search

EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
56 stars 13 forks source link

New term request for gRNA-seq #1267

Closed Jfortin1 closed 3 years ago

Jfortin1 commented 3 years ago

For new term requests, please provide the following information:

Preferred term label

gRNA-seq

Synonyms

gRNASeq, gRNA-Seq, grnaSeq, grna-seq, grna-Seq

Textual definition

Amplicon sequencing of gRNAs from CRISPR pooled genetic screens. PMID: 24336571

Suggested parent term

EFO:0003747 (Amplicon sequencing) EFO:0001456 (DNA assay)

Attribution

ORCID id: 0000-0001-9328-3852

paolaroncaglia commented 3 years ago

Dear @Jfortin1 ,

Thank you for your request. Could you please provide your ORCID iD if you have one, as a way of attributing new EFO terms to their submitters? Also, if applicable, could you please indicate one or more references for gRNA-seq (e.g. PMIDs of articles that describe the technique and/or its application in a given study). We'll then aim at including the new term in the next EFO release, scheduled for Oct. 18th, and will post the new term ID here when ready.

Best,

Paola Roncaglia

Jfortin1 commented 3 years ago

Updated, thanks!

paolaroncaglia commented 3 years ago

@Jfortin1 thank you!

paolaroncaglia commented 3 years ago

@Jfortin1 You requested 'gRNA-seq' ("Amplicon sequencing of gRNAs from CRISPR pooled genetic screens."), with PMID:24336571, and suggested EFO:0001456 'DNA assay' as one of the parent terms. May I please confirm that the term label should indeed be 'gRNA-seq' (the paper quotes _s_gRNA throughout) and the parent term 'DNA assay' (the suggested definition and the paper point to RNA molecules). I didn't have time to read the paper in detail though. Thanks. Paola

paolaroncaglia commented 3 years ago

@Jfortin1 The new term is EFO_0030033 (gRNA-seq). I added "sgRNA-seq" as an exact synonym, and made the term a subclass of 'RNA assay'. The term will be available after the EFO release scheduled for Oct 18th.

Jfortin1 commented 3 years ago

@paolaroncaglia Hi Paola, it should be DNA assay and not RNA assay (the amplicon sequencing is performed on the gRNA integrated into the cell genome, so the sequencing is done on genomic DNA).

paolaroncaglia commented 3 years ago

@Jfortin1 Thanks, this is fixed now. The change will be visible in the next EFO release, scheduled for Nov 15th.