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Re-evaluate readPairOrientation, readStrandOrigin #138

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allaway opened this issue Apr 13, 2022 · 1 comment
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Re-evaluate readPairOrientation, readStrandOrigin #138

allaway opened this issue Apr 13, 2022 · 1 comment
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@allaway
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allaway commented Apr 13, 2022

Describe the issue with the metadata

As written, the definitions for these two are somewhat confusing. One of the valid values for readPairOrientation is fr-firststrand which is actually a combination of both readPairOrientation and readStrandOrigin.

This blog post has a nice summary: https://littlebitofdata.com/en/2017/08/strandness_in_rnaseq/

I think that we could actually combine these two terms into one to simplify data entry for annotators and to also make these more useful for processing - ultimately, data users want to know what strandedness setting to use in their software of choice, and it's easier to provide a straightforward annotation instead of a multiple of terms that they'll have to interpret.

HTAN (which I believe adoped from GDC) use this, which pairs nicely with the potential options for strandedness that one might select:

term: Library Strand
definition: Library stranded-ness. (OK, this could be more specific)
values: Unstranded, FirstStranded, SecondStranded, NotApplicable
@allaway allaway added bug Something isn't working schema labels Apr 13, 2022
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allaway commented Apr 13, 2022

can add isStranded to this review too, for the same reason.

@anngvu anngvu removed the schema label May 9, 2023
@anngvu anngvu moved this to In Progress in NF-OSI Sprints Sep 3, 2023
@anngvu anngvu self-assigned this Sep 3, 2023
anngvu added a commit that referenced this issue Sep 5, 2023
@anngvu
Address issue #138
2db75d6
@anngvu anngvu mentioned this issue Sep 8, 2023
Merged
anngvu added a commit that referenced this issue Sep 22, 2023
@anngvu @nfosi-service
Feat/advanced templates (#342)
b995e81 
* Remove obvious notes, lint, define add'l props

* Address issue #138

* Resort and refactor templates (wip)

* Update supplemental prop

* Refine (wip)

* Add header

* Define some assay constraints (wip)

* Update some assay descriptions

* Define more relationships of templates to assay

* Update test to use local config when present

* Add more HTAN mappings

* More mappings

* Revise new prop

* Update matching to assay or datatype

* Fill in descriptions, lint

* Don't run tests on draft PR

* Various ugprades (wip)

* Update data definition

* Split up templates

* Clarify and lint some assays

* More revisions

* Update base props

* Keep tests

* Revert ci

* Build jsonld

* Test with schematic v23.9.1

* Lint

* Build jsonld

* Various fixes and refinements

* Build jsonld

* Update config in tests/validate as well

* Make required

* Update validation tests

* Build jsonld

* Fix test config

* Add notes and optional asset link

* Build jsonld

* Update test expectation

* Allow auxiliary links in more places

* Build jsonld

* Remove pre-split file

* Uncomment

* Build jsonld

* Update strandedness, HTAN-style, and update tests

* Build jsonld

---------

Co-authored-by: nf-osi[bot] <nf-osi@sagebionetworks.org>
@anngvu anngvu closed this as completed Oct 19, 2023
@github-project-automation github-project-automation bot moved this from In Progress to Done in NF-OSI Sprints Oct 19, 2023
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