EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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New EFO terms with missing definitions #825

Closed anjaf closed 4 years ago

anjaf commented 4 years ago

Dear EFO team,

This is regarding the new EFO terms that Ola created for the Expression Atlas curation team a while ago (see https://github.com/EBISPOT/efo/issues/545). While reviewing those, I discovered a few terms have their definition missing or the wrong one. It would be great if you can add/update those.

Definition to be added:

Term label Definition
inferred cell type A cell type classification that is determined as result of a single-cell analysis, such as cell clustering or trajectory analysis.
single cell identifier A unique identifier for a single cell specimen.
random An oligonucleotide primer with random sequence.
UMI barcode read The sequencing read that contains the UMI barcode.
UMI barcode offset The offset in the sequence where the UMI barcode starts.
UMI barcode size The length of the UMI barcode.
cell barcode read The sequencing read that contains the cell barcode.
cell barcode offset The offset in the sequence where the cell barcode starts.
cell barcode size The length of the cell barcode.
sample barcode read The sequencing read that contains the sample barcode.
sample barcode offset The offset in the sequence where the sample barcode starts.
sample barcode size The length of the sample barcode.

Definition needs correction:

Term label Correct definition
cell barcode A short nucleotide sequence that is added during a single cell library preparation to identify reads from an individual cell.
zoependlington commented 4 years ago

Thank you @anjaf, I will make sure these definitions are added/changed before our August release.

zoependlington commented 4 years ago

These are now updated/added and will be available at our next release. Please let me know if there are any issues.

anjaf commented 4 years ago

Thank you @zoependlington!