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[ITR] BD Rhapsody Targeted mRNA #128

Closed rachadele closed 1 year ago

rachadele commented 1 year ago

Source ontology identifier

EFO:0700004

Destination ontology

HCAO

Preferred term label

BD Rhapsody Targeted mRNA

Synonyms

Textual definition

A BD Biosciences-based technology that utilizes multiplex PCR to sequence mRNA from the 3' end of specific genes from a predetermined panel. [ https://scomix.bd.com/hc/en-us/articles/360023293851-Targeted-mRNA-Protocols https://www.bdbiosciences.com/en-us/products/reagents/single-cell-

Suggested parent term

single cell library construction EFO:0010183

Use case

to be used in library preparation protocol schema

Attribution

0000-0002-7431-4139

ghost commented 1 year ago

Hi, @rachadele, thanks for the ticket. This term appears in efo_slim.owl, which is part of the HCAO release. Can you clarify if something is missing?

rachadele commented 1 year ago

@willrockout can you help clarify why you thought it wasn't in HCAO?

willrockout commented 1 year ago

@rachadele @bvarner-ebi Same as my other comment searched HCAO for the term nothing came up.

rachadele commented 1 year ago

@bvarner-ebi thanks for clarifying!

rachadele commented 1 year ago

this term causes an ingest error: .library_construction_method.ontology : Provided term is not child of [http://purl.obolibrary.org/obo/OBI_0000711]

willrockout commented 1 year ago

@bvarner-ebi Similar to the other I think we need this term moved under EFO:0010183 single-cell library construction.

ghost commented 1 year ago

@willrockout, can you confirm which option you are requesting:

'BD Rhapsody Targeted mRNA' to be a child of 'single cell library construction' only

or

'BD Rhapsody Targeted mRNA' to be a child of 'single cell library construction' and 'single-cell RNA sequencing'

willrockout commented 1 year ago

@bvarner-ebi I think it should be moved under 'single cell library construction' only as the protocol is a library construction and doesn't include the sequencing step which is stated in the definition for single-cell RNA sequencing.

ghost commented 1 year ago

@rachadele, @willrockout,

Thank you again for this ticket. 'BD Rhapsody Targeted mRNA' has been added as a subclass under 'single cell library construction' and removed as a subclass from 'single-cell RNA sequencing' via PR https://github.com/EBISPOT/efo/pull/1938.

This change should be reflected in the next EFO and HCAO releases.