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submission script prep documentation #358

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raynamharris opened this issue Apr 12, 2022 · 1 comment
Open

submission script prep documentation #358

raynamharris opened this issue Apr 12, 2022 · 1 comment
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documentation Improvements or additions to documentation

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@raynamharris
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The first step in the Usage section of the submission script prep wiki reads like this:

"0. First build your file.tsv, biosample.tsv, biosample_disease.tsv, biosample_gene.tsv, biosample_substance.tsv, subject_disease.tsv, subject_phenotype.tsv, subject_role_taxonomy.tsv, subject_substance.tsv, and collection_disease.tsv tables. (Some of these can be left empty (as header-only TSVs) if desired: see the C2M2 table wiki for requirements.)"

I find this first step to be a little confusing because all of the files listed can be left blank while none of the files that cannot be left blank are mentioned. Also, there is no link to the blank tsv files. To make what files can and cannot be left blank a little more explicit, can we reword this section to something like:

  1. Prepare the required id_namespace.tsv, project.tsv, and dcc.tsv files.
  2. Then, prepare the tsv tables for associating meta data with files, biosamples, subjects, etc. tsv files can be left blank if there is no relevant metadata. Download blank tsv files here. See the C2M2 Table Summary for requirements. (Make sure all id_namespaces in the tsv files are represented in the id_namespace.tsv mentioned above.)
@raynamharris raynamharris added the documentation Improvements or additions to documentation label Apr 12, 2022
@abradyIGS
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Agreed on clarity/confusion: I think the whole page could benefit from reconstitution. (By generous arrangement with @raynamharris) I'll draft a top-down rewrite within 24 hours and re-present for further evaluation.

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