WBP-DPO logical alignment review

[matentzn]

@Clare72 (FlyBase) has kindly started a review of alignments between DPO and WBP. Here are her notes:

DPO	WBPHENOTYPE	Label DPO	Label WBP	Alignment	Note
FBcv_0000408	WBPhenotype_0000067	stress response defective	organism stress response variant	logical	does not need to be organism-wide
FBcv_0000409	WBPhenotype_0000876	osmotic stress response defective	organism osmotic stress response variant	logical	does not need to be organism-wide
FBcv_0000410	WBPhenotype_0001273	heat stress response defective	organism heat response variant	logical	does not need to be organism-wide
FBcv_0000683	WBPhenotype_0000146	temperature response defective	organism temperature response variant	logical	does not need to be organism-wide
FBcv_0000725	WBPhenotype_0001620	oxidative stress response defective	organism oxidative stress response variant	logical	does not need to be organism-wide

@chris-grove What do you think? Thanks @Clare72!!

[chris-grove]

@matentzn @Clare72
Thanks!
I'll need to look this over in more detail at some point when I get the time. One question is: what does it mean for the stress response to be "defective"? Would increased stress resistance also be considered "defective stress response"? The WBP "stress response variant" terms include (are parents or ancestors of) stress resistance increased terms. The "organism" environment response terms above for WBP are not, according to the logical definition or textual definition, necessarily organism-wide. We do have some cell stress response terms which are specific to a cell's response to stress (more specifically than just the whole organism).

[matentzn]

It depends on how you understand the word defective. I always understood it as a synonym to "abnormal" - so yes, abnormally increased stress response is a defective stress response..

[Clare72]

Yes, in dpo 'defective' is synonymous with 'abnormal' - any deviation from control/wild-type. I am considering changing our term labels at some point if all other phenotype ontologies prefer 'abnormal' and if 'defective' is causing confusion.

Ok, if "organism" in the labels does not mean "organism-wide" then I think these phenotypes are correctly matched, just wanted to flag it to check.

[chris-grove]

In WBP we have terms for "variant/abnormal" and separately subclass terms that have "defective". I think to worm biologists, "defective" means unable to function or complete the process or do so as effectively as wild type/control/normal. So, we wouldn't consider increased efficacy as "defective". This comes back to the whole "defective" pattern I was trying to create before and I still need to address our "defective" terms and finding appropriate patterns for them.