change 'abnormal flight' to 'abnormal flight behavior'

[Clare72]

FlyBase curators feel that this phenotype should represent behavior, rather than the ability to fly.

NB, 'flightless' will no longer be a subclass - is this ok @arzuozturk @vmt25

[vmt25]

NB, 'flightless' will no longer be a subclass - is this ok @arzuozturk @vmt25

I am OK with it as long as it remains a phenotypic class.

Many thanks

[gm119]

the 'abnormal flight' term has been historically used to capture cases where the ability to fly is less good than normal, but the flies can still fly a bit, so that is why flightless is currently a sub-class - as its the most extreme case (ability to fly is zero).

So to me, "FlyBase curators feel that this phenotype should represent behavior, rather than the ability to fly." sounds like the proposal to change 'abnormal flight' to 'abnormal flight behavior' would be 're-using' an existing term for a different concept ( I think, although I guess I'm not clear what the difference between 'ability to fly' and 'flight behavior' means exactly) . I don't think this would be good, as many of the existing 'abnormal flight' annotations would presumably then be incorrect ? (and what would the appropriate term be for "ability to fly is less good than normal, but the flies can still fly a bit" be if this change was made - would that no longer be curatable ?)

(apologies if I'm misunderstanding, but this sounds problematic to me).

[Clare72]

'flight behavior' 'flight'

Arzu and Vitor thought that the phenotypes being captured were behavioral, so 'flight behavior' was more appropriate.

If 'flight' also needs to be captured (or has been in the past), we should really make 'abnormal flight behavior' a new term.

[vmt25]

I see Gillian's point. The reason for the proposal is what is being observed/assessed is the behavior, which can be more, less (even absent), or qualitatively different flight. Of course, the reason for the abnormal behavior/abnormal flight can be purely anatomical (severe flight muscle anatomy, mitochondria, etc); many papers don't go into that. But for walking, for example, we currently only have the broad term 'abnormal locomotor behavior', whether the phenotype is more, less/absent, or qualitatively different walking. I don't see why flight should be different from any other type of locomotion (I was going to write 'type of locomotor behavior'...). Would an 'abnormal locomotion' term be more appropriate? Happy to chat about this

[Clare72]

An 'abnormal locomotion' phenotype would be a superclass to flight, cell motility and taxis phenotypes (and jumping phenotypes, due to NBO structure).

[vmt25]

An example for discussion. An abnormal copulation phenotype could be due to a physical impairment or be behavioural in nature. And the definition of the term 'abnormal copulation' term is "Phenotype that is any abnormality in copulation (GO:0007620). 'copulation' is defined as: 'The act of sexual union between male and female, involving the transfer of sperm.", which applies to both cases. However, 'abnormal copulation' is child of 'abnormal mating behavior', which is child of 'abnormal behavior'.

[Clare72]

GO does not split 'copulation' into behavior and movement the way it does with 'flight' - see 'flight involved in flight behavior'.

We have to work with what is in GO or ask them to change it (which may or may not happen).

[hattrill]

Hi @vmt25 - for most gross phenotypes, there is not a direct pheno to GO connection, in that an phenotype lies downstream of any number of potentially disrupted biological processes. GO does have "mating behavior" GO:0007617, if this is what you are looking for - this is what I would use to specifically describe as thing that directly impacts this behaviour.

[vmt25]

That example was just food for thought in terms of how the ontology is organized and how we do/should/can annotate - particularly for cases related to behavior.

We should have this topic for one of our weekly meetings.