Arctos: Parts

[Jegelewicz]

• Parts seem super weird?

In the linked page I see

Click that PID and then I can see the "part", but also I see it twice (seems like a weird GUM thing, but I don't understand it)?

[tucotuco]

The relevant records from the CSVs are:

Entity

https://arctos.database.museum/guid/MSB:Host:15217,MATERIAL_ENTITY,https://arctos.database.museum/collection/MSB:Host,,
https://arctos.database.museum/guid/MSB:Host:15217/PID22723022,MATERIAL_ENTITY,https://arctos.database.museum/collection/MSB:Host,,

MaterialEntity

https://arctos.database.museum/guid/MSB:Host:15217,ORGANISM,,,MSB,MSB,Host,https://arctos.database.museum/collection/MSB:Host,MSB,15217,,,,,,
https://arctos.database.museum/guid/MSB:Host:15217/PID22723022,part,media,discarded,MSB,MSB,Host,https://arctos.database.museum/collection/MSB:Host,MSB,15217,,,,,,

Organism

https://arctos.database.museum/guid/MSB:Host:15217,,https://arctos.database.museum/guid/MSB:Host:15217/IID11522185

EntityRelationship

600132059,,https://arctos.database.museum/guid/MSB:Host:15217/PID22723022,part of,https://arctos.database.museum/guid/MSB:Host:15217,,,1
600132060,,https://arctos.database.museum/guid/MSB:Host:15217/PID22723022,part of,https://arctos.database.museum/guid/MSB:Host:15217/PID22723022,,,1
600152580,,https://arctos.database.museum/guid/MSB:Host:15217,has genetic sequence,,http://www.ncbi.nlm.nih.gov/nuccore/FJ174557,,1
600152581,,https://arctos.database.museum/guid/MSB:Host:15217,has genetic sequence,,http://www.ncbi.nlm.nih.gov/nuccore/FJ174497,,1

[MortenHofft]

@Jegelewicz
Thanks for looking at this. I believe parts of it will be better with the next Arctos export.

There are several things that makes this feel wrong I think (it is far from ideal in my opinion as well).

self referential relationships in the data
Part of the weirdness is in the data. where A is listed as a part of A. That looks like a data error to me.
#111
That is why you see things appearing twice. It is a relation to itself as both a subject and an object.

aligning vocabularies for relationships
A second thing is that the lack of a vocabulary makes it really difficult to know what to do with these relations. I try to tease some of them out (e.g. images and sequences), but for the rest we just show them as a long list (and I do not know what is the interesting information to show for each of these related entities).
When #116 is fixed in the data then this well get a bit better as well.

But there might always be relationships that is unique, and for those I'm not sure what else to do than something along the current presentation.

When to show a new page
What to show and when to link to a new page - this is related to #117 (comment)

Perhaps we can revisit this issue once the data is updated? The current data export adds additional clutter to an already messy part of the UI - so it is difficult to evaluate it fairly based on above screenshots.

[tucotuco]

How does this look now that we have a latest greatest export @MortenHofft @Jegelewicz ?

[MortenHofft]

It now looks like I would expect it to at this point. The UI tease out a subset of relationships, but shows the remaining very crudely. I'm not sure what more I can do for the "rest" - assuming there will always be relations of types that I do not know.

But "hosts" and "part of" relationsships seem so common that it would make sense to display them more explicitly - similar to how we show image and sequence relationshships in a custom way.

The challenge for me with showing parts, is that it is hard to know what to include. For images and sequences it is quite natural to know what fields are most relevant (the accessURI). For a part that is a material entity that is more tricky I find. I can try to spell "parts" out and then create an issue asking for guidance.

[Jegelewicz]

This media part - http://labs.gbif.org:7003/?entityId=https://arctos.database.museum/guid/MSB:Host:15217/PID22723022

Looks OK as it relates to the catalog record, but it still doesn't have an identification.

Also, this is probably a bit of an exceptional case. The part "media" is being treated as if it were a material sample, but it isn't. This part is recording the existence of a ledger where the host information was recorded. Ideally, the part would be "whole organism" with the disposition = discarded and this fact is supported by the ledger or media that we have recorded here as "media" (FWIW, the media has not been discarded...).

We have had endless rounds of discussion about this scenario and I don't think we have figured out the best path for recording it. I'd love to hear y'all's ideas....

[tucotuco]

Also, this is probably a bit of an exceptional case. The part "media" is being treated as if it were a material sample, but it isn't. This part is recording the existence of a ledger where the host information was recorded. Ideally, the part would be "whole organism" with the disposition = discarded and this fact is supported by the ledger or media that we have recorded here as "media" (FWIW, the media has not been discarded...).

We have had endless rounds of discussion about this scenario and I don't think we have figured out the best path for recording it. I'd love to hear y'all's ideas....

Speaking from the GUM perspective, the media would not be a MaterialEntity, but rather a digital entity with a relationship to a MaterialEntity. Using this model we can do even more exceptional things, such as have a 3D printed MaterialEntity that is derived from a 3D mesh DigitalEntity which is a model of a skull (MaterialEntity) that is a part of an Organism (MaterialEntity) of which there is a digital image (DigitalEntity). Let creativity reign!

[Jegelewicz]

The challenge is that while sometimes digital media exists, this part is about the physical ledger page. As a physical object, the collection still wants to track its whereabouts and usage. Right now, the only way for us to track physical things is to use parts. Digital media would come across with an associated URI and could facilitate all that creative magic.

[tucotuco]

It may be about the physical ledger page, but it isn't the physical ledger page. It is an image of if. The physical ledger page too is a MaterialEntity.