WBP-DPO logical alignment review

[matentzn]

WBP-DPO logical alignment review

[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]

@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..

[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.