Ethology module: Reproductive behavior (incorporating ROBOT template updates) - by @DitchingIt

[matentzn]

Addresses #192

Problem 1: you cannot (at all) use OR in column O (Participant), see for example O6:

UBERON:0003134|CL:0000365 OR CL:0000025|ENVO:01001684

Why exactly is the OR needed?

[DitchingIt]

Thanks @matentzn The specific problem and a preferred solution is written up as UBERON issue https://github.com/obophenotype/uberon/issues/3124 I may have misunderstood @gouttegd who noted another option:

One possibility would be to state that ‘egg broadcasting’ has EITHER a ‘female gamete’ OR a ‘zygote’ as participant: ‘egg broadcasting’ has_participant (‘female gamete’ OR ‘zygote’) That’s a perfectly valid construct, however one that we generally try to avoid in the OBO foundry. It’s relatively uncommon and not all tools know how to deal with such constructs.

The easiest thing for now is for me just to withdraw the offending items and see if a solution turns up down the road, maybe from UBERON.

[DitchingIt]

@matentzn The other example was where either a female or a hermaphrodite (but not a male) was a participant. Anyway, the template has been amended. Thanks

[gouttegd]

I may have misunderstood @gouttegd who noted another option:

I had not realised you were trying to do everything with a ROBOT template. When I said that OR was a “perfectly valid construct”, I was referring to a valid OWL construct. That’s not necessarily valid in the context of a ROBOT template.

[DitchingIt]

I may have misunderstood @gouttegd who noted another option:

I had not realised you were trying to do everything with a ROBOT template. When I said that OR was a “perfectly valid construct”, I was referring to a valid OWL construct. That’s not necessarily valid in the context of a ROBOT template.

Sorry @gouttegd That explains it - let's see if anything comes of the UBERON issue.

[DitchingIt]

@gouttegd Are you able to help resolve any of the merge conversations above (particularly the first three)? My experience indicates that content review might tend to follow the first commit into the nbo-edit.owl rather than the publication of the initial issue (perhaps this triggers notifications or allows use of particular tools like Protege), so resolving blocks to the first commit, may help enable content debate.

[DitchingIt]

@gouttegd Are you able to help resolve any of the merge conversations above (particularly the first three)? My experience indicates that content review might tend to follow the first commit into the nbo-edit.owl rather than the publication of the initial issue (perhaps this triggers notifications or allows use of particular tools like Protege), so resolving blocks to the first commit, may help enable content debate.

The three technical conversations have been resolved: they were caused by a template problem fixed by @matentzn

[DitchingIt]

The repro-dict branch's nbo-edit file currently displaces all the ROBOT template work done on the ontology's NBO:0000010 'reproductive behavior' branch: classes are currently masquerading as annotated Datatypes! Watch this space for a resolution...

[matentzn]

@DitchingIt fixed (was the same issue as before, just different column, value N2 in your spreadsheet)

[aclark-binghamton-edu]

@DitchingIt @pmidford especially. I am coming in late, after I should have commented on (to me) essential miscalculations in setting up reproductive behavior relationships, inherent in the Reproduction NBO 231124 spreadsheet of definitions. Here are a few points--and then let me know if these comments are just too late in the process. (PLease understand that my tone is perhaps overly critical but I wrote these first points in reactive mode) Each term involved is in caps.

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1. In the "field" of Animal Behavior, the term "Mating Behavior" or "Mating" is usefully and necessarily separated from "Reproductive Behavior" writ large. Many of the terms and definitions make "Mating Behavior" essentially equivalent to "Sexual Reproductive Behavior" i.e. any aspect of reproduction where two gametes are involved at some point. This will make use in ethological circles extremely problematic. The problem would not be there if "reproductive organ" were not implicitly limited to those used in mating. But in some cases, transfer of sperm is not through the same organ or pathway that the egg-producer uses to release young at whatever stage. (There are cases in insects where sperm is introduced directly into the body of the female; and certainly an ovipositor is not also used in what I would call "mating behavior") Thus the definition of mating behavior as

<A movement behavior that stimulates, uses, or suppresses a reproductive organ in reproductive behavior>.

could stipulate that it is behavior involved in the process of transmitting sperm or receiving sperm or otherwise influencing the transmittal of sperm.

2. OVIPOSITION The problem in 1. is immediately obvious in "oviposition" being defined as a mating behavior. Oviposition in many if not most animals will take place spatially and temporally disassociated with mating (as I use it) and/or reproductive interactions with another animal, and it may include release of eggs that are NOT fertilized (including those that are functionally infertile, e.g. if used as food by existing hatched young, as in dendrobatid frogs). There are some other problems with it being called a "female mating behavior" because hermaphroditic species also oviposit. One might call it "female" by its association with an egg, but I suspect we are going to be avoiding such terminological divisions.

3.SEXUAL PLAY- Likewise "sexual play" might or might not include behaviors associated with mating, such as displays. But more importantly, the functional context gets pretty muddy if one calls "sexual play" mating behavior.

4. SEXUAL POSTURING: I have to say that I have never heard of "Sexual posturing" as a specific term, but fine if there is some need for it as a category or type of behavior. Its definition seems pretty unclear to me. What is "Control" of mating behavior? Posturing by a frog in amplexing a female is controlling, but is a female standing still "Controlling"? I would avoid this whole minefield of "control"

5. MATING AMPLEXUS and AMPLEXUS???? two terms?

6. SEXUAL ACTIVITY--I don't see the utility here (or why this reference is chosen?)--broadly speaking this is a familiar categorical term that is applied in a very non-individualistic way. "There follows a period of sexual activity in this species."--This does little to define even a group of behaviors, motivations, or states that in elephants includes associating with females.

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   Let me know if this focus on terms and the relationships that are implicit in their definitions is useful at this point. I can upload all comments together as one file.

[DitchingIt]

Thanks @aclark-binghamton-edu Do you mean in your final sentence that you have more comments? If so, it would be great to have everything that you have.

[DitchingIt]

My attempts over the last year to change the NBO have not made enough progress to justify pursuing it further. The most recent unmerged commits were made by @matentzn using my ROBOT template. I suggest they be removed to reduce confusion in future, since they are dependent on wholesale changes throughout NBO and cannot realistically stand alone.

Unlike anatomy or biochemistry, I doubt behaviour above the morpho-physiological level will (in the near future at least) be more than a set of more or less disputed opinions, although doubtless there will be individuals or 'schools' who believe in the universality of their own systematics.

Perhaps a more viable approach to cataloguing behaviour would be to map these opinions as a knowledge graph of behavioural ssertions (something I have already begun to explore) rather than to think there is a universally acceptable set of fixed behavioural entities which can be pinned down in a fixed ontology.

Even if I am wrong, at the very least, involvement, let alone consensus, has virtually disappeared over the last 12 years from the construction of the NBO. I now support @cmungall in his suggestion that the NBO be labelled functionally inactive, and declared as such on the OBO site (see#126).