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Arctos is a museum collections management system
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USNM: National Museum of Natural History #5994

Open dustymc opened 1 year ago

dustymc commented 1 year ago

Instructions

This is a template to facilitate communication with the Arctos Code Table Committee. Submit a separate request for each relevant value. This form is appropriate for exploring how data may best be stored, for adding vocabulary, or for updating existing definitions.

Reviewing documentation before proceeding will result in a more enjoyable experience.


Initial Request

Goal: Describe what you're trying to accomplish. This is the only necessary step to start this process. The Committee is available to assist with all other steps. Please clearly indicate any uncertainty or desired guidance if you proceed beyond this step.

All USNM: National Museum of Natural History should be replaced with other ID type = other identifier and issued by agent Smithsonian National Museum of Natural History

Proposed Value: Proposed new value. This should be clear and compatible with similar values in the relevant table and across Arctos.

Proposed Definition: Clear, complete, non-collection-type-specific functional definition of the value. Avoid discipline-specific terminology if possible, include parenthetically if unavoidable.

Context: Describe why this new value is necessary and existing values are not.

Table: Code Tables are http://arctos.database.museum/info/ctDocumentation.cfm. Link to the specific table or value. This may involve multiple tables and will control datatype for Attributes. OtherID requests require BaseURL (and example) or explanation. Please ask for assistance if unsure.

Collection type: Some code tables contain collection-type-specific values. collection_cde may be found from https://arctos.database.museum/home.cfm

Priority: Please describe the urgency and/or choose a priority-label to the right. You should expect a response within two working days, and may utilize Arctos Contacts if you feel response is lacking.

Available for Public View: Most data are by default publicly available. Describe any necessary access restrictions.

Project: Add the issue to the Code Table Management Project.

Discussion: Please reach out to anyone who might be affected by this change. Leave a comment or add this to the Committee agenda if you believe more focused conversation is necessary.

Approval

All of the following must be checked before this may proceed.

The How-To Document should be followed. Pay particular attention to terminology (with emphasis on consistency) and documentation (with emphasis on functionality).

Rejection

If you believe this request should not proceed, explain why here. Suggest any changes that would make the change acceptable, alternate (usually existing) paths to the same goals, etc.

  1. Can a suitable solution be found here? If not, proceed to (2)
  2. Can a suitable solution be found by Code Table Committee discussion? If not, proceed to (3)
  3. Take the discussion to a monthly Arctos Working Group meeting for final resolution.

Implementation

Once all of the Approval Checklist is appropriately checked and there are no Rejection comments, or in special circumstances by decree of the Arctos Working Group, the change may be made.

Review everything one last time. Ensure the How-To has been followed. Ensure all checks have been made by appropriate personnel.

Make changes as described above. Ensure the URL of this Issue is included in the definition.

Close this Issue.

DO NOT modify Arctos Authorities in any way before all points in this Issue have been fully addressed; data loss may result.

Special Exemptions

In very specific cases and by prior approval of The Committee, the approval process may be skipped, and implementation requirements may be slightly altered. Please note here if you are proceeding under one of these use cases.

  1. Adding an existing term to additional collection types may proceed immediately and without discussion, but doing so may also subject users to future cleanup efforts. If time allows, please review the term and definition as part of this step.
  2. The Committee may grant special access on particular tables to particular users. This should be exercised with great caution only after several smooth test cases, and generally limited to "taxonomy-like" data such as International Commission on Stratigraphy terminology.
dustymc commented 1 year ago

I will plan on proceeding with this about 2023-03-28 if there are no objections.

I will proceed immediately upon approval of each of the involved collections.

Data: temp_usnm_national_museum_of_natural_history.csv.zip

Summary: guid_prefix numrecs approved
ALMNH:Inv 7 changed
ALMNH:Paleo 1 changed
CHAS:Bird 36 yes
CHAS:Mamm 6 yes
CRCM:Bird 11 yes
DMNS:Bird 9
DMNS:Mamm 5
MLZ:Bird 68
MSB:Bird 33
MSB:Fish 1
MSB:Host 25
MSB:Para 45
MVZ:Bird 36 yes
MVZ:Herp 6
MVZ:Mamm 1 fixed
NMMNH:Paleo 1 fixed
UAM:Art 9
UAM:Herp 1
UAM:Inv 11
UAM:Mamm 25
UAMObs:Ento 33
UCM:Egg 3 yes
UCM:Fish 72 yes
UCM:Herp 2 yes
UCM:Mamm 9 yes
USNPC:Para 1
UTEP:ES 24 changed
UTEP:Inv 5 changed

Users: @ebraker @msbparasites @Nicole-Ridgwell-NMMNHS @mlbowser @mkoo @jessicatir @campmlc @ccicero @catherpes @amgunderson @atrox10 @DerekSikes @marecaguthrie @mvzhuang @cjconroy @wellerjes @kmkocot @jandreslopez @droberts49 @aklompma @acdoll @jrdemboski @kyndallh

See also https://github.com/ArctosDB/arctos/issues/5771

ccicero commented 1 year ago

Fine with me for MVZ:Bird

campmlc commented 1 year ago

Not OK for MSB:Host and MSB:Para collections until further discussion regarding impact on relationships.

On Tue, Mar 14, 2023 at 2:02 PM dustymc @.***> wrote:

  • [EXTERNAL]*

I will plan on proceeding with this about 2023-03-28 if there are no objections.

I will proceed immediately upon approval of each of the involved collections.

Data: temp_usnm_national_museum_of_natural_history.csv.zip https://github.com/ArctosDB/arctos/files/10973257/temp_usnm_national_museum_of_natural_history.csv.zip

Summary: guid_prefix numrecs ALMNH:Inv 7 ALMNH:Paleo 1 CHAS:Bird 36 CHAS:Mamm 6 CRCM:Bird 11 DMNS:Bird 9 DMNS:Mamm 5 MLZ:Bird 68 MSB:Bird 33 MSB:Fish 1 MSB:Host 25 MSB:Para 45 MVZ:Bird 36 MVZ:Herp 6 MVZ:Mamm 1 NMMNH:Paleo 1 UAM:Art 9 UAM:Herp 1 UAM:Inv 11 UAM:Mamm 25 UAMObs:Ento 33 UCM:Egg 3 UCM:Fish 72 UCM:Herp 2 UCM:Mamm 9 USNPC:Para 1 UTEP:ES 24 UTEP:Inv 5

Users: @ebraker https://github.com/ebraker @msbparasites https://github.com/msbparasites @Nicole-Ridgwell-NMMNHS https://github.com/Nicole-Ridgwell-NMMNHS @mlbowser https://github.com/mlbowser @mkoo https://github.com/mkoo @jessicatir https://github.com/jessicatir @campmlc https://github.com/campmlc @ccicero https://github.com/ccicero @catherpes https://github.com/catherpes @amgunderson https://github.com/amgunderson @atrox10 https://github.com/atrox10 @DerekSikes https://github.com/DerekSikes @marecaguthrie https://github.com/marecaguthrie @mvzhuang https://github.com/mvzhuang @cjconroy https://github.com/cjconroy @wellerjes https://github.com/wellerjes @kmkocot https://github.com/kmkocot @jandreslopez https://github.com/jandreslopez @droberts49 https://github.com/droberts49 @aklompma https://github.com/aklompma @acdoll https://github.com/acdoll @jrdemboski https://github.com/jrdemboski @KyndallH https://github.com/KyndallH

See also #5771 https://github.com/ArctosDB/arctos/issues/5771

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dustymc commented 1 year ago

impact on relationships

If you have a concern please open an Issue to it can be addressed.

campmlc commented 1 year ago

This is the issue I'm using for now. When I can stop reviewing the endless flow of new issues, I can consider taking a breath to create one.

campmlc commented 1 year ago

https://github.com/ArctosDB/arctos/issues/6004

wellerjes commented 1 year ago

Reviewed; okay to proceed for CHAS

ebraker commented 1 year ago

Ok for UCM

Jegelewicz commented 1 year ago

I think we can do more with this one.

I just worked on UTEP:Inv and I can find all of the related identifiers on the Smithsonian's Invertebrate Zoology database. This brings all of those records one step closer to an actual link with USNM:IZ.

image

image

Jegelewicz commented 1 year ago

Same goes for ALMNH:Inv

image

image

Jegelewicz commented 1 year ago

ALMNH:Paleo

image

image

Jegelewicz commented 1 year ago

NMMNH:Paleo

https://arctos.database.museum/guid/NMMNH:Paleo:43252

@Nicole-Ridgwell-NMMNHS I can't find the corresponding record on the USNM Paleo site - https://collections.nmnh.si.edu/search/paleo/

Jegelewicz commented 1 year ago

UTEP:ES

@mvzhuang I also could not find the UTEP USNM identifiers in their paleo site search - https://collections.nmnh.si.edu/search/paleo/

here is the list. https://arctos.database.museum/search.cfm?guid_prefix=UTEP%3AES&oidtype=USNM%3A%20National%20Museum%20of%20Natural%20History

dustymc commented 1 year ago

@Jegelewicz are you doing something with the variously-formatted possibly-random IDs or looking up ARKs manually or ??

(Mostly wondering if ARs in identifier should get some UI magic...)

(And who wrote their form?? EZID is an issuer/resolver, not an ID type!)

campmlc commented 1 year ago

That's great - I'd like to see if we can do that for MSB links. And again, if we can narrow down to an actual institutional catalog number at USNM, then that is the other ID type we would request.

On Thu, Mar 16, 2023 at 10:09 AM Teresa Mayfield-Meyer < @.***> wrote:

  • [EXTERNAL]*

I think we can do more with this one.

I just worked on UTEP:Inv and I can find all of the related identifiers on the Smithsonian's Invertebrate Zoology https://arctos.database.museum/agent/21347813 database. This brings all of those records one step closer to an actual link with USNM:IZ.

[image: image] https://user-images.githubusercontent.com/5725767/225681677-1220b3a4-a111-4215-b266-190589cf52dc.png

[image: image] https://user-images.githubusercontent.com/5725767/225681912-4f863405-0663-41f8-8049-56879b3b3a8e.png

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Jegelewicz commented 1 year ago

variously-formatted possibly-random IDs or looking up ARKs manually or ??

All of this comes straight from GRSciColl (not so useless now?)

Smithsonian Institution Page image

Contains links to all of their collections image

Collection pages like Invert Zoo image

Contain links to their database search page image

dustymc commented 1 year ago

Oh - I thought perhaps you were somehow getting from the shady IDs to ...

Screenshot 2023-03-16 at 9 45 08 AM

...the really great IDs.

Jegelewicz commented 1 year ago

Yeah, but that is a lot more work. Maybe we can figure out some way to go and get them all someday - but that seems to be a fundable project? Doing real digital extended specimen stuff?

Nicole-Ridgwell-NMMNHS commented 1 year ago

Ours is actually a USNM locality ID, I've changed the identifier to locality ID issued by USNM (specimen is ungeoreferenced and in a general catch-all locality for this particular adopted collection, otherwise I would have added the ID to the locality).

jessicatir commented 1 year ago

OK for CRCM:Bird.

Jegelewicz commented 1 year ago

I thought perhaps you were somehow getting from the shady IDs to ...

Screenshot 2023-03-16 at 9 45 08 AM

...the really great IDs.

But the problem is @campmlc added them as complete links and we are adding on a base url, so they just 404. See https://arctos.database.museum/guid/MSB:Host:11676 where I have also added an ARK that functions properly.

There is definitely opportunity to make all of these ACTUAL links, but we have two ways of doing this and to any user unaware, this can result in malformed links.

I am happy to do some cleanup to get these working - and even to get the ARKs for the other stuff that I can, it will just take a while.

Jegelewicz commented 1 year ago

EZID is an issuer/resolver, not an ID type!)

It is BOTH - the concept that I think we have been trying to get across for a while?

dustymc commented 1 year ago

added them as complete links and we are adding on a base url,

Blargh, why again is https://github.com/ArctosDB/arctos/issues/6163 not my only priority?!

And ARK is another place where that plus the issuer really shines - nobody cares that it's an ARK, we care that is DOES STUFF and that it's "theirs." Old model completely fails at that, current handles it elegantly. But here we are for some reasons...

It is BOTH

No (but I think what you're trying to say isn't wrong). EZID is an organization. They issue ARKs (which technically are part of the URL). They also resolve ARKs. You can also issue ARKs if you want, and you can resolve ARKs if you want, and EZID can resolve your ARKS (even though the URL might suggest otherwise) and vice-versa. It's complicated, even before we arbitrarily rip them apart for Arctos (in an effort to confuse everyone? It works!).

It ain't gotta be that way, and nobody needs to understand any of that. Just paste the thing that DOES STUFF in, save, and be done with it. Why is that contentious?!

also added an ARK

FWIW I'd call that one an identifier (if I could - I can't even find that issue! https://github.com/ArctosDB/arctos/issues/6005) - it's clearly not their catalog number, see above re: ARK type, there's no reason to complicate this.

Jegelewicz commented 1 year ago

Unable to find the UTEP:ES numbers in any of the Smithsonian databases, so changed them to issued by Smithsonian National Museum of Natural History

campmlc commented 1 year ago

I am concerned that someone thought these were USNM numbers, and from my experience, the fact they aren't in the USNM digital catalog does not mean they aren't. These could just not be cataloged yet, or they are older numbers that the Smithsonian has replaced with newer ones. When I choose a USNM identifier for a record, I am explicitly choosing that number because I have "USNM" written on a tag. There is a big difference between an explicit "USNM" identifier and "issued by the Smithsonian", which is a giant institution with two different administrations. Again, I am very, very concerned about the loss of data that is going on here with these conversions. Please stop until we can have a committee to discuss.

campmlc commented 1 year ago

You do not have MSB permission to make any changes to MSB records.

Jegelewicz commented 1 year ago

Ah-Ha! I am pretty sure those UTEP:ES numbers are locality identifiers! I just sent an email to Art to confirm.

Jegelewicz commented 1 year ago

FWIW - I did not "say they are not USNM numbers" - they are all prefixed with USNM and the issuer is Smithsonian Museum of Natural History which IS USNM. I even took the extra time to add the old USNM:National Museum of Natural History identifier to the remarks for the updated identifiers.

NOTHING has been lost and I stand by my work as making things better and more discoverable.

KyndallH commented 1 year ago

UAM:Mamm is taking care of the 25 they have on the list.

Jegelewicz commented 1 year ago

@KyndallH you might want to check out the additional conversation at https://github.com/ArctosDB/arctos/issues/6356

If you want to take time to look up the ARK's you could make some nice links...

campmlc commented 1 year ago

I do not question that some of this is valuable, or that it isnt being done for a good reason. I am asking, yet again, for any changes to MSB records to wait until MSB personnel are available to evaluate. We are all getting ready for a massive field season, and no one is available to look at what is being done or proposed.

campmlc commented 1 year ago

@mkoo

cjconroy commented 1 year ago

MVZ mammals has only one record related to this. I pulled the catalog card. It is a tissue sample-only that came to us via the NIH. However, the card reads that it originated with the National Zoological Park, #39700. I changed this other id to an other ID issued by the Smithsonian National Zoological Park and deleted the USNM reference.

Does this seem appropriate since we know it is from the zoo?

That agent is also used by MSB, DMNS:Mamm, UWBM:Mamm and UWZM:Bird in different ways.

Jegelewicz commented 1 year ago

@cjconroy that is the power of the issued by agent - The National Zoo can be a collector, determiner of many things and can issue identifiers for stuff! I think what you did makes perfect sense.

dustymc commented 1 year ago

Yes agreed - it's overwhelmingly obvious that the old types are being overloaded, and much (all??) of what they hold isn't what seems to be the general expectation, catalog numbers (that aren't attributed to collections for some reason...). There's no possible way we could have managed that under the old system, but it's trivial under the new.

with Project issuing an identifier or two isn't difficult to set up, isn't difficult to use, and I think isn't difficult to understand.

Or, skipping the cleanup and flopping the types to "institution" is exactly what's being said (however incorrectly...) now, it just brings the data into a system where they can be cleaned up.