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The Ontology for Biomedical Investigations
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NTR: amplicon sequencing #1098

Closed AlexandraPhil closed 1 year ago

AlexandraPhil commented 4 years ago

NTR: amplicon sequencing Defn: Amplicon sequencing is a highly targeted approach that enables researchers to analyze genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification and characterization (Source: Illumina https://emea.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/amplicon-sequencing.html) Subclass_of: DNA sequencing

I noticed that amplicon sequencing exists in EFO: http://www.ebi.ac.uk/efo/EFO_0003747 This would be a good one to import, perhaps?

jamesaoverton commented 4 years ago

Discussed on the 2020-01-13 OBI developer call.

OBI does not import terms directly from EFO -- it usually works the other way around. OBI can add a new term.

The EFO definition is simple but seems good: "An assay in which a DNA or RNA input molecule amplified by PCR is sequenced."

We think that OBI the parent would be the more general 'sequencing assay'. This term belongs in our assays.tsv template file.

Is there a methods paper we could cite for this assay? PubMed or Wikipedia would be better for our purposes than Illumina.

mgiglio99 commented 4 years ago

Hello, @nsuvarnaiari and I would like to check on the progress of this term as we have a need for such a term in our work.

Here is a slight tweak of the suggested definition from EFO: "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced."

Two papers you could cite are: PMID:29628929 - which uses the technique for genotyping PMID:31450270 - which uses the technique for microbiome analysis

Is there anything else this term needs?

Thanks, Michelle

mgiglio99 commented 4 years ago

This was discussed on the June 15 call. The amplicon term will be made as defined above. It will be part of the assay template update in https://github.com/obi-ontology/obi/issues/1178.

Also note: We will make NTR '16S ribosomal gene sequencing' an asserted child of this term. We will make 16S an inferred child of 'taxonomic diversity assessment by targeted gene survey' Will need to make equivalence axiom for 'taxonomic diversity assessment by targeted gene survey'.

jamesaoverton commented 1 year ago

'amplicon sequencing assay' http://purl.obolibrary.org/obo/OBI_0002767