copy barcodes of UAM:Ento to other id

[DerekSikes]

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Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

A few years back I had Dusty copy all the UAM:Ento specimen part barcodes to the 'other ID' field so these would be publicly visible. The reason for this was to allow those with loans of specimens to use Arctos to find data on the specimens they had borrowed. Because barcodes on specimens are not publicly shared this was a problem and this was a solution to that problem.

However, a new related problem has arisen. GBIF, iDigBio, and all the data aggregators can act as a form of data-backup in cases of a crash & data loss. However, they don't have the barcodes of the specimens since these are not publicly shared. They DO have the other IDs, however. Thus, if one ever wants to use GBIF data to restore lost data it would be best if GBIF also had the part barcodes with each record.

** Describe what you're trying to accomplish**
An clear and concise overview of the goals; why are you asking for this?

The past effort was a one-time script that copied part barcodes to the other id field. This was good but immediately became 'old' in that as new records were created they did not have barcodes copied into the other id field. Also, on rare occasions a specimen with a barcode value in the other ID field would get a new barcode leading to these two fields disagreeing. This can also happen from cloning records if the user forgets or doesn't know to edit the other ID field appropriately.

Thus, a better solution would be to have a script that UAM:Ento admin can run (or set to run on a schedule) that does the following:

1. copies all part barcodes to the other ID field if needed (if there isn't already a matching barcode in the other id field)
2. checks to see if barcodes in the other ID field match to those in the parts and if not, replaces them so they match.

Describe the solution you'd like
How might we accomplish your goals?

If this were a script that could be scheduled to run weekly that would be great.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Alternatively, can some collections choose to share their part & barcode data with GBIF et al. (are there even DWC fields to map to?) if so, this would be an easier solution - just let whomever chooses share these data publicly.

Personally, I'd feel a lot safer if all my collection's part barcode & other data were shared in all the aggregators so if Arctos vanishes or suffers some horrible crash I don't end up with 400k+ records with no barcode data!!

Additional context
Add any other context or screenshots about the feature request here.

Priority
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immensely high

[Jegelewicz]

Alternatively, can some collections choose to share their part & barcode data with GBIF et al. (are there even DWC fields to map to?) if so, this would be an easier solution - just let whomever chooses share these data publicly.

This seems like the better option. Maybe the barcode could be built into the material sample ID?

[campmlc]

I agree absolutely with this issue as I've just lost a month of barcodes and object tracking. Whatever method works most effectively.

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On Thu, May 14, 2020, 1:23 PM Teresa Mayfield-Meyer < ***@***.***> wrote: * [EXTERNAL]* Alternatively, can some collections choose to share their part & barcode data with GBIF et al. (are there even DWC fields to map to?) if so, this would be an easier solution - just let whomever chooses share these data publicly. This seems like the better option. Maybe the barcode could be built into the material sample ID <https://dwc.tdwg.org/terms/#dwc:materialSampleID>? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2685 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADQ7JBGGL2OOXEBDTKXS3ATRRRAMTANCNFSM4NA42DTA> .

[dustymc]

on rare occasions a specimen with a barcode value in the other ID field would get a new barcode leading to these two fields disagreeing.

This seems like a very good thing to me - it's the only approach that can serve the stated objective of using barcodes to persistently identify records (rather than just find parts from current data). I suggest this should be additive, not a replacement.

are there even DWC fields to map to

There could be (but "fields" not actual fields) - ArctosDB/documentation-wiki#258

material sample ID

Seems more correct, I can map that, I'll probably need guidance, I'm not sure if GBIF accepts it or not.

Anything involving site-wide exposure of barcodes requires discussion - I think some collections see barcodes as "private."

I think the realistic immediate approach is a barcode-->otherID script that runs for a hard-coded list of collections.

Whatever method works most effectively.

@campmlc I think that's your call. Most insects have a single barcoded part, so having the value somewhere in the Occurrence is almost as good as anything else that could happen. Having 30 barcode values mixed in with the 30 non-barcode values in https://dwc.tdwg.org/terms/#dwc:otherCatalogNumbers, and 30 not-obviously-related parts in https://dwc.tdwg.org/terms/#dwc:preparations, is a different situation.

immensely high

I am incredibly hesitant to do anything that might stress Oracle, and this would. That is hopefully 100% paranoia. Please advise, @ArctosDB/arctos-working-group-officers.

[Jegelewicz]

I'm not sure if GBIF accepts it or not.

Even if they don't, the DwC file will be at VertNet as a backup, No?

Anything involving site-wide exposure of barcodes requires discussion - I think some collections see barcodes as "private."

If they are embedded in a larger identifier, I think we can get everyone on board.

barcode-->otherID
Holy crap, some MSB records will end up with 10 or more of these....plus, what @dusty said.

As with pretty much everything right now - I think this needs to wait a few weeks until PG migration.

[dustymc]

DwC file will be at VertNet

I believe that's correct; I think they version.

MSB records will end up with 10 or more

http://test.arctos.database.museum/guid/MSB:Mamm:292039 has 42

[campmlc]

Can they be a specific kind of other ID that can be displayed separately in UI, like relationships?

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On Thu, May 14, 2020, 4:23 PM dustymc ***@***.***> wrote: * [EXTERNAL]* DwC file will be at VertNet I believe that's correct; I think they version. MSB records will end up with 10 or more http://test.arctos.database.museum/guid/MSB:Mamm:292039 has 42 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2685 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADQ7JBAMKCRQZ5CA7BFWDQLRRRVNFANCNFSM4NA42DTA> .

[dustymc]

specific kind of other ID

Yes but no?

displayed separately

That sounds incredibly confusing.

[dustymc]

This is now possible via search-->part/table-->download-->otherID loader - is some other action necessary?

[Jegelewicz]

Candidate for a workflow as discussed in Object tracking today?

[campmlc]

This relates to idea of Other ID metadata and linking of Other IDs to parts and events for e.g. GenBank sequences derived from loaned parts. Ideally we could associate Other ID barcodes with their respective parts and solve the problem of the 42 barcodes (isn't that the answer to life, the universe, and everything?)

[Jegelewicz]

I was about to close this, but I am thinking that the "barcode" identifier should actually be a part attribute? This was not a thing when we were discussing this before, but it would eliminate the issue of

MSB records will end up with 10 or more

http://test.arctos.database.museum/guid/MSB:Mamm:292039 has 42

thoughts? @DerekSikes @campmlc

[DerekSikes]

I don't understand, sorry.

…

-D

On Fri, May 13, 2022 at 2:06 PM Teresa Mayfield-Meyer < ***@***.***> wrote: I was about to close this, but I am thinking that the "barcode" identifier should actually be a part attribute? This was not a thing when we were discussing this before, but it would eliminate the issue of MSB records will end up with 10 or more http://test.arctos.database.museum/guid/MSB:Mamm:292039 has 42 thoughts? @DerekSikes <https://github.com/DerekSikes> @campmlc <https://github.com/campmlc> — Reply to this email directly, view it on GitHub <#2685 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFNUMYGMRZ4PH3WSOQC2ELVJ3G5TANCNFSM4NA42DTA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- +++++++++++++++++++++++++++++++++++ *Derek S. Sikes*, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 ***@***.*** phone: 907-474-6278 he/him/his University of Alaska Museum <https://www.uaf.edu/museum/collections/ento/> - search 357,704 digitized arthropod records <http://arctos.database.museum/uam_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

[Jegelewicz]

@DerekSikes the original request was to add the barcode attribute to your records (great when you only have one part), but now we have part attributes and I was wondering if this would be a better part attribute so that records with 20 parts can match their barcodes with the appropriate part.

[DerekSikes]

Ah, I see. The reason for adding barcodes to the attributes was to make them publicly available so users who borrow specimens with barcodes on them can search for them & see them etc. Will your new solution allow this?

…

-Derek

On Fri, May 13, 2022 at 2:15 PM Teresa Mayfield-Meyer < ***@***.***> wrote: @DerekSikes <https://github.com/DerekSikes> the original request was to add the barcode attribute to your records (great when you only have one part), but now we have part attributes and I was wondering if this would be a better part attribute so that records with 20 parts can match their barcodes with the appropriate part. — Reply to this email directly, view it on GitHub <#2685 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFNUM7UDFNLNJCUROA23GLVJ3H6VANCNFSM4NA42DTA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- +++++++++++++++++++++++++++++++++++ *Derek S. Sikes*, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 ***@***.*** phone: 907-474-6278 he/him/his University of Alaska Museum <https://www.uaf.edu/museum/collections/ento/> - search 357,704 digitized arthropod records <http://arctos.database.museum/uam_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

[Jegelewicz]

Will your new solution allow this?

Yep! It would be right here along with preservation

[DerekSikes]

Then that sounds good. Will people (the public without accounts) be able to search for these barcodes using our search form?

…

-Derek

On Fri, May 13, 2022 at 3:00 PM Teresa Mayfield-Meyer < ***@***.***> wrote: Will your new solution allow this? Yep! It would be right here along with preservation [image: image] <https://user-images.githubusercontent.com/5725767/168399455-c8582b8a-1b13-4ea4-b2f0-34a7a6f4ca27.png> — Reply to this email directly, view it on GitHub <#2685 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFNUM4IH47RSI7CVPBWWXLVJ3NKDANCNFSM4NA42DTA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- +++++++++++++++++++++++++++++++++++ *Derek S. Sikes*, Curator of Insects, Professor of Entomology University of Alaska Museum (UAM), University of Alaska Fairbanks 1962 Yukon Drive, Fairbanks, AK 99775-6960 ***@***.*** phone: 907-474-6278 he/him/his University of Alaska Museum <https://www.uaf.edu/museum/collections/ento/> - search 357,704 digitized arthropod records <http://arctos.database.museum/uam_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

[dustymc]

Yep, the "curatorial" search pane was made public a while back, anyone can search by barcode.

Persistent part identifiers is #3630

Tentatively closing.

[Jegelewicz]

Nope - barcodes are not visible to public users

So, should they be? Should we move the "barcode" attribute to be a part attribute? Or is everyone just happy with the way things are?

[campmlc]

Barcodes as part attributes make sense. That is public info. Might not be where most people would look. For Derek, he can also just use the ID for a single barcode.
Maybe we need GenBank IDs as part attributes too.