Additional Behavioral terms

[malcolmfisher103]

Erik asked previously for some other behavioral terms that should be included in the behavior class (#30) besides swimming and hatching. From a review of the literature we identified several types of behavior associated with Xenopus phenotypes. Of these 8 have precise GO terms ...

ID	Name
GO:0071625	vocalization behavior
GO:0007619	courtship behavior
GO:0048266	behavioral response to pain
GO:0042048	olfactory behavior
GO:0007638	mechanosensory behavior
GO:0007632	visual behavior
GO:0007634	optokinetic behavior
GO:0035176	social behavior

We also identified 3 types of behavioral phenotypes that lack a clear GO term equivalent ...

Name
collision avoidance behavior/ visual avoidance behavior
schooling behavior
escape behavior

Can these non GO terms be added as is or is the correct procedure to request additional terms be added to GO and then use those new GO terms as the basis for XPO terms?

All of these that can be added should probably have 'abnormal behavior' and 'abnormal absence of behavior' terms. Sorry I didn't have these ready in time for the last release.

[matentzn]

@malcolmfisher103 There are two options here.

1. You go the long way via GO; if you want to try, feel free!
2. You go for NBO, which we also use for behavior. The advantage here is that we can create terms quickly ourselves. (Check here) if interested!

[malcolmfisher103]

Thanks for directing us to the NBO, we'll consider that as an a alternative option.

[Xenbase2]

request: increased rate [PATO_0000912]/decreased rate[PATO_0000911] abnormal, absent 'surface breathing', ; increased rate/decreased rate/abnormal 'swimming behaviour', abnormal 'resting posture', absent/abnormal/increased rate/decreased rate 'locomotory behavior'. request. increased rate/decreased rate/abnormal/absent feeding behaviour

(surface breathing would be an additional request for new term with NBO).

[Xenbase2]

abnormal/absent mating behaviour (GO:0007617)

[malcolmfisher103]

ID	Name
GO:0007631	Feeding behavior
GO:0007626	locomotory behavior
NBO:0000358	resting posture

[seger]

Summary of terms that still need to be added/requested.

Q	E
abnormal	collision/visual avoidance behavior - NBO request
abnormal	schooling behavior - NBO request
abnormal	escape behavior - NBO request
increased rate/decreased rate/abnormal/absent	surface breathing - NBO request
increased rate/decreased rate	GO:swimming behavior
abnormal	NBO:resting posture
increased rate/decreased rate	GO:locomotory behavior
increased rate/decreased rate	GO:feeding behavior

@matentzn We need to set up NBO imports in the XPO.

[matentzn]

Done.

[seger]

Awesome! I am writing up the new NBO term requests and will submit tickets soon.

[matentzn]

Actually: would you feel comfortable to just make pull requests instead?

[seger]

Sure! So I just edit src/ontology/nbo-edit.owl, correct?

[matentzn]

I send you an email with instructions. Thank you!

[seger]

@seger will add subsumptions to GO terms to NBO so that the behaviors classify correctly.