NHMDenmark / DanSpecify

Important files regarding the Danish instance of the Specify database system for collections digitisation and management, plus placeholder for issue tracking. Guidelines, manuals and other kinds of documentations will be gathered on the wiki.
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updating fields in birds database #206

Open peterhosner opened 1 year ago

peterhosner commented 1 year ago

Some minor changes would improve and streamline the birds database, and also bring fields more in line with DarwinCore. If I could get Fedor or Zsuzsanna to assist me I would appreciate it!

Catalog numbers:

Alt Cat Number (or, collection codes?)

Currently, we use this field for any non-NHMD, non-Tilvaeksjounral number. However, some specimens have multiple numbers that fit this field. I would instead prefer to have fields for each of the previous number series:

Tilvaeksjournal – This is the oldest cataloging system, the data of accession to the museum followed by a unique sequential number, each specimen accessioned that data received a unique number. These are physically cataloged in the Tilvaeksjournal.

C.N. – This very old catalog system (to early 1900s) had a sequential number for each species. This system had the disadvantage that any taxonomic changes made it obsolete. These are physically cataloged in the old CN catalog book.

ZMUC AVES (Ny Kat) – This number series is one of the most common in our collection (mid 1900s–early 2000s), a 6-digit sequential number. This system was retired when the NHMD system began. These are physically catalogued in the

NHMD – Assigned automatically when catalogued in Specify.

Field number – This is individually variable, and recorded under the collector field

Biota – This is a tissue number, a sequential number from the old “Biota” tissue database. It is a 6 digit number starting at 100,000. Beginning in 2022 it has a “B” prefix (e.g. B-123456), but update older recordings to include a B-prefix to prevent confusion with Ny Kat

Aeg – This is from the old set of egg catalogs, contemporary with the “Ny Kat”

Løpp. – This is the number series for the large Løppenthen egg collection

Col Obj Attribute:

Sex – This field currently has compound information, sex and sex determination. These fields should be separated.

Age – Pullus should be updated to Pullus/chick. “Hatchling” records should be shifted to Pullus and deleted.

Weight – Change to mass

Molt, bill color, leg color, feet color, and iris color should allow addition of descriptors

Add field “mouth lining” (string)

Add field “Bursa” (string)

Add field “fat” (categories, no, light, medium, heavy)

Add field “habitat” (string)

Change “Wing length” to “Wing chord” (float)

Add field “Culmen” (float)

Add field “Hand-wing Index” (float)

Add field “Hallux length” (float)

Collecting Information

Method – add “shot”, “salvaged”

Other:

Also: change default to “publish”

Change date to DD/MM/YYYY

Add tissue degradation score

Sosannah commented 1 year ago

Adding alternative catalog numbers

Updating existing records to have the different catalogue numbers

Col Obj Attribute: - the preferred order is coming soon

Collecting Information

Other:

Sosannah commented 1 year ago

Here is an order for the Col Obj Attributes.

Cheers, -Pete

Bill color Mouth lining color Leg color Feet color Iris color Ring number Habitat Mass

Molt Fat Stomach contents (double width)

Sex Sex determination Gonads (double width)

Bursa Skull ossification Age

Culmen Bill length Bill width Bill height

Wing chord Hand-wing Index Tail length Tarsus length

Middle toe length Hallux length

Other

Sosannah commented 1 year ago

Further discussion on alternative catalog numbers:

I proposed a different approach with the different cataloging systems in the Ornithology collection.

The original idea was to create new fields for each alternative cataloging systems: • Tilvaeksjournal, • C.N., • ZMUC AVES, • Field number, • Biota, • Aeg, • Løpp

Data entry form was modified in line with this, but I haven’t updated the existing records yet.

several_cat_numbers

Before the update I’d like to consider the Other Identifiers concept.

Sosannah commented 1 year ago

Comments from Ornithology collection:

This is an interesting option, thanks for bringing it to our attention. The flexibility is useful.

Are there other optional fields? For us, the vast majority of the numbers are our own institution, making this field less useful. Maybe if we had Prefix (e.g., TVJ, ZMUC, Aeg, C.N.), then identifier (the number), then institution? /Pete/

Thanks for showing the possibility! I think this is a good solution. The cataloging would be faster and the “data entry mask” would be cleaner, without many rows. /Gloria/

If we decide to go ahead with this solution, would we do series of batch changes to manage the data already in Specify? /Pete/

Sosannah commented 1 year ago

Implementing batch changes would be necessary, but I would happen directly in the SQL database.

The field in Other Identifiers table can be customized. The suggested structure would look like this, but there's plenty of room to play around (https://files.specifysoftware.org/schema/version/2.10/#otheridentifier):

image

Currently it is available only in the test database waiting for approval.

peterhosner commented 1 year ago

Hi Zsusanna,

I’ve gone through the database and found all the different ways that the “alt cat number” and “alt cat number prefix” have been used in the past. With this update, we can also fix those records that were not entered in a standardized way.

Cheers, -Pete


Peter A. Hosner Assistant Professor Curator of Birds Curator of Cryo-collections Natural History Museum of Denmark Center for Global Mountain Biodiversity Center for Macroecology, Evolution, and Climate Globe Institute University of Copenhagen Universitetsparken 15, 465 DK-2100 Copenhagen Denmark

TEL: +45 52753248 Email: @.**@.> Twitter: @peter_hosner

From: ZsuzsannaPapp @.> Reply-To: NHMDenmark/DanSpecify @.> Date: Thursday, June 22, 2023 at 2:31 PM To: NHMDenmark/DanSpecify @.> Cc: Peter Andrew Hosner @.>, Author @.***> Subject: Re: [NHMDenmark/DanSpecify] updating fields in birds database (Issue #206)

Implementing batch changes would be necessary, but I would happen directly in the SQL database.

The field in Other Identifiers table can be customized. The suggested structure would look like this, but there's plenty of room to play around (https://files.specifysoftware.org/schema/version/2.10/#otheridentifierhttps://files.specifysoftware.org/schema/version/2.10/#otheridentifier):

[Image removed by sender. other_identifiers]https://user-images.githubusercontent.com/70754439/247930533-f56dc971-043a-4dce-87ad-6262407ce2a3.jpg

Currently it is available only in the test database waiting for approval.

— Reply to this email directly, view it on GitHubhttps://github.com/NHMDenmark/DanSpecify/issues/206#issuecomment-1602555526, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ3LP2GUHDY2SVWV3ZKEVEDXMQ3LNANCNFSM6AAAAAATOY7SSQ. You are receiving this because you authored the thread.Message ID: @.***>

Sosannah commented 1 year ago

That's great! Let's sort that out when we are all back from field work/holiday.