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 TruDrop #1759

Closed jychien closed 2 years ago

jychien commented 2 years ago

Preferred term label

TruDrop

Synonyms

TruSeq-inDrop

Textual definition

A droplet-based microfluidic library construction platform based on inDrop that incorporates dual-indexing to detect index hoping and standard Illumina sequencing primers for high-throughput sequencing.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06843-0

Suggested parent term

Parent terms should be comparable to what inDrop has as parents:

"TruDrop" has_part "inDrop" (EFO:0008780)

ghost commented 2 years ago

Thanks for the new term request, @jychien. Can you confirm "index hoping" should be "index-hopping" in the text definition?

Could you have a look at the conversation at https://github.com/HumanCellAtlas/ontology/issues/118 and advise if this new term really should be a subclass of 'RNA assay'?

jychien commented 2 years ago

@bvarner-ebi Oops! Yes, I meant "index-hopping". Thanks for catching that.

As for parent terms, I was mirroring where inDrop is currently in the ontology tree. Thank you for linking to the updated discussion. For our needs at CELLxGENE, the assay can be either a child of "assay by molecule" (EFO:0002772) or "single cell library construction" (EFO:0010183). So, we would be fine if you want to drop "RNA assay" as parent.

ghost commented 2 years ago

Hi @jychien, your new term has been added to EFO and will appear in the next release. You can refer to the linked PR to view the specific edits.

EFO:0700010 'TruDrop'