a feedback question from Kim Pruitt(NCBI) #12
Description
I shared the GA4GH Experiments Metadata checklist Open-for-Comment period with the rest of the INSDC Experiments Metadata minimal specifications group.
Question from Kim Pruitt of NCBI (she said that I can share)
Has there been any discussion as to whether single-cell transcriptomics should be called out as an additional category? What about things like epitranscriptomics (chemical modifications of RNA molecules) which is another purpose of sequencing.
Answer from Peter
No not yet. Thanks for asking, good points. Is it okay to share those (with the GA4GH team) alongside the feedback we have had from others?
We had focused on core attributes and that took far longer than anticipated.
I think you are right, we are going to have a plethora of additional categories. David B( the co-lead) invited HCA to talk with us two months ago, they have just been going through an overhaul of their metadata - they are keen to keen to work with us on the sequencing experiment metadata. Just for single-cell transcriptomics, the ArrayExpress people have provided some input too - we need to go though that in detail. The COPO(Earlham Institute) have single-cell genomics data.
Epitranscriptomics has not come up at all, to my knowledge. But yes, the scope going to have cope with all sequencing.
I had been working through metadata needed on the “targeted sequencing” and then picked on metabarcoding and exome sequencing experiments, and the extra important metadata needed for those was mainly different. It did help the the core metadata is fairly solid now, so we can mainly focus on the specialist metadata for different types of omics.