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Term issue: #327

Closed ValWood closed 4 months ago

ValWood commented 4 months ago

All H3-K9Me terms

For H3-K9 to be methylated, histone must be deacetylated at H3-K14. https://pubmed.ncbi.nlm.nih.gov/11283354/

In this case , would it be OK to add the K14-dAc to with this reference? id: PR:000027578 id: PR:000027593 id: PR:000027604 id: PR:000085727 id: PR:000085728 id: PR:000085731

nataled commented 4 months ago

Hi Val, Here is what I have concerning pombe histones with K9 methylation: PR:000027578 (mentioned above) PR:000027593 (mentioned above) PR:000027604 (mentioned above) PR:000044697 PR:000044698 PR:000044699 PR:000044700 PR:000044701 PR:000044702 PR:000044703 PR:000044704 PR:000044705 PR:000085726 PR:000085727 (mentioned above) PR:000085728 (mentioned above) PR:000085729 PR:000085730 PR:000085731 (mentioned above)

I assume this applies to all the above cases and not just the ones mentioned?

Also, I can approach this in one of four ways: 1) Deprecated current terms; replace with new terms with the more-complete information 2) Keep terms as-is; instead add new terms with the K14 information 3) Add the K14 information, and rename all terms accordingly 4) Add the K14 information, but keep current names

I'm thinking the first option is suboptimal, because if you are already pointing to the current terms, you'd have to remap. It's also more overhead for PRO. Same applies to option 2. I initially thought those were the only two ontologically-acceptable avenues. However, the criteria for deprecation/replacement is guided (for these cases) by the notion that deprecation is only required if the entities that are part of a class will change with the revision. I don't think that's the case here, since (as you mentioned) none of the K9-methylated proteins can exist without K14 acetylation. For that same reason, I think it would be okay to keep the current names. Doing so will break a few PRO sanity checks, but that's not too much of an issue since I can make 'exceptions' to these checks. Let me know your preference.

ValWood commented 4 months ago

OK, I have been digging around for confirmation of this, because I'm worried that it only diminishes binding but in fact they can co-occur. So far I have been unable to find any corroboration, so I am asking around. I'll continue to concentrate on the single modifications and return to the cross-talk later.

If we go ahead later, I think option 3 would be best.

Let's close this one for now.