Code Table Request - New Catalog Record Attribute: cause of death

[Jegelewicz]

Initial Request

See discussion in https://github.com/ArctosDB/data-migration/issues/889#issuecomment-1503495144 (including the initial request in comments in the same issue).

there are attributes for our deer collection that we would like to record but that I don't see; namely cause of death,

cause of death - this has traditionally ended up in collecting event remark (a lot of herpetological records include "DOR" or "dead on road"). Would you want a list of choices to select from or just a free text description?

we are needing to categorize hunter harvest, dead on road, euthanized, disease, vehicle, depredation, and predation as causes of mortality.

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

cause of death

• record attribute mortality cause
• code table ctmortality_cause WITHOUT collection-specific filtering

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

The method by which the cataloged organism died.

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

If I have missed that we are somehow recording this consistently elsewhere, please let me know. The code table ctkill_method exists, but I cannot figure out where/how it is being used.

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.

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

with categorical values in a new code table - ctcause_of_death (or can/should we use the table above?)

hunter harvest - Killed by humans for food or to control a population. euthanized - Humanely put to death. disease – Death caused by disease condition. vehicle – Killed by a motor vehicle. depredation – Killed by humans to mitigate damage to crops, landscaping, or other property. predation – Killed by predator species.

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

Bird Herp Mamm Amph Rept Host Teach

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.

yes

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)._

• [x] Code Table Administrator[1] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval
• [x] Code Table Administrator[2] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval
• [x] DBA - The request is functionally acceptable. The term is not a functional duplicate, and is compatible with existing data and code.
• [ ] DBA - Appropriate code or handlers are in place as necessary. (ID_References, Media Relationships, Encumbrances, etc. require particular attention)

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.

@ArctosDB/arctos-code-table-administrators @hkevans

[cjconroy]

What about herps that are taken from the wild (collecting event) in a group, but are kept for possibly years before euthanasia on different dates? Seems like the cause and date of death should be independent of collecting event.

[Jegelewicz]

Yes, the case that @cjconroy brings up is what is getting to me. In reality, I think that collection and death often do not happen at exactly the same time (hunting, a trap that kills), more often, the death occurred at some undetermined time before collection (DOR) or at some known time after collection (removed from a trap, euthanized at camp or taken to the lab and euthanized there).

While I am in favor of a second full event to record those scenarios, I do not think the community is willing to do that. And so, a record attribute seems the best place to put this.

habitat, collecting_method and mortality_source need to be in the same place

I disagree because the mortality source may not have been AT the event. The habitat and method definitely should have been though and I think that is where those belong.

[campmlc]

I agree that the ideal way to deal with all this is through multiple collecting events, but that it isn't realistic to expect collections to add this level of complexity to workflows. Something else to consider: in addition to cause of death (which I strongly prefer to "source of mortality"; if we are worried about public perception let's make this encumberable), we also need time of death, and time of preservation (specifically, our institution needs something like "time of tissue archive") - as we are recording these data to track the time between death and when tissues are dropped in liquid nitrogen. Time of death can be a record attribute, but time of tissue archive, or some variant ("time between death and preservation"?), should probably be a part attribute? Different parts have different preservation times, but for our puposes, it is the tissues/genetic materials that need the time stamp or time metric, typically minutes to hours, to track RNA quality. Seems like whatever solution we use should be able to track all these variables. I'm in favor of record attribute for cause of death and date/time of death. The latter could be used to track difference in dates between collecting event and death event for captive or experimental animals, and provide a means to flag records for those collections that would like to add a second collecting event for these purposes.

[jldunnum]

Yes I will second Mariel's suggestions. Need to track time between death and freezing at the part level. Needs to be in a searchable field where we can do a search such as: find all Peromyscus maniculatus with lungs frozen within 15 minutes of death.

---

Jonathan L. Dunnum Ph.D. (he, him, his) Senior Collection Manager Division of Mammals, Museum of Southwestern 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: Mariel Campbell @.> Sent: Wednesday, August 9, 2023 11:06 AM To: ArctosDB/arctos @.> Cc: Jonathan Dunnum @.>; Team mention @.> Subject: Re: [ArctosDB/arctos] Code Table Request - New Catalog Record Attribute: cause of death (Issue #6115)

[EXTERNAL]

I agree that the ideal way to deal with all this is through multiple collecting events, but that it isn't realistic to expect collections to add this level of complexity to workflows. Something else to consider: in addition to cause of death (which I strongly prefer to "source of mortality"; if we are worried about public perception let's make this encumberable), we also need time of death, and time of preservation (specifically, our institution needs something like "time of tissue archive") - as we are recording these data to track the time between death and when tissues are dropped in liquid nitrogen. Time of death can be a record attribute, but time of tissue archive, or some variant ("time between death and preservation"?), should probably be a part attribute? Different parts have different preservation times, but for our puposes, it is the tissues/genetic materials that need the time stamp or time metric, typically minutes to hours, to track RNA quality. Seems like whatever solution we use should be able to track all these variables. I'm in favor of record attribute for cause of death and date/time of death. The latter could be used to track difference in dates between collecting event and death event for captive or experimental animals, and provide a means to flag records for those collections that would like to add a second collecting event for these purposes.

— Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/arctos/issues/6115#issuecomment-1671824057, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED2PAZRMTAIWLHCKMPWUNDXUO7RZANCNFSM6AAAAAAW2OSZGM. You are receiving this because you are on a team that was mentioned.Message ID: @.***>

[Jegelewicz]

I'm in favor of record attribute for cause of death and date/time of death.

That is just one attribute. Record cause of death and let determined date be the time?

time of tissue archive

isn't this just the determined date/time of part preservation attribute?

[campmlc]

Technically yes, but it isn't clear how that would be obviously searchable between record attribute metadata and part attribute metdata, or that "determination date" actually means "date of death" and "date of preservation" in each case. I also use preservation determination date to say that "I checked these tissues on this date and confirmed they are in -80C freezer" without making an assertion that this is the date they were transferred there. I'd love to have some way of auto-time-date stamping a container check or scan event in object tracking so that it automatically creates a "storage temperature" or "preservation" or "condition report" part attibute . . . but that doesn't exist. Anyway, that discussion can be continued in a separate issue. For the purposes of this issue, I support "cause of death" as a record attribute. We can certainly put the time of death in as determination date for the moment until we decide whether that needs it's own attribute.

[Jegelewicz]

Yes, this gets back to the definition of determiner and determined date, which I don't think we use the same everywhere, but we probably should...

[dustymc]

determiner and determined date, which I don't think we use the same everywhere

Definitely should (and https://github.com/ArctosDB/arctos/issues/6413 if something's missing from the model). At least some of these would be of the form...

cause of death=whatever (necropsy @ date - person)

... and nothing says person didn't dig it out of some decades-old corner of the freezer and leave it laying around a week to thaw before performing the necropsy and determining that whatever happened on date.

[Jegelewicz]

Here is another set of data - I will probably use verbatim attribute for this stuff

Mortality DB Number	Necropsy Results
1999	Emaciation
2000013	Undetermined.  Carcass too decomposed.
2002012	Final:  Undetermined.  Carcass too decomposed.  Kidney too autolyzed to be able to distinguish nephritis
2005020	Nothing definitive.  Samples taken for submission to Steven Rafferty.
2006003	Gross necropsy only, slight endocarditis, but nothing definitive upon investigation.
2006005	No specific cause of death.  Thoracic and abdominal cavities contained considerable fluid.  Left testes enlarged and contained fluid.  Samples taken for Steven Rafferty
2007005	Undetermined.  Carcass too decomposed.
2008014	COD=head trauma.  Poor body condition, no fat present.  No ingesta in the GIT.  Severe skull fracture that involved predominantly with hemorrhage into the muscles, swelling of the brain, and hemorrhage on the undersurface of the brain.  No other lesions, but lungs were red and collapsed, however, they didn't have an unusual texture as though they were pneumonic.
2010005	Final Diagnosis:  Mild blunt Trauma.  Negative for moribillivirus and paralytic shellfish poisoning.    Open diagnosis, suspect maternal separation during storm, PCR negative for morbillivirus  ; Prelim=good body condition, lots of milk in her stomach.  Only notable thing at necropsy was some bruising on the body cavity, but not likely enough to be lethal.
2011003	Final Diagnosis:  Protozoal meningoencephalitis (Sarcocystis neurona-like).  Widespread inflammation in brain associated with protozoal parasites.  Toxoplasma gondii was isolated from tissues.  Negative for leptospirosis, and morbilliviruses.  Negative for domoic acid and PSP on liver
2011005	Final Diagnosis:  Severe meningoencephalitis due to Sarcocystis neurona-like protozoan; Bite wound to the throat.   Bite wound severed the tongue from larynx and tore most of the muscles ventral to the upper vertebral column.  This was a terminal traumatic injury, but the animal was likely to have been incapacitated by severe protozoal encephalitis.  Actively dividing protozoan were observed in lesions.  Otter had lumpocytic inflammation in adrenal gland.  Brain and kidney negative for morbillivirus.  Negative for leptospirosis.
2011013	Final Diagnosis:  Meningoencephalitis and hepatitis due to suspect Sarcocystis neurona parasitsm; Intestinal trematodiasis.   Negative for morbillivirus and leptospira.
2011019	Final Diagnosis:  Bacterial septicemia; bacterial abscess.  Bacteremia/septicemia secondary to deep bacterial abscess present in the subcutaneous tissue and muscle of the dorsum over the lumbar spine.  Streptococcus Group G bacteria were cultured from this abscess and fro mutliple other organs, including the lung, liver, and brain.  No evidence of protozoan parasites.  Negative for morbillivirus.
2011022	Final: Emaciation, dilated cardiomyopathy, mild multifocal meningoencephalitis (etiology not determined).    Prelim: emaciated, negative for morbillivirus.
2011025	Final: Bacterial septicemia (Streptococcus Group B); lympoid depletion, intestinal trematodiasis.     Prelim:emaciated, no other remarkable findings on necropsy.  Negative for morbillivirus.
2011026	Final: Sarcocystis neurona meningoencephalitis; Brain tested positive for morbillivirus by PCR.    Prelim:emaciated, puss observed in one mammary gland suggestive of mastitis; however, animal did not appear to be nursing.  Moderate osteochondrosis of one of the femoral heads but only mild arthritis in that joint.
2011030	Final Diagnosis:  Dilated cardiomyopathy.  Otter in fair nutritional condition.  Heart was markedly rounded and was enlarged and there was both pulmonary edema and fluid accumulation in the abdomen.  DA was detected in stomach contents and urine; while these concentrations not considered high enough to have caused death, this level of toxicity may have played a role in the heart condition.  Negative for morbillivirus
2011031	Final:  emaciation, no underlying cause identified.  ToDate:  emaciation and lesions suggestive of enteric stress hemorrhage.
2012001	Final:  COD massive crushing trauma, resulting fractures of the mandible, thoracic spine, and lumbar spine.  A lacerating wound was also present in the wall of the abdomen; this wound extended into the abdomen, resulting in rupture of the colon and spillage of colonic content into the adbominal cavity.  No significant bacteria were cultured; no parasites were seen in GI tract; negative for morbillivirus; no protozoa.  Biotoxin testing results still pending.
2012002	Final:  presumptive COD was dilated cardiomyopathy.  Otter had grizzling throughout the haircoat and the teeh were worn, with missing and broken incisors and canines, compatible with aged adult class.  Liver negative to Leptospirosis; Liver toxicology was negative for toxic compounds; Brain and kidney negative for morbilliviruses.  Biotoxin results pending.  Protozoa results pending.
2012012	Final:  COD meningoencephalitis due to sarcocystis neurona infestation; acute blunt trauma to the thorax; emaciation.   Negative for morbillivirus.  Biotoxin results pending.
2012013	Final:  COD severe meningoencephalitis associated with sarcosystic neurona-like protozoans.  Negative for morbillivirus.  Biotoxin results pending.
2012021	Final:  COD dilated cardiomyopathy resulting in chronic passive congestion of liver;  meningoencecphalitis and hepatitis due to protozoal infection (sarcocystis neurona); bacterial septicemia (Streptococcus group F) suspected.  Domoic Acid toxicity may have played a role in this mortality, but the evidence is somewhat mixed and insubstantial.  No saxitoxin detected in the liver.  Negative for morbilliviruses.
2012023	Final:  Meningoencephalitis and mycoarditis due to infestation by Sarcocystis neurona (suspect) and mild interstitial pneumonia.  Negative for morbillivirus; trace amounts of DA present in stomach contents; no saxotoxin present in stomach.      9/5/2012 Findings to Date:  COD could not be determined at necropsy, but observations by pathologist indicate otter may have had pneumonia.  A mixed growth of streptococcus bacteria was isolated from several tissues but the signficance of this bacteria to be determined from histopathology.
2012025	Final COD:  Parasitic pneumonia and meningoencephalitis - paragonimus sp. Tematodes; Emaciation; and Mild dilated cardiomyopathy; negative for morbillivirus, negative for saxotoxin.   9/19/2012 Findings to Date:  evidence of emaciation and possible dilated cardiomyopathy.
2012029	9/19/2012 Findings to data:  major findings at necropsy were emaciation and possible dilated cardiomyopathy.  Multiple dog bite wounds were noted but they were considered non-fatal.
2012030	Final:  Trauma-suspect propeller strike; mild multifocal lymphocytic and suppurative meningoencephalitis-suspect protozoal etiology (protozoal infection in brain suspected, more suggestive of toxo); mild multifocal lymphoplasmacytic and suppurative myocarditis.  Negative for morvillivirus.  High level of domoic acid (204.3 ng/g). 10/25/2012 Findings to date:  gross observations suggested trauma (shark or boat propeller) as a COD.   Urine tested positive for domoic acic (204.3 ng/g).  This level is considered high enough to possible cause symptoms.
2012033	FinalCOD:  chronic non-healing fracture of left frong leg due to gunshot, emaciation, and multifocal suppurative bronchopneumonia, bacterial, moderate;  negative for morbillivirus; negative for saxotoxin, minimal amount of DA:    2/5/2013 Findings to date:  Emaciated.  Radiographs showed abnormality of left ulna and left proximal radius.  Histology revealed abnormality to be a result of remodeling secondary to a fracture.  This otter also had osteomyelitis.
2012035	11/30/2012 Findings to data:  Gross observations support field obs that likely COD was due to trauma caused by sharkbite.
2013001	Final:  systemic toxoplasmosis; marked intestinal trematodiasis (Spelotrema sp); intestinal cryptocprodiciosis; and mild intestinal acanthocephaliasis.  Otter was emaciated, protozoa seen in the brain, liver, and adrenal glands.
2013002	Final:  bacterial septicemia secondary to chronic soft tissue abscess.  A large, chronic, pus-filled abscess was present in the subcutaneous tissue and skeletal muscle of the left hind leg; likely a result of a bite wound, however, no bite wound was seen.  Tested negative for morbillivirus.
2013003	Final:  Severe hemorrhagic gastroenteritis; suspect clostridial enteritis.  Bacterium Clostridia perfringens was isolated from the intestinal tract and rod-shaped bacteria consistent in appearance with Clostridia sp. Were seen associated with areas of intestinal destruction on histopathology.  Negative for parvovirus, morbillivirus.
2013008	Final COD Trauma and suspect mild toxoplasmosis, negative for morbillivirus, small amount of DA (11.2 ng/g) in stomach contents;  Findings to date:  no significant finding during gross exam
2013011	Final:  Septic peritonitis; uterine torsion (suspect).  Bacteria (Pasteurella mutlocide) cultured from multiple tissues (may have been pathogenic).  Female had recently given birth.  Negative for protozoa, saxotoxin, morbillivirus. Findings to Date: yellow-orange exudate found in mammary tissue, light-red thick fluid filling abdomen.  Tongue had protozoal cysts, which were also rarely observed in diaphragm and heart.
2013016	Final COD:  Gunshot (shotgun) and Meningoencephalitis consistent with protozoal infestation and significantly elevated Domoic Acid levels (432 ng/g).      Preliminary: Shot with shotgun; negative for morbillivirus
2013019	Final:  dilated cardiomyopathy and emaciation.  Negative for morbillivirus. Neg for DA, positive for Saxotoxin, but below detection limits.  Findings to Date: negative for morbillivirus, heart was enlarged, liver was congested and mildly swollen.  Suspect COD is dilated cardiomyopathy combined with stress of pregnancy and birth.
2014001	Final: Not Determined.  Juvenile was in fair nutritional condition.  Negative for morbillivirus, avian influenza, and chlamydia.
2014012	Final:  Emaciation.  Negative for canine parvovirus and morbillivirus.  Findings to date:  negative for morbillivirus, extensive bruising of soft tissues of the neck, but no penetrating wounds seen.  Exact COD not obvious at necropsy, but suspect enteritis or sepsis.
2014014	Final:  Bacterial septicemia secondary to tooth rot abscess; Mild to moderate protozoal meningoencephalitis (Toxoplasma gondii susptected).  Negative for morbillivirus
2014026	Final:  neoplasia due to carcinoma, ascites, emaciation, tongue (suspect herpesvirus), sarcocystosis, gastric ulceration (focal).
2014028	Final:  Emaciation, bacterial sepsis, mild multifoval protozoal meningoencephalitis associated with suspect toxoplasma sp. Cysts.
2015007	Final:  protozoal encephalitis (S. neurona and T. gondii), secondary findings included emaciation, mild dilation of the heart, pulmonary edema and congestion, gastric and duodenal ulceration, and lymphoid depletion.  Negative for AI, morbillivirus.  Positive for Saxotoxin exposure in liver, but BDL in urine for Saxotoxin and DA
2015012	Final:  Undetermined; suspect intestinal perforation with adhesions; subcutaneous, mediastinal, pulmonary and perirenal emphysema; mocardial necrosis; suspect Sarcocystis, tongue and skeletal muscle; gastric ulceration; and emaciation.  Negative for AI and morbillivirus
2015020	Final:  Severe dilated cardiomyopathy; ascites and hydrothorax, severe, secondary to heart disease; moderate protozoan meningoencephalitis (suspect S. neurona)
2015024	Final:  Colonic volvulus.  Negative for morbillivirus.  DA level of 2.46 ng/ml detected in urine. Negative for saxotoxin.
2016005	Final: Pasteurella multicoda bacterimia and marked multifocal subacute protozoal meningoencephalitis with suspect Sarcocystis neurona protozoa.  Brain and kidney negative for morbilli
2016007	general necropsy only.  No significant findings.  No COD identified
2016018	Final: Protozoal meningoencephalitis
2016030	Final: Severe heart disease (dilatative cardiomyopathy); necrotizing lymphadentitis of multiple lymph nodes by uknown cause; muscle parasite infection by Sarcocystis sp.
2016038	Final: necrotizing and non-suppurative protozoal meningoencephalitis; necrotizing bacterial hepatitis; emaciation
2016043	Final: congestive heart failure, negative for morbillivirus.  Positive detections of DA and saxotoxin, but both below detection limits.
2016048	Final:  Emaciation - suspect starvation.
2017001	Final: Protozoal meningoencephalitis due to sarcocystis-like protozoa; saxitoxin and DA below detectable levels in stomach and urine contents.
2017002	Final: protozoal meningoencephalitis by sarcocystis protozoa and emaciation.  Neg for AI, morbillivirus.  DA, Saxotoxin below detection levels.
2017009	Final:  Protozoal meningoencephalitis Sarcocystis neurona; emaciation, myocarditis.  Negative morbillivirus, influenza A.  Positive Domoic Acid detected in urine (1.1 ng/ml) indicates exposure.  Levels in stomach below detection levels.  Saxitoxin below detection levels.
2017016	Final: Dual infection of Sarcocystis and Toxoplasmosis; Dialated cardiomyopathy; Saxitoxin and DA below detectable levels in stomach contents, DA level of 0.4ppb in urine
2017026	Final:  Acute necrotizing hepatitis, bacteremia, pneumonia.  Bacteremia and pneumonia likely due to liver damage.  Negative for herpes virus, drugs, pesticides, and industrial chemical residues.  Cause of hepatitis likely poisoning from microcystin-LA.  Positive for saxitoxin (3.3 ng/g) in urine, stomach content negative. Positive for DA (36.6ng/g) in urine, stomach content negative
2017032	Final: acute and severe protozoal pneumonia and meningoencephalitis, likely sarcocystis neurona.  Negative for AI.  Below detectable levels for DA/saxotoxin.
2018008	Final:  Heart Failure secondary to loss of myocardial tissue; trauma to head with signficant loss of soft tissue and with accompany hemorrhage from unknown cause.  Negative for saxitoxin and DA
2019003	Final COD: tubular mammary adenocarcinoma, bacterial septicemia secondary to tumor necrosis
2019024	COD - Protozoal encephalitis due to Sarcocystis neurona; pancreatic cestodiasis; emaciation; hemorrhage and hemothorax.  Immunohistochemistry positive for sarcocystis neurona.  DA detected in urine at 0.59 ng/ml.  DA not detected in stomach contents.  No saxotoxin detected in stomach contents or urine
2019043	Final:  meningoencephalitis, mild with focal protozoal cyst; septicemia, acute; emaciation.  Negative for morbillivirus.
2020013	COD: Acute bacteremia, emaciation.  Cocci bacteria were present most prominently in the blood vessels of brain and meninges.  Avian Influenza, CDV negative
2020014	COD: Acute bacterial septicemia and peritonitis due to Streptococcus phocae cultered from multiple organs, emaciation.  Likely that septicemia and peritonitis originated in the necrotic area in the muscle of the left inguinal region, likely as a result of a bite wound.  Avian Influenza negative.
2020026	COD:  poor body condition with severe adipose atrophy; subcutaneous and mediastinal emphysema (severe, diffuse); splenic depletion (mild); multifocal gastric ulceration

[wellerjes]

Does this have a chance of moving forward? It would be great to have, especially to record our window strike salvage specimens. Could it be free text? We currently record time of collection, estimated time of death, and cause of death in event remarks.

[dustymc]

@wellerjes put it on the issues agenda and show up tomorrow, I think this probably needs an advocate to guide it through the process and keep it out of the weeds.

FWIW I'm still at https://github.com/ArctosDB/arctos/issues/6115#issuecomment-1552220337 - I like this as a 'life event' catalog record attribute because it's simple (even though record-event would probably be more correct), expandable (it'll probably work for that thing the next new-to-Arctos collection needs), seems to cover the original request, and avoids any possibility of a "we'd like to use for lichens but 'dead' is usually a bit of an overstatement for them" situation.

[Jegelewicz]

At AWG we agreed to add this term, but we did not agree to the code table for it. Should it have a code table or remain free text? @ArctosDB/arctos-code-table-administrators @dustymc @wellerjes

[dustymc]

I think it's a new code table, but I don't know if if needs collection partitioning or not.

[ebraker]

At AWG we agreed to add this term, but we did not agree to the code table for it. Should it have a code table or remain free text? @ArctosDB/arctos-code-table-administrators @dustymc @wellerjes

I'd be fine with free text. There's a million ways to die, right?

But I guess if we have "other" and a code table that works as well.

[ewommack]

There's a million ways to die, right?

mwahahaha

That requires a mad scientist laugh.

[dustymc]

The original request was looking to get at things like roadkill vs harvest and would have needed a CT/categorical value set - IDK if that's still current or not, but https://github.com/ArctosDB/arctos/issues/4203 (900 ways to spell DOR) makes me think there's some value in the idea.

"other" and a code table

Seems reasonable when/if we find something that can't be categorized and still have something to say about it.

[Jegelewicz]

OK - I think a code table makes sense, otherwise we should just keep putting this in remarks somewhere?

Adding other as suggested to the original request gets us:

hunter harvest - Killed by humans for food or to control a population. euthanized - Humanely put to death. disease – Death caused by disease condition. vehicle – Killed by a motor vehicle. depredation – Killed by humans to mitigate damage to crops, landscaping, or other property. predation – Killed by predator species. other - place the cause in the method of this attribute

Any additions to this list? Changes to the definitions?

[ebraker]

I'd like to add "collision," which could include vehicles, or we could keep these as separate categories. Window strikes into buildings are probably my biggest source of salvaged birds.

collision - killed by impact, including static structures (window strikes) or by moving objects, such as cars and wind turbines

Also, does it make sense to add "collected"? It might be worth pulling out from "euthanized" to make the distinction from a wildlife rehab or wildlife "dispatch" situation (sheriff, state DNRs, etc.) to indicate that an organism was specifically targeted for scientific research.

I think an "unknown" value would also be useful.

[dustymc]

I sorta think the terms should come in as issues with use cases/discussion/data - this already seems to be turning into a recipe for needing to change a lot of stuff....

Can we limit this issue to the table? From some comments above, I'll propose

• code table ctmortality_cause WITHOUT collection-specific filtering, and
• record attribute mortality cause

[Jegelewicz]

Ahhhh - I always assumed we needed values to create a code table...

[Nicole-Ridgwell-NMMNHS]

code table ctmortality_cause WITHOUT collection-specific filtering, and record attribute mortality cause

Looking back through this issue, will check a box for this.

[wellerjes]

I agree with @ebraker's definition of collision. If we are going with code table definitions, there needs to be something like "incidental" to cover unintentional deaths, i.e., an owl eating a mouse that had eaten rodenticide.

I'm also happy to go with a free text field!

[dustymc]

@wellerjes please see https://github.com/ArctosDB/arctos/issues/6115#issuecomment-2093897686 - are you OK with the proposed attribute type (and can you find someone to check a box if so)? We can address attribute values in separate issues.

See also https://github.com/ArctosDB/arctos/issues/6115#issuecomment-2093600866 for my current understanding of the need for controlled/categorical values, and please let me know if that's changed.

[campmlc]

I support and checked a box. We may also need something free text at some point, or use media, for long free text descriptions e.g. necropsy reports. But this is a good start.

[Jegelewicz]

I was going to add, but I feel like everyone is talking about cause of death and the request is:

mortality cause - The method by which the cataloged organism died.

Is that what we are all agreeing to?

[campmlc]

Is there a reason not to just be clear and use "cause of death"? Are we just hoping the euphemism flies under the radar? It doesn't really matter to me, and I approve either way, but just curious.

[wellerjes]

@wellerjes please see #6115 (comment) - are you OK with the proposed attribute type (and can you find someone to check a box if so)? We can address attribute values in separate issues.

Agree with attribute type and @campmlc has checked the box.

See also #6115 (comment) for my current understanding of the need for controlled/categorical values, and please let me know if that's changed.

"other" will work.

Thanks!

[Jegelewicz]

@dustymc I think this is ready, but the code table needs to be created.

[dustymc]

As https://github.com/ArctosDB/arctos/issues/6115#issuecomment-2093897686? I thought we were starting over....

[dustymc]

wrong tab....

[Jegelewicz]

@dustymc I don't want to create the term without a table to associate it with or we will immediately have people using it as free text. The table doesn't need any values, it just needs to exist?

[dustymc]

Sorry, I think I checked my box when we were considering recycling a table, please don't do anything until I (re)check all the boxes.

[dustymc]

Done.

To add values, file a code table request

To add to a collection, click collection settings from https://arctos.database.museum/info/ctDocumentation.cfm?table=ctattribute_type or manage collection