ghost
commented
1 year ago Thank you for the ticket, @Wkt8.
Regarding EFO:0010022 Smart-3Seq:
- "Smart-seq3" was added as an exact synonym with https://www.biorxiv.org/content/10.1101/2022.02.14.480352v1.full and your ORCiD added as references
- EFO:0010184 Smart-like was added as a parent class
This work is reflected in https://github.com/EBISPOT/efo/pull/1913 and should be present in the next EFO release.
Source ontology identifier
EFO:0010022 Smart-3Seq
Destination ontology
The term already exists in the HCAO, but hierarchically it is under: experimental process -> assay -> assay by molecule -> RNA assay -> Smart-3Seq
To fulfil our metadata hierarchy restrictions we need it to hierarchically be under library preparation: OBI:0000711
Ideally under: Smart-like EFO:0010184
Preferred term label
Smart-3Seq
Synonyms
Smart-seq3
Textual definition
As per (https://ontology.archive.data.humancellatlas.org/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0010022) the definition is:
Method that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. Modified 3Seq method - omitted poly (A) enrichment and replaced dsDNA ligation with template-switching cDNA synthesis
Suggested parent term
Smart-like EFO:0010184
Use case
When the paper says that they use Smart-seq3 as a library preparation method (e.g. https://www.biorxiv.org/content/10.1101/2022.02.14.480352v1.full)
Attribution
0000-0002-6583-8504