Code Table Request - new catalog record attribute: pathology

[Jegelewicz]

Goal record details about pathology detected

Context https://github.com/ArctosDB/data-migration/issues/667#issuecomment-1255312947

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

Proposed Value pathology

Proposed Definition Non-normal skeletal conditions that include lytic, proliferative and deformative lesions, as well as accessory bones, non- fusion anomalies and antemortem trauma.

Collection type Bird, Mamm, Fish, Herp, Amph, Rept, Vert, Teach

Attribute data type free-text

Available for Public View Yes

Priority [ Please choose a priority-label to the right. ]

[Jegelewicz]

Non-normal skeletal conditions that include lytic, proliferative and deformative lesions, as well as accessory bones, non- fusion anomalies and antemortem trauma.

Could this be applied to things other than bones? Should we generalize the definition if so? @ehalverson26

[dustymc]

Why is this separate from https://github.com/ArctosDB/arctos/issues/5087?

[Jegelewicz]

Because it is kinda independent of it - we will ask for this either way that goes and I don't want to hold this up for that (which needs some considering...)

[dustymc]

independent

I don't see it - the other thing has a 'just stumbled on it' option (if that's the concern), I can't see any reason anyone would ever need more, this just looks like simple denormalization (==hiding data from users by having many arbitrary places for it) from here at the moment.

[Jegelewicz]

See https://github.com/ArctosDB/data-migration/issues/667#issuecomment-1255312947

[dustymc]

Not sure what I'm looking for there, still two ways of saying the same thing.

Definitely agree that this belongs at the record level, unless we're prepared to have records for parts which no longer exist (eg something like/beyond https://github.com/ArctosDB/arctos/issues/3630)

[ehalverson26]

I have been thinking about your question about if pathology could be applied to things other than bones. I was thinking about other possible deformities and pathologies. Examples might include a beak deformity on a bird, or a carapace shell deformity, but in those cases it would still fall under the skeletal structure. Possibly something like melanism in mammals or birds, but I think that would not really be considered a "pathology". Of course that can be pathology in tissues but I don't foresee that being a part of a museum specimen record that would need to be recorded so specifically in a catalog record. That might be more cause of death and be noted elsewhere. I think we should be okay leaving pathology in relation to bones, however pathology is a pretty broad range of things, so if someone can think of an example where it might apply to a broader scenario and be applicable to museum specimen records, I would certainly be open to changing the definition.

[dustymc]

pathology in tissues

"enlarged spleen" and similar are very common notations (at least when there's a parasitologist in the camp), I think that would end up in a better place if such a place were available.

[ewommack]

When you work with whole animals from vet labs, zoos, or rehab clinics you might get the pathology information from them.

[campmlc]

Following up with this as we are getting a lot of these data in a format that cannot easily be parsed by tissue type/part attributes. And to the previous point, this includes a lot of information on pathology in tissues but which needs to be recorded at the catalog record level. There is a ton of this info in the Rausch records at MSB that all got shoved into remarks. I strongly support making this record level attribute available.

[campmlc]

Alternately, we could use the Examined for/Detected/Not Detected proposed attributes, and have pathology as a value in the code table.

[jldunnum]

We just received serology data for >8000 records of Panamanian rodents. Where can I put it?

---

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 @.> Sent: Thursday, March 16, 2023 3:06 PM To: @.> Cc: @.***> Subject: Re: [ArctosDB/arctos] Code Table Request - new catalog record attribute: pathology (Issue #5101)

[EXTERNAL]

Alternately, we could use the Examined for/Detected/Not Detected proposed attributes, and have pathology as a value in the code table.

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[dustymc]

Example data would be most useful in figuring that out. "All of it" is my preferred sample size.

I think the biggest hangup at the moment is probably https://github.com/ArctosDB/arctos/issues/5688 - there was a long discussion then everything reset as the meeting was ending and I have no idea what to do about that.

[Jegelewicz]

We have a meeting set for 2023-03-21 at 10AM MDT, perhaps we can figure it out now that we have a use case? But, yes, data in advance would be helpful.

[dustymc]

pruning offshoots