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oborel
NTR: Sleeps in
I was looking for the most relevant relation for a primate using a specific tree species as a sleep sites. I couldn't find more generic "sleep", "rest" or "roost" relations between a animal and a plant. The two most closely related current terms are "creates habitat for" and "visits". Does "creates habitat for" have an inverse relation? Maybe visits could have subset of visit use such as feeding vs. resting? Let me know if a new term getting to specific and I should utilize a more generic term. I do think animal-habitat associations for sleeping would be widely applicable.
any ideas @diatomsRcool @jhpoelen?
Planning for the future, are we likely to need a relation for every term in the behavior ontology, or can we come up with a good generic relation as @arw36 suggests
Weren't we having this discussion with a bird roosting in a specific tree in another issue? I think "sleeps in" should not only be an inverse of "creates habitat for" but also a subclass. Are the primates sleeping in the tree similar to a bird roosting in a tree? or are the primates constructing "beds" on the ground using branches from the tree? That implies something a bit different. I think "visits" was originally meant for pollinator data where an insect was observed "visiting" a plant, but you can't assume that actual pollination occurred just from an observation of that sort.
Thanks for these comments. To clarify, if "sleeps in" is too specific a term, I could see utilizing the inverse of "creates habitat for" as a more general term for this animal-plant relationship. However, as of yet, I don't see an inverse term for interaction.
Visits could also suffice for this interaction, as I don't see a definition clarifying taxa or length of time focusing on certain animal-plant interactions.
If a new term is warranted, I think "sleeps in", or whichever term is decided on, would be generalizable across lots of taxa. Te case study I describe is primates sleeping on branches of a live tree, similar to birds sleeping in nests in a tree. Other primates do construct nests, both up a tree (chimpanzees) and on the ground (gorillas).
(That being said, has it been addressed by https://github.com/biolink/biolink-model/issues/850 or is there still a new term needed?)
@diatomsRcool said "Yes, this can be closed" in biolink/biolink-model#850. Since that issue was already closed, I'm assuming she's referring to this one.
Hi @arw36, sorry this is taking so long. RO is a volunteer effort, and we currently meet only once every 8 weeks. I have added this request to the agenda for our next meeting (March 8).
I think we need a term that implies that one taxon is using another to create a structure, like a primate makes a bed, a bird makes a nest, etc. Or we could be even broader and have a term that says that one taxon uses parts of another taxon for carrying out its life or some life process. The we could also include crabs that live in discarded mollusk shells. Then maybe making a structure is a subclass of that.
The current definition for "creates habitat for" is: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." I propose that we create inverse for this "uses for habitat" or something. Then perhaps we include subset such as "is modified for habitat by" (and the inverse "modifies for habitat") in the case of a of plant material being used to make a nest.
Thinking of a bird putting a nest together. Some just fetch twigs, but also mud? And various animals dig through dirt etc. to make tunnels. So a top-level habitat making model from creature's perspective, symbiotic or otherwise, should allow interventions that apply to inanimate materials as well as organisms.
I'm wondering now if every behavioural object relation is a shortcut connecting between behavioural process model components?
A "habitat creation process" has:
- output some habitat
- has participant some organism (as homebuilder, or in OBI speak, performer)
- occurs in some [host organism or place]
- has input some inorganic material and/or organism resource
A model should provide for the distinction between inorganic and organism material, and may reference the location the behaviour process occurs in.
The "creates habitat for" relation sounds a bit intentional (ok if it is an evolved symbiotic relationship.) "establishes habitat for" might be more on-target: "An interaction relationship wherein a structure or environment established by one organism can be lived in by another organism.". But this invites the inverse relations, and the need for material/nonmaterial reference:
- organism utilizes for habitat creation some material entity
- organism utilizes for habitat creation some inorganic material
- organism utilizes for habitat creation some organism material
- organism utilizes for habitat location some organism ...
Each of these maps from one part of the habitat creation process to another. And it looks like one gets into the categories of habitat location, for sleeping, eating, surveying, etc. Throw in complexity of obtaining building materials etc.
Are there still action items here to be addressed, or can this be closed now?
@arw36 @diatomsRcool is the term "sleeps in" still to be added for your research?
No. That project didn't get funding. This can be closed from my perspective.
@diatomsRcool bummer to hear that the project didn't get funded ; (
@arw36 would you still be interested in having "sleeps in" added to the Relations Ontology ?
I've added this topic to the agenda for the upcoming Nov. 1 meeting.
Let me know if you do not wish to discuss.
@cmungall @diatomsRcool will add a "has roost" under "has habitat" relation.
@arw36 Will this work for you?