Request - symbiont vs parasite

[happiah-madson]

Help us understand your request (check below):

• search or data request (help with SQL or provide the specific fields you are trying to retrieve for your collection)
• add a new Github user to the Arctos Users team
• a new barcode series
• a new term for data entry or management
• a change or new report or label
• update to an Agent (split, merge, or other type of change)
• bulkload changes (to Agents, Identifiers, etc that are not already available as a bulkloading tool)
• new feature or otherwise a good idea to make Arctos even better
• quarantine taxon name and suggested replacement (please supply links)
• other

Describe what you're trying to do
I'm having feelings about only being able to do host/parasite relationships. We have a lot of host/symbiont relationships. I'm not interested in creating unnecessary complexity, but is there any way to either make this more general and change the language to symbiont or make the term "parasite or symbiont" ? Do other collections have this host-symbiont relationship that isn't explicitly parasitic?

For instance, we have some records w/ notes like this: Host, Desmarestia antarctica, thallus maintained in culture approx 1 year; emergent endophyte filaments cultured and identified as Geminocarpus sp. This specimen was endophytic in Desmarestia antarctica

where we have physical parts for the endophyte and observations for the hosts. I don't feel super awesome about calling this a host/parasite situation.

We also have a ton of shipworm + bacteria records where the bacteria are explicitly good and so I really don't want to use host/parasite for those.

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctid_references#parasite_of

@dustymc @campmlc

[campmlc]

I believe we have switched to using "associated with" (changed from "physically associated with" and more specific info in remarks. We had a discussion awhile ago about phoretic mites etc and how to deal with similar situations. @DerekSikes

[happiah-madson]

I get that; I considered using "associated with" it's just so hard to not use host when it's there 😬

[campmlc]

Otherwise we'd also need "symbiont of" and "host of symbiont" and "commensal of" and "host of commensal" and "mutualist of" etc. Perhaps we do need "culture of" and "cultured from"? We are starting discussions about archiving cultures.

[dustymc]

In #1842 / #5349 I (unsuccessfully) argued that we really need a first-level 'they sure spend a lot of time together...' relationship (which I think would cover about 99% of what's known about Arctos records), backed up by some optional evidence-based 'this is actually parasitism' sort of thing. I'm not sure I'd make the same arguments today (simple/general and properly used seems to result in much better data than complex/precise but poorly used because it's poorly understood), but there's some background....

#8355 from here looks like compelling evidence that fine-scale relationships will be arbitrarily used.

I'm not much of a fan of 'list of possibilities' terms, but I think I like "parasite or symbiont" better than trying to make the split (which would assuredly end up with some same-things in two evidence-free piles meaning that no researcher will find them both).

'associated with' seems too broad a brush, even if there's something useful in method. (Possibly https://github.com/orgs/ArctosDB/discussions/6742 might eventually spawn something that trickles down here and makes that look more realistic, but I ain't holdin' my breath...)

¯\_(ツ)_/¯

[campmlc]

There is a major difference between parasites and symbionts, and we have a lot of funded initiatives and long-term Arctos projects specifically dedicated to delineating known host/parasite relationships. We have entire collections and collection types explicitly for parasites. I would not want these well-known and universally used terms muddied, and I'm sure others @gracz-UNL @acdoll @msbparasites would agree.
I suggest we don't reinvent the wheel and consider modifications of the terms in use by GloBI, since they explicitly work with data from many different sources and collections to map to their fields: https://www.globalbioticinteractions.org/data

[dustymc]

consider modifications of the terms in use by GloBI,

Those are https://github.com/oborel/obo-relations, but

1. Ripping ontology terms out the context of an ontology has limited benefit (still useful in understanding things like whether a term might be appropriate in a code table), if we want to ontology then let's stop talking about it and just do that, but
2. That particular ontology does not seem to scale to Arctos, and
3. GloBI and Arctos data models are very different, that really has to be understood before we can usefully talk about changes of this scope.

[msbparasites]

I recently visited a collection where they had an amazing lifetime collection of army ants and all their symbionts, parasite, mutual, commensal etc. I was thinking if that was in Arctos, how would we have a relationship other than "parasite of" as the concern was made up above. What about having a tiered list, Symbiont--> then select from parasite, mutualist, commensal, culture (or whatever). There are some awesome books just on symbionts and there is terminology there that if interested, I could come up with a list that can be looked at by others who have other types of symbionts than parasites.

[campmlc]

I was thinking this would work if we could use an ontology . . .

[dustymc]

tiered list,

That idea is in #5349. The big picture still seems correct (which may or may not have any overlap with 'usable') to me, and I'm sure we could find a way to implement if someone wants to lead the charge (with a functional use case Issue, please).

ontology

I started an Issue, feel free to volunteer to write the proposal over there!

[DerekSikes]

Back in the 1990s the specimen database Biota made by Rob Colwell used the terms 'host-guest' (he had done lots of work with hummingbird mites that use the bills of hummingbirds to get from flower to flower, like a taxi service). I like this because it has more information than 'associated with' which I find to be too vague, but does not go so far as to imply whether the relationship is +/+ (mutualism), +/- (parasitism) -/- (competition), etc. which can often be unknown for many mites (the niches of taxa like lice, fleas, ticks, are more obvious than mites). It also makes it clear which partner is big (the host) and which is small (the guest) although perhaps the more important bit of info is that the guest is OF the host - ie on, in, or otherwise more or less physically associated with (ah, but what about nest symbionts like beaver lodge beetles? They are guests who scavenge detritus in the lodge).

I think I would be in favor of a solution that allows us to assign the relationship term (eg parasitism, mutualism, etc) separately from the host-guest relationship.

[campmlc]

I like that idea. Similarly, what if we could choose what the reciprocal relationship would be, rather than automatically defaulted pairs? Or at least have this be an option, with the default being set? That way we could choose "host of" for the host without "parasite of" being the default. We could choose other options for a given host relationship, e.g. "commensal of" or "symbiont of". We also need the ability to describe viruses/fungi, bacteria that may or may not be pathogens or causing infection, but which are still extracted from a given host.

[dustymc]

'associated with' which I find to be too vague

That level of specificity being necessary keeps showing up when we talk about things like your taxi service. I think those generally have two levels of resolution, first a 'this fell out of there' link at the time of cataloging, hopefully/eventually followed up by a (possibly very specific) "here's why" from some expert (involving methods and publications and such).

Finding a tapeworm somewhere inconvenient for the host seems to lead directly to the latter level (and that's probably justified) so probably not a simple 'do A then B' workflow - seems like we'd need to retain the ability to assert nearly anything without introducing any dependencies/complexities.

I do (sometimes) think we need to better separate 'natural' and 'curatorial,' but there's also a lot of stuff in between - collected with==hint of a relationship and cultural stuff involving the intent of the maker and such, so even that's probably not as simple as I wish it was.

what if we could choose what the reciprocal relationship would be

There's never been a limit on what you can choose, but there's also been a long-standing desire to have some automation and I think you've just proposed to kill that possibility.

@happiah-madson I'm not sure if we're circling in on your request or not, please feel free to hide anything that doesn't seem productive.

I've started https://github.com/orgs/ArctosDB/discussions/8386 for general discussion.

[campmlc]

I agree with moving this to general discussion.

what if we could choose what the reciprocal relationship would be

There's never been a limit on what you can choose, but there's also been a long-standing desire to have some automation and I think you've just proposed to kill that possibility.

I very much appreciate the bots and don't want to lose that option- so my question is more could we opt in for the bots using specified reciprocals, but have the ability to manually choose alternate relationships? We'd have to have the permissions to edit both related records/collections.

[happiah-madson]

I feel like I've just re-opened a whole can of worms 😆

In our old system we had Host (big organism); symbiont (little organism); co-occcuring (coincidentally together).

I was thinking this would work if we could use an ontology

Does this mean a hierarchical series of relationships? If we don't have to use host/parasite AND people are okay with me adding additional terms to relationships, I'm ok with that solution but note that I don't use the bots...

[campmlc]

We could do like GLoBI :
"Parasite of" / Host of Parasite "
Symbiont of / Host of Symbiont
Virus of / Host of virus
Etc