alanruttenberg
commented
8 years ago Communication with Colin. He says create NCRO terms for the material entities and relate the SO terms to them. I'm still following up with Mike Bada
Open alanruttenberg opened 8 years ago
alanruttenberg
commented
8 years ago Communication with Colin. He says create NCRO terms for the material entities and relate the SO terms to them. I'm still following up with Mike Bada
This is from a discussion thread. Putting them here so they are easy to find. Should probably split into separate issues.
AR We have to figure out what to do about SO.
JH See comments below.
AR figure out what to do with unused, non-reference terms.
JH Make them obsolete terms?
AR Fix where ncRNA goes. Currently it is a sequence feature under mature transcript. But sequence features aren't material entities and ncRNA is.
JH There is an unpublished version of SO (molecular SO) where ncRNA is defined as material_entities. Discussed with Karen earlier, a temporary solution is to place the current ncRNA underneath material_entities and later on switch to the correct ncRNA (in molecular SO).
AR Moreover ncRNA is under mature transcript, but aren't there mature and immature e.g. miRNA?
JH As far as I understand, immature miRNA has another name (something like pri miRNA). We may not need to worry about this b/c we have not utilized, and most likely will not utilize, such pri miRNA.
AR Organize the hierarchy below ncRNA
JH How about keeping the current structure of small_regulatory_ncRNA and adding other high-level place holders like ribosomal RNA (rRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), and small interfering RNA (siRNA)?
AR Review other content. e.g. assertion that Every miRNA has_predicted_target some gene. I don't think that's necessarily true.
JH Discussed earlier with some biologists and got different opinions. Maybe leave it for right now?