Preservation modes

[ecurrano]

Our preservation modes do not exactly match the PBDB choices for their collection entry. How shall we handle this? Do I remember correctly that this is a node?

PBot has: charcoalification, compression, impression, mold/cast, other, permineralization, unaltered remains, unknown

PBDB has: body, trace, permineralized, cast, mold/impression, adpression/compression, soft parts, recrystallized, concretion, dissolution traces, charcoalification, coalified.

I think it is fine to have a subset of the PBDB values, as things like "soft parts" don't really make sense for plants. the main problems I see:

• we have choices PBDB does not, and this is a required PBDB field.
• we lumped molds & casts, whereas PBDB has cast as an option and lumped mold & impression.

[aazaff]

Yes, you should pick an exact subset of pbdb choices

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From: Ellen Currano @.> Sent: Wednesday, July 12, 2023 2:15:18 PM To: paleobot/pbot-dev @.> Cc: Zaffos, Andrew - (azaffos) @.>; Assign @.> Subject: [EXT][paleobot/pbot-dev] Preservation modes (Issue #147)

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Our preservation modes do not exactly match the PBDB choices for their collection entry. How shall we handle this? Do I remember correctly that this is a node?

PBot has: charcoalification, compression, impression, mold/cast, other, permineralization, unaltered remains, unknown

PBDB has: body, trace, permineralized, cast, mold/impression, adpression/compression, soft parts, recrystallized, concretion, dissolution traces, charcoalification, coalified.

I think it is fine to have a subset of the PBDB values, as things like "soft parts" don't really make sense for plants. the main problems I see:

• we have choices PBDB does not, and this is a required PBDB field.
• we lumped molds & casts, whereas PBDB has cast as an option and lumped mold & impression.

— Reply to this email directly, view it on GitHubhttps://github.com/paleobot/pbot-dev/issues/147, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPQSQ7CBV3XIITGBXDIHA3XP4HWNANCNFSM6AAAAAA2IBHHKM. You are receiving this because you were assigned.Message ID: @.***>

[doricon]

I would like to keep our current PBot options for the specimen node's Preservation field. This is just internal PBot info and doesn't pipe over to PBDB.

For the PBDB field list on collections: I think the following subset should suffice: trace, permineralized, cast, mold/impression, adpression/compression, recrystallized, concretion, charcoalification, coalified

(i don't know how soft parts, body, or dissolution traces would relate to plants - so those are the ones I would nix)

I totally understand if other folks don't want two different lists on different nodes, in which case we will have to standardise to the PBDB version. I don't like their groupings, but also don't have strong sentiment either way! :)

[aazaff]

To clarify.

What Dori said makes sense to me. Use whatever the PBOT team wants for specimens, but make the options for collections consistent with PBDB as she described.

RE: the question about why it exists for both collections and specimens – the short answer is simply for legacy compatibility reasons.

From: doricon @.> Date: Thursday, July 13, 2023 at 9:35 AM To: paleobot/pbot-dev @.> Cc: Zaffos, Andrew - (azaffos) @.>, Assign @.> Subject: [EXT]Re: [paleobot/pbot-dev] Preservation modes (Issue #147)

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I would like to keep our current PBot options for the specimen node's Preservation field. This is just internal PBot info and doesn't pipe over to PBDB.

For the PBDB field list on collections: I think the following subset should suffice: trace, permineralized, cast, mold/impression, adpression/compression, recrystallized, concretion, charcoalification, coalified

(i don't know how soft parts, body, or dissolution traces would relate to plants - so those are the ones I would nix)

I totally understand if other folks don't want two different lists on different nodes, in which case we will have to standardise to the PBDB version. I don't like their groupings, but also don't have strong sentiment either way! :)

— Reply to this email directly, view it on GitHubhttps://github.com/paleobot/pbot-dev/issues/147#issuecomment-1634551739, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPQSQ6GWRXCNXFYAPRGVDDXQAPTPANCNFSM6AAAAAA2IBHHKM. You are receiving this because you were assigned.Message ID: @.***>

[aazaff]

Can we consider asking Mark if they would be willing to add our new/additional types to PBDB as options?

[aazaff]

Either way this is too complex to be handled before hackathon.

[ecurrano]

For the Hack-a-Thon we do need to match the collection node preservation modes to PBDB's. Here is the subset of PBDB entries that we would like to include: Body Trace Permineralized Cast Mold/impression Adpression/compression Recrystallized Concretion Charcoalification Coalified

@doricon : I left Body since otherwise I wasn't necessarily sure where to put pollen. You can select multiple, so really someone could select body and many of the choices below. Botany team needs to come up with definitions of charcoalification vs. coalified for the cheat sheet.

[aazaff]

We have agreed to go with this final list for both specimen and collection.

[NoisyFlowers]

This is in 2062b7f33d73f9104699c60445aab62849f783dd