search

miRTop / mirGFF3

GFF3 format with miRNA and isomiR information from sequencing data
14 stars 6 forks source link

Remove miRNA_ref #3

Open lpantano opened 6 years ago

lpantano commented 6 years ago

Hi all,

we are discussing whether to remove miRNA_ref from the type column and use always isomiRs, and if the reference was used to annotate it, just leave Variant as NA.

Any inputs on this?

xbdr86 commented 6 years ago

But, wouldn't that conflict with the gene ontology definition of miRNA_ref and isomiR, since isomiR it's by definition a modification of one or multiple ref_miRNA?

Otherwise, we could go for the parental category of miRNA SO:0000276, but to me that looks like losing a valuable annotation. http://www.sequenceontology.org/miso/current_svn/term/SO:0000276

ThomasDesvignes commented 6 years ago

That's kind of tricky indeed. Originally we defined the isomiRs as variants of a miRNA_ref so that we could have a base to compare it to and at the same time set, arbitrarily, one isomiR as a standard. I would think that we need to keep this information somewhere.

lpantano commented 6 years ago

Thank for chime in, I think we can leave for now, and se how things go when we have more experience on this.