Closed dustymc closed 4 years ago
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.
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...).
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.
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......"
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.
@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 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?
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.
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.
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.
"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
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
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.
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
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.
/remind me to finalize this in 2 weeks
@dustymc set a reminder for Oct 16th 2019
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
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.
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
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
Bueno?
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
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
Bueno?
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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?
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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
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.
taxonomic revision is no more
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/ +++++++++++++++++++++++++++++++++++
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
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?
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-- 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/
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
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
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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
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
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
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.
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/ +++++++++++++++++++++++++++++++++++
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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:
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.
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
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
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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
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....
What about "external phenoype" (looks like moose") vs "anatomy" (internal morphology/structure) vs "microscopy"?
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?
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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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.
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.
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"
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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-- 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/
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
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.
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.
'feature examination' ? pretty vague but works & is better than 'unknown'
I think this is confounding some stuff.
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.
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?
@ccicero