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polyA+ & polyA- RNA-seq distinctions #863

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jahilton opened this Issue Sep 11, 2017 · 7 comments

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jahilton commented Sep 11, 2017

Hello,
The ENCODE project is exploring how to distinguish various RNA-seq assays, including those that involve steps in the protocol to enrich, or deplete, polyAdenylation. Would these be appropriate terms?

editor preferred term: polyA-selected RNA sequencing assay
alternate terms: polyA RNA-seq, polyA mRNA RNA-seq, mRNA-seq
textual definition: An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing.
definition source for the textual definition: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419
logical definition: RNA-seq assay --> polyA RNA-seq

editor preferred term: polyA-depleted RNA sequencing assay
alternate terms: polyA-depleted RNA-seq
textual definition: An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing.
definition source for the textual definition: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733, http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676
logical definition: RNA-seq assay --> polyA-depleted RNA-seq

Thanks!

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turbomam Apr 26, 2018

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Hi, Jason. This is a good request. I'd like to discuss it during the OBI phone call at noon EDT on this Monday, April 30th. I assume the group will approve it, but I'll be suggesting that we follow some OBI templates and define these assays in terms of what their specified input is. That may require creating a few additional terms (which may or may not interest you.)

Would you be willing to join the call to make sure your needs and perspective are understood?

see http://obi-ontology.org/#contact-us

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turbomam commented Apr 26, 2018

Hi, Jason. This is a good request. I'd like to discuss it during the OBI phone call at noon EDT on this Monday, April 30th. I assume the group will approve it, but I'll be suggesting that we follow some OBI templates and define these assays in terms of what their specified input is. That may require creating a few additional terms (which may or may not interest you.)

Would you be willing to join the call to make sure your needs and perspective are understood?

see http://obi-ontology.org/#contact-us

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jahilton Apr 27, 2018

Yes, I think the ENCODE DCC will have some representation on next week's call.
Thank you.

jahilton commented Apr 27, 2018

Yes, I think the ENCODE DCC will have some representation on next week's call.
Thank you.

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turbomam Apr 30, 2018

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I just noticed that you have several additional term requests, all from mid to late 2017. I'll try to orient myself regard the others, in case you or a colleague want to go over them, too.

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turbomam commented Apr 30, 2018

I just noticed that you have several additional term requests, all from mid to late 2017. I'll try to orient myself regard the others, in case you or a colleague want to go over them, too.

@turbomam turbomam self-assigned this Apr 30, 2018

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turbomam Apr 30, 2018

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OBI has related terms using at least two notations: " polyA..." and "poly(A)..."

Should we make these consistent?

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turbomam commented Apr 30, 2018

OBI has related terms using at least two notations: " polyA..." and "poly(A)..."

Should we make these consistent?

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turbomam Apr 30, 2018

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For the assays that take RNA enriched for poly adenylation, we could say that the specified input is Class: 'polyA RNA extract', http://purl.obolibrary.org/obo/OBI_0000869 (or that eh assay has polyA RNA extraction as one of its parts?)

BTW, the parent class, 'RNA-seq assay' is http://purl.obolibrary.org/obo/OBI_0001271

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turbomam commented Apr 30, 2018

For the assays that take RNA enriched for poly adenylation, we could say that the specified input is Class: 'polyA RNA extract', http://purl.obolibrary.org/obo/OBI_0000869 (or that eh assay has polyA RNA extraction as one of its parts?)

BTW, the parent class, 'RNA-seq assay' is http://purl.obolibrary.org/obo/OBI_0001271

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turbomam May 11, 2018

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...selected assay: OBI_0002571
...depleted...
extraction: OBI_0002574
extract: OBI_0002573
assay: OBI_0002572

@jahilton would you be willing to help me find definitions or examples of use for polyA depleted extraction, extract and sequencing assay?

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turbomam commented May 11, 2018

...selected assay: OBI_0002571
...depleted...
extraction: OBI_0002574
extract: OBI_0002573
assay: OBI_0002572

@jahilton would you be willing to help me find definitions or examples of use for polyA depleted extraction, extract and sequencing assay?

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turbomam May 14, 2018

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New issue? Single cell RNAseq as a new term? Includes special preparative steps and special analytical steps.

General issue... how far to go with pre-composition?

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turbomam commented May 14, 2018

New issue? Single cell RNAseq as a new term? Includes special preparative steps and special analytical steps.

General issue... how far to go with pre-composition?

turbomam added a commit that referenced this issue May 21, 2018

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