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[ITR] BD Rhapsody Whole Transcriptome Analysis #127

Closed rachadele closed 1 year ago

rachadele commented 1 year ago

Source ontology identifier

EFO:0700003

Destination ontology

HCAO

Preferred term label

BD Rhapsody Whole Transcriptome Analysis

Synonyms

Textual definition

A BD Biosciences-based technology that sequences mRNA from the 3' end in an unbiased manner. [https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-Rhapsody-WTA-Amplification-Kit.pdf]()

Suggested parent term

EFO:0010186 single cell library construction

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 we needed the terms added?

willrockout commented 1 year ago

@rachadele @bvarner-ebi I searched for it on the OLS site under the HCAO ontologies and nothing came up. @bvarner-ebi is there another spot to be able to search the efo_slim?

ghost commented 1 year ago

Hi @willrockout, I don't believe any EFO term is found on OLS when just looking at HCAO. EFO terms are packaged separately in the HCAO release file in ontology/efo_slim.owl. That contains all the EFO terms that are part of the HCAO release.

If you download the release files and open the ontology/efo_slim.owl in Protégé or some other editor, you would be able to search that way.

rachadele commented 1 year ago

@bvarner-ebi thanks for clarifying!

rachadele commented 1 year ago

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

willrockout commented 1 year ago

@bvarner-ebi Thanks for the clarification. I think this is a case where 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 Whole Transcriptome Analysis' to be a child of 'single cell library construction' only

or

'BD Rhapsody Whole Transcriptome Analysis' 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 Whole Transcriptome Analysis' 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.