gonad #7504

dustymc · 2024-03-08T14:45:10Z

2024-03-07 AWG meeting https://docs.google.com/document/d/12NEMEwuQEMgjvdymggJNrp68RNroZdfrRm1tJZaS9Y0/edit
- unanimous decision to merge on fewer attributes, more use of metadata
2024-08-05 AWG meeting https://docs.google.com/document/d/1WvDYixTFZU9ZIFREwF5t605cywxkkQWOW42FfgOV8I8/edit#heading=h.q3pk226foene

Cleanup

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#gonad

gonad needs cleaned up, very few records, easy if we act before it gets used more

 guid_prefix | count 
-------------+-------
 MLZ:Bird    |     1
 ANSP:Host   |  1625

(no contacts available)

Please note that this has about 1624 more records than it did when we started this, if values The Community does not want to support are in the tables they WILL be used, if we are going to do something let's do it now.

Suggest we move this to reproductive data if we are to remove this term.

#6189

right gonad width (already misconfigured, nonsense data cannot be trusted) needs migration - suggest we move this to reproductive data, including a note about the conflict between the definition and term, if we plan to remove this term.

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#right_gonad_width


 guid_prefix | count 
-------------+-------
 UMNH:Mamm   |     1
 BYU:Bird    |   465
 UCSC:Mamm   |     1
 MVZ:Mamm    |    22
 UNR:Mamm    |     1
 MMNH:Bird   |    18
 MMNH:Mamm   |     1
 MVZ:Herp    |    40
 HSUVM:Mamm  |     6
 KSB:Mamm    |     1
 UAM:Mamm    |     1
 UMZM:Bird   |    22
 UMNH:Bird   |     8
 OWU:Bird    |     7
 MLZ:Bird    |     9
 UMZM:Mamm   |    23
 UCM:Bird    |    47

@amgunderson
@adhornsby
@mkoo
@cjconroy
@atrox10
@ebraker
@kderieg322079
@asemerdj
@jrpletch
@byuherpetology

right gonad length [ link ]


 guid_prefix | count 
-------------+-------
 UMNH:Mamm   |     2
 BYU:Bird    |   465
 UCSC:Mamm   |     1
 MVZ:Mamm    |    22
 UNR:Mamm    |     1
 MMNH:Bird   |    18
 UTEP:Bird   |     1
 MMNH:Mamm   |     1
 MVZ:Herp    |   177
 HSUVM:Mamm  |     6
 UAM:Mamm    |     1
 UMZM:Bird   |    22
 UMNH:Bird   |     5
 UWBM:Mamm   |    85
 OWU:Bird    |     7
 MLZ:Bird    |     9
 UMZM:Mamm   |    23
 UCM:Bird    |    47

@amgunderson
@adhornsby
@mkoo
@cjconroy
@atrox10
@jebrad
@mvzhuang
@ebraker
@kderieg322079
@asemerdj
@jrpletch
@byuherpetology

left gonad length [ link ]


 guid_prefix | count 
-------------+-------
 UNR:Mamm    |     2
 MMNH:Bird   |    37
 MVZ:Herp    |   153
 HSUVM:Mamm  |     6
 APSU:Bird   |   112
 MLZ:Bird    |   217
 UMZM:Mamm   |    21
 UCM:Bird    |    50
 UMNH:Mamm   |     1
 UCSC:Mamm   |     4
 UTEP:Bird   |     2
 KSB:Mamm    |   308
 UMZM:Bird   |    44
 UMNH:Bird   |    10
 MSB:Mamm    |     2
 UWBM:Mamm   |   111
 OWU:Bird    |     5
 BYU:Bird    |   510

@ebraker
@byuherpetology
@mkoo
@campmlc
@kderieg322079
@atrox10
@mvzhuang
@asemerdj
@adhornsby
@jebrad
@gradyjt
@jrpletch
@AdrienneRaniszewski
@jldunnum

left gonad width [ link ]

 guid_prefix | count 
-------------+-------
 UNR:Mamm    |     2
 MMNH:Bird   |    37
 MVZ:Herp    |    62
 HSUVM:Mamm  |     6
 APSU:Bird   |   112
 MLZ:Bird    |   218
 UMZM:Mamm   |    21
 UCM:Bird    |    49
 UMNH:Mamm   |     1
 UCSC:Mamm   |     4
 UTEP:Bird   |     1
 KSB:Mamm    |   303
 UMZM:Bird   |    44
 UMNH:Bird   |     7
 OWU:Bird    |     4
 BYU:Bird    |   510

@ebraker
@byuherpetology
@mkoo
@kderieg322079
@atrox10
@mvzhuang
@asemerdj
@adhornsby
@gradyjt
@jrpletch

Done

#7503

gonad weight - already there, updated definition

added
https://github.com/ArctosDB/code-table-work/issues/63

New gonad width attribute, needs approved and implemented

added

https://github.com/ArctosDB/code-table-work/issues/14

New gonad length attribute, needs approved and implemented

20240906 still no action

The text was updated successfully, but these errors were encountered:

Jegelewicz · 2024-03-21T22:28:10Z

Email to AWG today:

Arctos Working Group Member,

In an effort to increase discoverability of data and keep the Arctos Code Tables efficient, changes will soon be made to catalog record attributes related to gonads.

For a summary of the issues and effort, please see #7504

When this process is completed, there will be three gonad attributes:

gonad length - Measurement of the long axis of the gonad (which may be testes or ovary and can be indicated in Remarks or by implication of attribute of sex). Left or right side gonad should be indicated in the Methods.

gonad width - Measurement of the short axis of the gonad (which may be testes or ovary and can be indicated in Remarks or by implication of attribute of sex). Left or right side gonad should be indicated in the Methods.

gonad weight - Weight measurement of the gonad (which may be testes or ovary and can be indicated in Remarks or by implication of attribute of sex). Left or right side gonad should be indicated in the Methods.

The following terms will be removed from the catalog record attribute code table and the values currently there will be migrated as detailed.

right gonad width - will become gonad width with right placed in the attribute method.

right gonad length - will become gonad length with right placed in the attribute method.

left gonad width - will become gonad width with left placed in the attribute method.

left gonad length - will become gonad length with right placed in the attribute method.

If you have concerns about your data, please comment on the various issues. Migration to the new terms will take place on April 11, 2024. If you want to handle your data on your own, this allows time for that, or you may request assistance in any of the issues.

Thank you!

Teresa J. Mayfield-Meyer

dustymc · 2024-08-27T17:55:48Z

I'm adding to AWG agenda; we're 6 months into what seems like it should have been a half-day problem, suggest we convert all involved data to https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#reproductive_data and drop the individual attributes if a better and actionable solution cannot be identified.

campmlc · 2024-08-27T17:59:22Z

These data are being converted out of https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#reproductive_data as part of the grant funded Ranges project. These stakeholders need to be involved.
@jldunnum @bryansmclean @mkoo

dustymc · 2024-08-27T18:02:49Z

need to be involved

PLEASE! I believe all issues are linked above, proceeding with the initial plan is still perfectly fine with me and I'm happy to do whatever I can to facilitate that. Getting stuck in the middle where nobody can understand the increasingly-scattered data (where we are now) should not be an acceptable position for anyone. HELP!

bryansmclean · 2024-08-27T19:30:04Z

I would love to help sort this out and finalize the consensus decision.

AWG @ Thursday, September 5, 2024?

jldunnum · 2024-08-27T19:42:30Z

I'll be traveling on the 5th so can't attend. Frankly don't even remember where we left off, I know some of the trait attributes were incorporated but maybe not all????

…

______________________________________________________________ Jonathan L. Dunnum Ph.D. (he, him, his) Senior Collection Manager Division of Mammals, Museum of Southwestern Biology Research Assistant Professor (LAT) Department of Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351 Chair, Systematic Collections Committee, American Society of Mammalogists Latin American Fellowship Committee, ASM 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: bryansmclean ***@***.***> Sent: Tuesday, August 27, 2024 1:30 PM To: ArctosDB/arctos ***@***.***> Cc: Jonathan Dunnum ***@***.***>; Mention ***@***.***> Subject: Re: [ArctosDB/arctos] gonad (Issue ArctosDB/arctos#7504) [EXTERNAL] I would love to help sort this out and finalize the consensus decision. AWG @ Thursday, September 5, 2024? — Reply to this email directly, view it on GitHub<#7504 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AED2PA2R7AHA4JESOV6OVQLZTTHVFAVCNFSM6AAAAABEM52VW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJTGM2TAMJZGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

campmlc · 2024-08-28T15:13:01Z

@bryansmclean @jldunnum can you suggest a meeting time for when you are both available to discuss? I think it would be good to go over this outside of the AWG to review what has been done so far and what is still needed. @mkoo

bryansmclean · 2024-08-28T15:16:04Z

This Friday (30 Aug) from 11-1 ET
anytime next Monday (2 Sept) or Wed (4 Sept)

dustymc · 2024-08-28T15:16:55Z

consensus

As far as I know that is done and does not need more. The first comment outlines what is needed - the addition of one attribute, and ~5 cleanup issues.

bryansmclean · 2024-08-28T15:31:19Z

consensus

As far as I know that is done and does not need more. The first comment outlines what is needed - the addition of one attribute, and ~5 cleanup issues.

I am not seeing discussion or documentation of a consensus on other related proposed repro attributes

I agree that it would be great to finalize but my memory of how we decided to do that is now hazy

dustymc · 2024-08-28T15:40:03Z

discussion

Link to AWG notes in first comment.

That said: I wholeheartedly agree, we need a mechanism to finish to the things we start on a timeline. The Community has made a decision, there's a clear path to implementation, hanging out for months while the data get worse and more confusing at that point should not happen. I'm always happy to update, just need a little direction and support.

bryansmclean · 2024-08-28T20:18:33Z

We will prepare to discuss this on 5 Sept @ AWG if that sounds good to all. I think a short recap of the community consensus makes sense at that mtg. Please let me know if this doesn't work

dustymc · 2024-09-06T14:27:04Z

rediscussed 20240905 AWG meeting, I don't know if progress was made or not - @bryansmclean ??

I'm going to consolidate some things here, I can't keep up with the scattered issues, maybe I'm not alone...

dustymc · 2024-09-06T14:44:54Z

This just keeps getting more messy, and has now become disruptive to incoming collections. Can we find some quick conclusion and implement that, please? @bryansmclean @mkoo help!

FWIW all of this still looks a lot like https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type#reproductive_data to me, and several collections have cleaned up parts of this in that direction.

bryansmclean · 2024-09-06T14:50:11Z

I think that our consensus was to move left and right gonad lengths and widths to the "gonad length" and "gonad width" fields

The one pre-requisite is to create a controlled vocabulary for methods with all possible positions (left, right, left and right combined, side unknown)

bryansmclean · 2024-09-06T14:51:48Z

The one pre-requisite is to create a controlled vocabulary for methods with all possible positions (left, right, left and right combined, side unknown)

FWIW, Creating this structural change will benefit pending requests for future mammal traits since placental scars, embryo counts, etc all require position statements

Should I log a new issue for that?

dustymc · 2024-09-06T15:05:03Z

pre-requisite is to create a controlled vocabulary for methods

That would be some model other than the one we have, please comment here: #6742

EDIT: Even if someone has a clear vision for a model which will solve all of our attribute woes (I do not!), I don't think we should wait for it to be developed and implemented. This is clearly and demonstrably causing problems for incoming collections, that is in my view WAY more evil than eg tossing these data into reproductive data for safe keeping while we decide on a better path.

campmlc · 2024-09-06T15:21:53Z

We have a consensus on what to do here: follow the March 21 recommendations above. All the ANSP data recently loaded by @Jegelewicz ( and more of the same in the attribute component loader that I have control over) need to be converted to gonad length and gonad width attributes as soon as they exist,which should be immediately.
@bryansmclean and others in the issues meeting yesterday discussed a code table for positions, eg left, right, left and right, unknown etc, that could be used for methods for these types of dimensional attributes. There was general support for this. It needs a new issue. As that may take some time to discuss, in the meantime, these positional values should go in methods as free text.
I recommend making the above changes immediately and getting rid of the gonad attribute.

bryansmclean · 2024-09-06T15:23:45Z

getting rid of the gonad attribute

I agree with this as well. Any other gonad attributes besides measurements are good for free text in the reproductive data field.

dustymc · 2024-09-06T15:31:52Z

converted to gonad length and gonad width attributes

If you're volunteering, here are the data:

temp_gonad.csv.zip

dustymc · 2024-09-06T15:36:05Z

as soon as they exist,

Done, I'm not letting that impede any momentum here.

dustymc · 2024-09-06T15:38:31Z

@campmlc or anyone else: if you need any other data, please let me know. There are now eg 3 'gonad length' attributes, that should not exist any longer than absolutely necessary. I'll plan to move whatever's left of the things that shouldn't exist to repro data in ~a week.

campmlc · 2024-09-06T15:48:12Z

Gonad length and gonad width should exist, correct? We don't want to get rid of them. We are trying to move all applicable data out of reproductive data as part of this process.
I will convert all ANSP data including what is pending in the loaders to gonad length and gonad width.
Ah, I understand your comment. Yes, agree.

jrpletch · 2024-09-06T22:46:56Z

OWU's should be all fixed

campmlc · 2024-09-06T22:52:10Z

ANSP gonads are deleted; converted gonad length and width attributes loading now

campmlc · 2024-09-10T14:05:36Z

all ANSP should be fixed.

bryansmclean · 2024-09-10T15:00:58Z

gonads are deleted

If someone outside Arctos knew the kinds of things that were going on here...

dustymc · 2024-10-03T18:16:47Z

AWG issues meeting - this is all approved and can be migrated, DLM will figure it out and leave any data that changes. Try to get the bulkloader too.

dustymc · 2024-10-03T18:18:14Z

TODO: Check documentation, some confusion over method vs. remarks for left/right/etc. (Consensus on method, I think.)

dustymc · 2024-10-03T20:12:22Z

gonad was used one time for https://arctos.database.museum/guid/MLZ:Bird:69262, manually updated

dustymc · 2024-10-03T20:25:01Z

right gonad width

EDIT: I'm going with @adhornsby 's plan from #7504 (comment) - probably most people guess definitions from terms, the remarks should make everything clear, and my original plan would lose datatype and make recovery more difficult. Moving on to reproductive data from here will be easy if anyone wants to do so, just let me know.

Note that this is defined as "Length measurement of the left gonad." and I'm very hesitant to do anything more precise than what's proposed below from a 3-way mess.

Data:

temp_rgw.csv.zip

Summary:


 guid_prefix | count 
-------------+-------
 UMNH:Mamm   |     1
 BYU:Bird    |   465
 UCSC:Mamm   |     1
 MVZ:Mamm    |    22
 UNR:Mamm    |     1
 MMNH:Bird   |    18
 MMNH:Mamm   |     1
 MVZ:Herp    |    40
 HSUVM:Mamm  |     7
 KSB:Mamm    |     1
 UAM:Mamm    |     1
 UMZM:Bird   |    22
 UMNH:Bird   |     8
 MLZ:Bird    |     9
 UMZM:Mamm   |    23
 UCM:Bird    |    47

Users:

@amgunderson
@adhornsby
@mkoo
@cjconroy
@atrox10
@ebraker
@kderieg322079
@asemerdj
@byuherpetology

I will plan to move this to reproductive data [ link ] with "Formerly right gonad width, which was defined as Length measurement of the left gonad." appended to remark unless someone shows up with a better plan before ~early next week.

dustymc · 2024-10-03T20:27:50Z

right gonad length

Data:

temp_rgl.csv.zip

Summary:


 guid_prefix | count 
-------------+-------
 UMNH:Mamm   |     2
 BYU:Bird    |   465
 UCSC:Mamm   |     1
 MVZ:Mamm    |    22
 UNR:Mamm    |     1
 MMNH:Bird   |    18
 UTEP:Bird   |     1
 MMNH:Mamm   |     1
 MVZ:Herp    |   177
 HSUVM:Mamm  |     7
 UAM:Mamm    |     1
 UMZM:Bird   |    22
 UMNH:Bird   |     5
 UWBM:Mamm   |    85
 MLZ:Bird    |     9
 UMZM:Mamm   |    23
 UCM:Bird    |    47

contact

@amgunderson
@adhornsby
@mkoo
@cjconroy
@atrox10
@jebrad
@mvzhuang
@ebraker
@kderieg322079
@asemerdj
@byuherpetology

I'll update to gonad length [ link ] and append 'right gonad length' to method unless someone shows up with a better plan before ~early next week.

dustymc · 2024-10-03T20:29:40Z

left gonad length

data

temp_lgl.csv.zip

summary

 guid_prefix | count 
-------------+-------
 UNR:Mamm    |     2
 MMNH:Bird   |    37
 MVZ:Herp    |   153
 HSUVM:Mamm  |     7
 APSU:Bird   |   112
 MLZ:Bird    |   217
 UMZM:Mamm   |    21
 UCM:Bird    |    50
 UMNH:Mamm   |     1
 UCSC:Mamm   |     4
 UTEP:Bird   |     2
 KSB:Mamm    |   308
 UMZM:Bird   |    44
 UMNH:Bird   |    10
 MSB:Mamm    |     2
 UWBM:Mamm   |   111
 OWU:Bird    |     1
 BYU:Bird    |   510

users

@ebraker
@byuherpetology
@mkoo
@campmlc
@kderieg322079
@atrox10
@mvzhuang
@asemerdj
@adhornsby
@jebrad
@gradyjt
@jrpletch
@AdrienneRaniszewski
@jldunnum

I'll update to gonad length [ link ] and append 'left gonad length' to method unless someone shows up with a better plan before ~early next week.

dustymc · 2024-10-03T20:30:50Z

left gonad width

data

temp_lgw.csv.zip

summary


 guid_prefix | count 
-------------+-------
 UNR:Mamm    |     2
 MMNH:Bird   |    37
 MVZ:Herp    |    62
 HSUVM:Mamm  |     7
 APSU:Bird   |   112
 MLZ:Bird    |   218
 UMZM:Mamm   |    21
 UCM:Bird    |    49
 UMNH:Mamm   |     1
 UCSC:Mamm   |     4
 UTEP:Bird   |     1
 KSB:Mamm    |   303
 UMZM:Bird   |    44
 UMNH:Bird   |     7
 BYU:Bird    |   510

users

@ebraker
@byuherpetology
@mkoo
@kderieg322079
@atrox10
@mvzhuang
@asemerdj
@adhornsby
@gradyjt

I'll update to gonad width [ link ] and append 'left gonad width' to method unless someone shows up with a better plan before ~early next week.

adhornsby · 2024-10-07T04:46:58Z

For all MMNH & UMZM:
Instead of having 'right gonad width' sent to reproductive data, can I have it handled like the other traits -- i.e. updated to 'gonad width' with method 'right gonad width.' I know we were using that trait at face value, so the old mismatched definition in the table doesn't bother me.

MMNH & UMZM are otherwise good to be updated as planned.

dustymc · 2024-10-07T15:04:45Z

@adhornsby sure and thanks!

@amgunderson
@mkoo
@cjconroy
@atrox10
@ebraker
@kderieg322079
@asemerdj
@byuherpetology

would you like to make any adjustments to #7504 (comment)?

cjconroy · 2024-10-07T16:30:03Z

Fine with MVZ mammals. I added this info to reproductive data, so there would be something like verbatim data as well.

dustymc · 2024-10-09T15:56:09Z

Final data stash:

temp_rgw(1).csv.zip
temp_rgl(1).csv.zip
temp_lgl(1).csv.zip
temp_lgw(1).csv.zip

dustymc added this to the Active Development milestone Mar 8, 2024

bryansmclean mentioned this issue Mar 25, 2024

reproductive category #7364

Closed

dustymc modified the milestones: Active Development, Clean / Migrate Apr 9, 2024

dustymc modified the milestones: Clean / Migrate, Next AWG Meeting Aug 27, 2024

This was referenced Sep 6, 2024

Code Table Cleanup - Record Attribute = gonad #4774

Closed

Code Table Request - right gonad width #6189

Closed

migration: right gonad length #7506

Closed

migration: left gonad length #7509

Closed

migration: left gonad width #7508

Closed

dustymc modified the milestones: Next AWG Meeting, Active Development Oct 3, 2024

dustymc closed this as completed Oct 9, 2024

gonad #7504

gonad #7504

Comments

dustymc commented Mar 8, 2024 • edited Loading

Cleanup

Done

Jegelewicz commented Mar 21, 2024

dustymc commented Aug 27, 2024

campmlc commented Aug 27, 2024

dustymc commented Aug 27, 2024

bryansmclean commented Aug 27, 2024

jldunnum commented Aug 27, 2024 via email

campmlc commented Aug 28, 2024

bryansmclean commented Aug 28, 2024

dustymc commented Aug 28, 2024

bryansmclean commented Aug 28, 2024

dustymc commented Aug 28, 2024

bryansmclean commented Aug 28, 2024 • edited Loading

dustymc commented Sep 6, 2024

dustymc commented Sep 6, 2024

bryansmclean commented Sep 6, 2024

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campmlc commented Sep 6, 2024 • edited Loading

jrpletch commented Sep 6, 2024

campmlc commented Sep 6, 2024

campmlc commented Sep 10, 2024

bryansmclean commented Sep 10, 2024

dustymc commented Oct 3, 2024

dustymc commented Oct 3, 2024

dustymc commented Oct 3, 2024

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adhornsby commented Oct 7, 2024

dustymc commented Oct 7, 2024

cjconroy commented Oct 7, 2024

dustymc commented Oct 9, 2024

dustymc commented Mar 8, 2024 •

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