Open sjm41 opened 2 years ago
I don't know this biology very well, and I have been flummoxed by these terms.
For RefSeq annotations, we've traditionally mapped Cajal body-specific RNAs (http://rfam.xfam.org/family/RF00283) to INSDC 'guide_RNA', which in turn is mapped to SO guide_RNA (SO:0000602). INSDC used to not have a separate term for scaRNA, but now it does, so we should probably switch to using that.
Looking at INSDC submitted records, it looks like INSDC guide_RNA is used for CRISPR-related features (e.g. MH683611.1) and mitochondrion-related guide RNAs (FJ416603.1).
There's also SO sgRNA (SO:0001998), which is specific for CRISPR oligos.
So maybe the intent is SO guide_RNA is for biologically-occurring examples, and SO sgRNA is for CRISPR, and INSDC guide_RNA combines both? And with that logic, is it the case that CRISPR sgRNAs never really have genes, so it would be better to name SO:0001264 as guide_RNA_gene?
Proposed Actions:
Some relevant feedback from Zasha Weinberg: _guide_RNA is maybe an overarching term. I think the specific term "guide RNA" in the ontology spreadsheet refers to RNAs in mitochondria of I think trypanosomes that are antisense to mRNA and direct nucleotide insertions, deletions or changes. snoRNAs could also be considered to be guide RNAs to direct pseudouridylation/methylation, and one could make a case for CRISPR RNAs or miRNAs. If guide_RNA is kept as a top-level term, maybe its name could be altered to make it more specific, e.g., RNA_editing_guideRNA
@keilbeck Do you have any objections to @murphyte's list of proposed actions?
I like this RNA_editing_guide_RNA
Agree with the rest of @murphyte sensible suggestions.
Hi @keilbeck Just to clarify, are you suggesting: guide_RNA (SO:0000602) -> RNA_editing_guide_RNA and gRNA_gene (SO:0001264) -> RNA_editing_guide_RNA_gene ?
What is the SO term name and accession? gRNA_gene (SO:0001264)
Describe what you would like to change. Current def is "A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system."
Need to change start of this definition to say "A gene that encodes a..."
Also, is this term meant to be the corresponding 'gene' term to the ncRNA term 'guide_RNA (SO:0000602)' (that has synonym of 'gRNA')? But the definition of that term seems rather different: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA."
'guide_RNA' is an INSDC term, so maybe @murphyte has insights?