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The Ontology for Biomedical Investigations
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circulome-seq term #872

Open jahilton opened 6 years ago

jahilton commented 6 years ago

Since the inclusion of OBI:0002144, the lab has posted a publication referencing circulome-seq. http://www.g3journal.org/content/ggg/early/2017/08/11/g3.117.300141.full.pdf

Do you think it would be appropriate to add 'circulome-seq' as a synonym to the existing term or more appropriate to create a new term underneath it?

The distinction, if we were to make one, is in the DNA enrichment, so the definition might be... An extrachromosomal circular DNA sequencing assay which utilizes a combination of biophysical (CsCl) and enzymatic (ExoV) approaches for circular DNA enrichment, followed by Tn5 tagmentation allowing library construction from a very low quantity of input material and providing informatic advantage at analysis stages of the sequencing data.

bpeters42 commented 6 years ago

My gut feeling: Adding it as a synonym might be more useful in practice; too fine distinctions tend to not get used and/or confused. But I am not expert in this field.

On Mon, Nov 6, 2017 at 4:59 PM, jahilton notifications@github.com wrote:

Since the inclusion of OBI:0002144, the lab has posted a publication referencing circulome-seq. http://www.g3journal.org/content/ggg/early/2017/08/11/ g3.117.300141.full.pdf

Do you think it would be appropriate to add 'circulome-seq' as a synonym to the existing term or more appropriate to create a new term underneath it?

The distinction, if we were to make one, is in the DNA enrichment, so the definition might be... An extrachromosomal circular DNA sequencing assay which utilizes a combination of biophysical (CsCl) and enzymatic (ExoV) approaches for circular DNA enrichment, followed by Tn5 tagmentation allowing library construction from a very low quantity of input material and providing informatic advantage at analysis stages of the sequencing data.

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-- Bjoern Peters Associate Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

jahilton commented 6 years ago

That was my feeling as well because the goal & general method is the same.

bonitalam commented 4 years ago

Hello, have there been any updates on adding Circulome-seq as a synonym for OBI:0002144?

DanBerrios commented 4 years ago

Discussed on call. The value to users can first be addressed by simply making this an alternative term. We could subclass it later if requested. Also, could add that both classes/terms output DNA Sequence data and therefore are DNA Sequencing Assays.

bonitalam commented 4 years ago

Currently, Circulome-seq doesn't appear under DNA sequencing assays and is under the broader "assay" class. Can we have it under the DNA sequencing assay class?

turbomam commented 4 years ago

Apolgies, @bonitalam . I'm surprised you see 'Circulome-seq' as an alternative term for extrachromosomal circular DNA sequencing assay already. I added it, but not via the optimal route (an assay template), so thought it hadn't been pushed to a release. I'm going to fix that now and reclassify extrachromosomal circular DNA sequencing assay as a DNA sequencing assay, instead of assay

@DanBerrios @jamesaoverton Since we were talking about the placement of nucleotide sequencing assays on Monday #1098, do you want to review this?

see also original request #830