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Ontology term request for bulk ATAC-Seq #98

Closed ami-day closed 2 years ago

ami-day commented 2 years ago

Preferred term label

ATAC-seq

Synonyms

Textual definition

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. The ATAC-Seq method relies on next-generation sequencing (NGS) library construction using the hyperactive transposase Tn5.

Suggested parent term

library preparation http://purl.obolibrary.org/obo/OBI_0000711

Use case

library construction method ontology term (library preparation protocol schema)

paolaroncaglia commented 2 years ago

Hi @ami-day , Commenting briefly as I'm in the middle of something else, but it looks like the existing term EFO:0007045 ATAC-seq would fit your need? It's a child of DNA-seq, and descendant of assay by molecule and assay by sequencer.

paolaroncaglia commented 2 years ago

@ami-day It's also in the EFO HCA subset, see here.

paolaroncaglia commented 2 years ago

@ami-day Would you strictly need the parent 'library preparation' to be added to the existing ATAC-seq term in order to be able to use it?

ami-day commented 2 years ago

Hi @paolaroncaglia yes exactly, the existing term is not working for me because the parent is not 'library preparation'. Would it be possible to add it?

paolaroncaglia commented 2 years ago

@ami-day I think so, there are other terms in the 'library preparation' branch that are also descendants of 'assay'. I'll do the edit in EFO in time for the next EFO release (Feb 15th), and it will then percolate to the HCA ontology, and be visible after the next HCAO release (Feb 16th). EFO ticket: https://github.com/EBISPOT/efo/issues/1437

paolaroncaglia commented 2 years ago

Hi @ami-day , ATAC-seq is now (also) a child of 'library preparation'. The change will be in the EFO release scheduled for Feb 15th, and will then be imported in the HCAO release the following day.