confidence? When they don't include their confidence ratings do we leave this field null despite the fact we know the specimens have been examined by a specialist? Or do we introduce some level of educated interepretation (>80%?)? If so, I think ranges vs. straight integers allows us to accurately convey confidence without getting overly precise.

[Jegelewicz]

As long as I can leave the rating slider null (not zero, NULL), I don't care, because I am not going to make any judgement calls about the relative expertise of anyone's ID (nor do I want to have the person who made the ID rate themselves). The move to objective means of identification is awesome an I totally support it.

[dustymc]

I think much of that's documentation??

I can round to any precision....

UAM@ARCTOS> select round(45.9995476788,-1) from dual;

ROUND(45.9995476788,-1)
-----------------------
             50

but that might be more misleading/confusing.

At some point the ID (and probably specimen) bulkloader will likely need to accept a NUMBER and downloads will contain a NUMBER as well; we have limited control over UI.

The documentation should stress that this is a subjective thing which should be set to "that feels about right."

Any query access will need carefully and similarly documented; most of these data will be NULL, and so setting this to any value will exclude most specimens. I don't think it will be useful for "normal" specimen searches, it will be used by "us" to find the situations we created by using the tool.

I'm inclined to just accept whatever I'm given (within some defined range), mostly because I think it's least confusing. I suppose if someone really wants to set up some distinction between 89.00000345 and 89.00000346 they can, all we can do it make the documentation clear....

[campmlc]

I changed back to "molecular" because this can include proteins, immunology, RNA, future tech we don't know about yet . . . Otherwise we have to specify each one . . .

On Sat, Jul 20, 2019 at 6:43 PM dustymc notifications@github.com wrote:

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to DNA from CC's suggestion, I'm not attached to that (or anything else, except the idea).

I'm not 100% attached to the idea, but I think there's a distinction between audio where you have only one kind of information and video where you potentially have much more. I suppose we can sort it out when we get some data...

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[campmlc]

I'm not a fan of the slider concept. How are students going to use this in data entry? How do we assign in the field on a rapid assembly line? What does it mean, anyway? It seems most useful for specimens that have been subsequently examined curatorially to indicate if something has indeed been examined by an expert on that particular taxonomic group. Everything else by anyone else is "not enough info to assess confidence".

On Mon, Jul 22, 2019 at 10:38 AM Mariel Campbell campbell@carachupa.org wrote:

I changed back to "molecular" because this can include proteins, immunology, RNA, future tech we don't know about yet . . . Otherwise we have to specify each one . . .

On Sat, Jul 20, 2019 at 6:43 PM dustymc notifications@github.com wrote:

changed it back to genomics

Edit history says I did, but certainly not intentionally. I changed it to DNA from CC's suggestion, I'm not attached to that (or anything else, except the idea).

I'm not 100% attached to the idea, but I think there's a distinction between audio where you have only one kind of information and video where you potentially have much more. I suppose we can sort it out when we get some data...

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[dustymc]

include proteins, immunology, RNA, future tech we don't know about yet. . . Otherwise we have to specify each one . . .

This is a question for users, but perhaps specifying each one is important - eg, species hypotheses built on "future tech we don't know about yet" [do|do not] align with species hypotheses built on {something else} and users will want to find those specimens and request loans.

Or we could see this as a not-so-precise category and get at "future tech we don't know about yet" via id_sensu (publications).

I think one category, whatever we call it, is probably OK for now, just something to keep in mind...

I'm not a fan of the slider concept.

So don't use it.

What does it mean, anyway?

By definition, probably something like 'subjective measure of how confident the identifier is in the identification." By usage, whatever Curators want it to mean...

It provides a pathway to get at the things Derek mentioned without engaging in an endless vocabulary debate, and it does it without requiring anything from anyone who doesn't want to use it or taking anything of value from identifications which haven't specified a 'confidence.'

"not enough info to assess confidence"

That's NULL, which would be the default condition.

[ebraker]

I imagine using NULL in the majority of cases for our collection so I am not all out opposed to the slider. That said, I wonder if it is more straightforward to have some sort of toggle, e.g., "ID tentative" rather than attempting to quantify the degree of uncertainty for an identification in an unmethodical way across multiple collection types and personal assertion styles (and essentially reintroducing subjectivity, e.g., 80 vs 85% cetain). A flagged record could still be elaboarated upon with a textual description (or alas, even a numeric rating) in the ID_remarks if desired and is easily searched. It just seems like if we create some sort of Confidence-o-Meter and then find a better structure down the line, we then have to migrate all of these [overly] precise values into the new model that hold varying degrees of meaningfulness and which will likely be interpreted as [overly] significant for future users. For me, just knowing an ID is uncertain is valuable - regardless of whether the determiner was 80% or 45% confident, I know that specimens needs further examination and should likely be excluded from niche models, etc.

[campmlc]

I prefer Emily's alternative to the slider.

As for: get at "future tech we don't know about yet" via id_sensu (publications)

Yes, we just need to rely on liking to the publication. It is hard enough for curatorial staff to just find and link publications. To add a requirement that we read through the entire methods section of each pub to figure out exactly what technique they used and translate that into some Arctos terminology would not be reasonable. It is hard enough for me to find those studies just based on "genetic" or "molecular" vs "morphology". Parsing it further would require an enormous amount of time and effort.

On Mon, Jul 22, 2019 at 11:03 AM Emily Braker notifications@github.com wrote:

I imagine using NULL in the majority of cases for our collection so I am not all out opposed to the slider. That said, I wonder if it is more straightforward to have some sort of toggle, e.g., "ID tentative" rather than attempting to quantify the degree of uncertainty for an identification in an unmethodical way across multiple collection types and personal assertion styles (and essentially reintroducing subjectivity, e.g., 80 vs 85% cetain). A flagged record could still be elaboarated upon with a textual description (or alas, even a numeric rating) in the ID_remarks if desired and is easily searched. It just seems like if we create some sort of Confidence-o-Meter and then find a better structure down the line, we then have to migrate all of these [overly] precise values into the new model that hold varying degrees of meaningfulness and which will likely be interpreted as [overly] significant for future users. For me, just knowing an ID is uncertain is valuable - regardless of whether the determiner was 80% or 45% confident, I know that specimens needs further examination and should likely be excluded from niche models.

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[dustymc]

toggle, e.g., "ID tentative"

I'm certainly fine with that, but it didn't look like we were headed for vocabulary resolution above. Something symbolic (slider, stars, whatever) doesn't require us to define terms - that's essentially all of my "recommendation." Derek seems to the the one with a solid use case; I'm happy enough to do whatever he tells me to do, as long as nobody else is screaming too loudly....

ID_remarks

No free-text field anywhere is usefully searchable, at least not as long as we let humans provide the values. Wee maek typograaphical eerors n etc....

It is hard enough for curatorial staff to just find and link publications.

I don't doubt that, but it provides a level of precision that nothing else can. It's certainly never going to be anything like a requirement, but if it's there it becomes a powerful tool that users can access for all sorts of reasons; it makes your data more able to answer more questions.

entire methods section of each pub to figure out exactly what technique they used and translate

That would be (can be now) up to the user, not "us." Any translation would be a downgrade. Maybe users want specimens IDed genetically using some primer that they don't trust - they can get that from id_sensu, it's not something we'd realistically be able to to predict, summarize, and/or categorize.

"genetic" or "molecular"

Those two values in the same list would probably lead to ambiguous usage.

[DerekSikes]

I've been considering the slider idea and have fears there will be unforeseen undesirable consequences. Mariel brought one up I hadn't considered - how to bulkload the data? Also, how do we search on the field if we don't know what's in it? or would a value 0-100 appear as the slider is set? We could then search on those values?

I still think this brings in massive over-precision. I might set a value of 85 one day and 87 another and 90 or 86 another day all for the same basic ID job.. it's asking users to split hairs and make impossible decisions. Even if we just had the scale run from 1-10 (an improvement) it would still be hard to decide.

I really like a binary choice - is this a reliable ID or not? (or null for unknown)

-Derek

On Mon, Jul 22, 2019 at 9:30 AM dustymc notifications@github.com wrote:

toggle, e.g., "ID tentative"

I'm certainly fine with that, but it didn't look like we were headed for vocabulary resolution above. Something symbolic (slider, stars, whatever) doesn't require us to define terms - that's essentially all of my "recommendation." Derek seems to the the one with a solid use case; I'm happy enough to do whatever he tells me to do, as long as nobody else is screaming too loudly....

ID_remarks

No free-text field anywhere is usefully searchable, at least not as long as we let humans provide the values. Wee maek typograaphical eerors n etc....

It is hard enough for curatorial staff to just find and link publications.

I don't doubt that, but it provides a level of precision that nothing else can. It's certainly never going to be anything like a requirement, but if it's there it becomes a powerful tool that users can access for all sorts of reasons; it makes your data more able to answer more questions.

entire methods section of each pub to figure out exactly what technique they used and translate

That would be (can be now) up to the user, not "us." Any translation would be a downgrade. Maybe users want specimens IDed genetically using some primer that they don't trust - they can get that from id_sensu, it's not something we'd realistically be able to to predict, summarize, and/or categorize.

"genetic" or "molecular"

Those two values in the same list would probably lead to ambiguous usage.

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[dustymc]

how to bulkload the data?

The slider would just be an abstraction of some range of values - 0-1 or 0-10000000000 or whatever - I think it's become "percent confidence" in my head but that's probably overly precise/wrong.

Arctos is unicode, so something like a code table of

IN (NULL,⭐,⭐⭐,⭐⭐⭐,⭐⭐⭐⭐,⭐⭐⭐⭐⭐)

is completely possible as well. Not suggesting we should, but we could - we are not limited to text/ASCII.

I might set a value of 85 one day and 87 another and 90 or 86 another day all for the same basic ID job.

Yep, probably - I guess in addition to the terminology thing, you (or someone) mentioned some "expert" threshold above that sounded really low for some use cases. The slider would let you-the-user and you-the-operator define "expert" (or "unreliable" or whatever) however you want, assuming there's some sort of grouping around sliding the widget ALMOST all the way to the right for "I'm pretty confident in this" - and that may be an unjustified assumption.

binary

I'm certainly fine with that if we can find acceptable vocabulary. It's a lot easier to code too!

null for unknown

It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. (https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

[Jegelewicz]

null for unknown

It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. (https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

[campmlc]

agree.

On Mon, Jul 22, 2019 at 1:00 PM Teresa Mayfield-Meyer < notifications@github.com> wrote:

null for unknown

It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. ( https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

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[DerekSikes]

Agreed

4 options for ID confidence, how about:

reliable uncertain reliability unknown NULL

I really think we should avoid making clear statements that the reliability is poor or unreliable etc. because that seems too strong & we don't want to be making former nature of IDs with 'student' = 'unreliable'... a much better term is ' uncertain reliability'

-D

On Mon, Jul 22, 2019 at 11:00 AM Teresa Mayfield-Meyer < notifications@github.com> wrote:

null for unknown

It's overly pedantic for this conversation, but those are not the same thing. NULL ==> we say nothing (including about why we're saying nothing). "Unknown" ==> we don't have the information. ( https://arctos.database.museum/info/ctDocumentation.cfm?table=CTSEX_CDE contains a couple more ways we can get at not having anything to say.)

I think it is an important distinction...

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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'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

[campmlc]

Perhaps we need to treat these as flags going forward, but legacy data will have to be left as null. I would not want to convert all our "student" IDs to uncertain reliability if that meant those records would be excluded from niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

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[DerekSikes]

I keep forgetting to mention this but in that case, when you want to indicate unreliable, why not just use ID formula A ?

-D

On Mon, Jul 22, 2019 at 11:15 AM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

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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

[DerekSikes]

Mariel,

If we did go this route then it sounds like you'd like your 'student' IDs changed to 'reliable' ? I suppose Dusty could do this on a case-by case basis. But then how would you distinguish 'world expert/taxonomic authority' based IDs from the rest in your collection?

-Derek

On Mon, Jul 22, 2019 at 11:17 AM Mariel Campbell notifications@github.com wrote:

Perhaps we need to treat these as flags going forward, but legacy data will have to be left as null. I would not want to convert all our "student" IDs to uncertain reliability if that meant those records would be excluded from niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

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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]

We have expert for some of our IDs made by experts in that group who have examined the specimens through some criteria. But most of our IDs are made by collection managers who use "student" because they are not experts in a particular group, even though they are qualified taxonomic professionals. This is what we've been instructed to consider "student" to mean. Even our "field" IDs are usually made by people who are consulting keys and have some knowledge of the taxa involved - but we are missing key characters (e.g. cleaned dentition) to make a full diagnosis; and the confidence depends largely on the species richness and geographic distribution of the taxonomic group at a particular locality . . .

On Mon, Jul 22, 2019 at 1:21 PM DerekSikes notifications@github.com wrote:

Mariel,

If we did go this route then it sounds like you'd like your 'student' IDs changed to 'reliable' ? I suppose Dusty could do this on a case-by case basis. But then how would you distinguish 'world expert/taxonomic authority' based IDs from the rest in your collection?

-Derek

On Mon, Jul 22, 2019 at 11:17 AM Mariel Campbell <notifications@github.com

wrote:

Perhaps we need to treat these as flags going forward, but legacy data will have to be left as null. I would not want to convert all our "student" IDs to uncertain reliability if that meant those records would be excluded from niche modeling, for example. Most everything we have is "student".

On Mon, Jul 22, 2019 at 1:15 PM dustymc notifications@github.com wrote:

I'm OK with that, but there have also been times when I might have used an "unreliable" option. Something's not some Eurasian species so I know more than genus (the next-highest taxonomic pigeonhole), but I'm still not entirely confident that the species I've picked is correct. I suppose "A {string}" gets there too, but it isn't as searchable as I'd like.

There would need to be some clear separation between "uncertain reliability" and "unknown" (and NULL) - I'm not sure I see that just from the vocabulary.

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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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[ebraker]

Was just typing what Derek said re: formula A ?. A slider also wouldn't convey that you are certain about genus designation, still wavering between a couple species but can confidently rule out all Eurasian taxa in a given group. The pick list: reliable/certain, unreliable/tentative, unknown, null (or whatever values we choose) would be an intuitve way to flag records without having to think too hard as well as a means to conviently call up records with uncertain IDs in a search. ID_remarks and/or formulas would then further detail the thinking behind tentative determinations.

If we decide to map all student IDs to NULL, perhaps we can integrate the confidence flag into the Manage menu. That way we could do global updates for taxa (yes, all skulls identified as Alces alces are reliably moose) or by agent (yes, this collection manager or grad student is good for bird IDs) or whatever parameter. I will very likely leave current student values NULL and make opportunistic changes when I happen upon them, but would use the flag moving forward for new records.

[dustymc]

legacy data will have to be left as null

I can deal with that by collection (or any other criteria ya'll want to put together). I don't think anything global will or should happen. Pushing some confidence value for CollectionA 'expert' IDs and doing something different in CollectionB and ..... isn't much of a problem, and I think hinges on how the existing values have been used up to this point. I'm pretty sure we can do this without losing anything or forcing anyone in any direction they don't want to go in.

meant those records would be excluded from niche modeling,

We obviously can't control how people use data, but I can't really see why anyone would want to do that.

The flag doesn't/can't say anything about the ID, it's just how confident a particular user is in a particular ID. My "oh yea, I think I totally nailed it" is (in light of my "expertise" via my agent record and perhaps my cited publication) almost certainly of less value than Derek's "I'm not very sure about this" on the same beetle, for instance. This field does not and cannot live in isolation, and it should not be seen that way.

why not just use ID formula A

... {string} presumably. Searchability - if you CAN mis-type strings, you WILL mis-type strings, so it's not as discoverable in certain search fields. You can still search by the taxonomy component - I suppose you could mix all that up to say "I'm leaning towards Sorex tundrensis" (ID to species, low confidence) or "it's definitely one of the northern tricolored shrews (ID to genus, a bit more info via the text-based ID, high confidence).

[ccicero]

Rather than 'reliable' and 'uncertain reliability' which sounds really awkward to me and am not sure what it really means or how to use it, what about this:

ID certain ID uncertain ID certainty unknown null

[DerekSikes]

Hate to belabor this but I keep worrying about us stating falsehoods.

ID certain is not the same as ID reliable.

The former means 100% - error is impossible, the latter means it's trustworthy but of course, humans being humans...

so if we don't use 'reliable' I hope we can find an actual synonym

-Derek

On Mon, Jul 22, 2019 at 12:20 PM Carla Cicero notifications@github.com wrote:

Rather than 'reliable' and 'uncertain reliability' which sounds really awkward to me and am not sure what it really means or how to use it, what about this:

ID certain ID uncertain ID certainty unknown null

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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 think we moved away from certain because it implies immutability?

On Mon, Jul 22, 2019, 2:20 PM Carla Cicero notifications@github.com wrote:

Rather than 'reliable' and 'uncertain reliability' which sounds really awkward to me and am not sure what it really means or how to use it, what about this:

ID certain ID uncertain ID certainty unknown null

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[dustymc]

As above, "ID bla" should be taken to mean "the person(s) making this identification say they're bla of it" and not, ever, under any circumstances, "this identification is actually bla." I think we're trying to put meaning that can't exist into this.

[DerekSikes]

If the person making the IDs is also the person entering the ID data into Arctos we can say "I'm certain/uncertain" of it but in many cases we're entering IDs made by others... and we still want some way to say how reliable the IDs are and 'certain' shouldn't be an option.

-D

On Mon, Jul 22, 2019 at 1:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this identification say they're bla of it" and not, ever, under any circumstances, "this identification is actually bla." I think we're trying to put meaning that can't exist into this.

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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]

How about: field: "ID confidence" values: high, medium, low, unknown, null

On Mon, Jul 22, 2019 at 3:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this identification say they're bla of it" and not, ever, under any circumstances, "this identification is actually bla." I think we're trying to put meaning that can't exist into this.

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[DerekSikes]

I'm ok with these... but to which would 'student' map? medium? or low? (or let each collection decide which)

Rarely an expert will return specimens with a ? next to the ID. How would we record this? ID confidence = high but use ID formula A ?

-D

On Mon, Jul 22, 2019 at 1:19 PM Mariel Campbell notifications@github.com wrote:

How about: field: "ID confidence" values: high, medium, low, unknown, null

On Mon, Jul 22, 2019 at 3:08 PM dustymc notifications@github.com wrote:

As above, "ID bla" should be taken to mean "the person(s) making this identification say they're bla of it" and not, ever, under any circumstances, "this identification is actually bla." I think we're trying to put meaning that can't exist into this.

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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]

or let each collection decide which

Yes - and if a particular collection also wants THAT student to "medium" and THIS one to "low" and some other to NULL I can accommodate that too.

? next to the ID

Ideally you'd ask them (eg, by way of sending them some form that you can upload to Arctos), but if you're assigning things you can obviously do whatever you think they meant or just leave confidence NULL. "I'm sure it might be that" certainly fits....

[DerekSikes]

Ok, are we good with Mariel's suggestion?

field: "ID confidence" values: high, medium, low, unknown, null

-D

On Mon, Jul 22, 2019 at 1:58 PM dustymc notifications@github.com wrote:

or let each collection decide which

Yes - and if a particular collection also wants THAT student to "medium" and THIS one to "low" and some other to NULL I can accommodate that too.

? next to the ID

Ideally you'd ask them (eg, by way of sending them some form that you can upload to Arctos), but if you're assigning things you can obviously do whatever you think they meant or just leave confidence NULL. "I'm sure it might be that" certainly fits....

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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

[ccicero]

I'm fine with that.

[dustymc]

Are we good to go with this? If so I can

• add "identification_confidence" using...
  • high==>Determiner(s), or collection personnel on behalf of determiners(s), have high confidence that the identification is correct.
  • medium==>Determiner(s), or collection personnel on behalf of determiners(s), have moderate confidence that the identification is correct.
  • low==>Determiner(s), or collection personnel on behalf of determiners(s), have low confidence that the identification is correct.
  • unknown==>Determiner(s), or collection personnel on behalf of determiners(s), have expressed that they do not know how confident the identification is.
  • (NULL==>nobody asserts anything)
• add the values from the spreadsheet to the code table
• set up a temporary trigger to disallow using 'old' values
• work with ya'll to migrate existing data to the new structure
• clean up old values

---

From https://github.com/ArctosDB/arctos/issues/1868: When implementing add drag-drop ordering, replace the JS checks with HTML5 controls

[DerekSikes]

Could we change "Identifier(s)" to "Determiners"

The latter is a synonym of the former but the former is a homonym of those numbers and codes we assign to specimens... and homonyms can lead to confusions.

Otherwise, I'm happy with this.

-Derek

On Wed, Jul 24, 2019 at 12:19 PM dustymc notifications@github.com wrote:

Are we good to go with this? If so I can

• add "identification_confidence" using...
  • high==>Identifier(s), or collection personnel on behalf of identifier(s), have high confidence that the identification is correct.
  • medium==>Identifier(s), or collection personnel on behalf of identifier(s), have moderate confidence that the identification is correct.
  • low==>Identifier(s), or collection personnel on behalf of identifier(s), have low confidence that the identification is correct.
  • unknown==>Identifier(s), or collection personnel on behalf of identifier(s), have expressed that they do not know how confident the identification is.
  • (NULL==>nobody asserts anything)
• add the values from the spreadsheet https://docs.google.com/spreadsheets/d/1JfbcpVYTK73DKRkgJQ0jNrFziS9zcbx7lEq872WrfYs/edit#gid=115578899 to the code table
• set up a temporary trigger to disallow using 'old' values
• work with ya'll to migrate existing data to the new structure
• clean up old values

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From #1868 https://github.com/ArctosDB/arctos/issues/1868: When implementing add drag-drop ordering, replace the JS checks with HTML5 controls

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[dustymc]

Determiners

Edited above.

[campmlc]

What about saying that high confidence means high confidence that the determiner asserts that the identification is correct according to currently accepted taxonomy?

On Wed, Jul 24, 2019 at 3:22 PM dustymc notifications@github.com wrote:

Determiners

Edited above.

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[dustymc]

according to...taxonomy

That's what ID_Sensu does, and confounding it with something else could only result in conflicting and low-quality data.