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The Ontology for Biomedical Investigations
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NTR: Genotyping by HiC #828

Closed jahilton closed 5 years ago

jahilton commented 7 years ago

editor preferred term: genotype phasing by HiC textual definition: An assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples definition source for the textual definition: https://www.ncbi.nlm.nih.gov/pubmed/19815776 (for HiC, but there is no publication yet on using this assay for genotyping) logical definition: genotyping assay --> genotype phasing by HiC, carbon-copy chromosome conformation capture assay followed by sequencing assay --> genotype phasing by HiC

(updated term name reflects a recent change by the lab)

jahilton commented 7 years ago

Here is another appropriate reference: https://www.nature.com/nbt/journal/v31/n12/full/nbt.2728.html

beckyjackson commented 6 years ago

Hi @jahilton - we recently added the term 'HiC assay' as OBI:0002440, with definition: "A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes."

I would guess this isn't specific enough for your use case, though, correct?

jahilton commented 6 years ago

Correct. We are looking for a child term to 'HiC assay' to specify using the technique for the purpose of genotyping.

beckyjackson commented 5 years ago

Term added as OBI:0002459 ('genotype phasing by Hi-C assay') in 984887b