Link to the C2M2 GitHub pages on https://github.com/MaayanLab/DRC-Portals/blob/main/drc-portals/app/info/standards/markdown/C2M2.md

[mano-at-sdsc]

The current description at

https://github.com/MaayanLab/DRC-Portals/blob/main/drc-portals/app/info/standards/markdown/C2M2.md

is great, and I suppose it is evolving. It will be useful to add a link to the page

https://github.com/nih-cfde/published-documentation/wiki/Quickstart where complete details of table columns, etc., can be obtained. After, April 1st, 2024, we can edit this relevant GitHub pages, e.g., https://github.com/nih-cfde/published-documentation/wiki/Quickstart as we see fit. For example, any links that take us to https://docs.nih-cfde.org should be pointed to a corresponding respective page on the new portal, e.g., https://info.cfde.cloud/info/standards/C2M2, or to a GitHub page such as https://github.com/nih-cfde/c2m2, or https://github.com/nih-cfde/published-documentation/.

[sxie04]

Hi @mano-at-sdsc I've updated the C2M2 Documentation on the portal to include the content from the original documentation pages, specifically the table descriptions. I opted not to include the Quickstart page which references the old submission pipeline, but please let me know if there is anything else you think is missing.

[mano-at-sdsc]

Hi @sxie04: Thank you. This is tremendous effort. Just some minor fixing:

1. At https://info.cfde.cloud/documentation/C2M2#c2m2-tables, the URL in the first item: All table files listed in this summary must be bundled together, along with the C2M2 datapackage JSON Schema file (https://osf.io/vzgx9/), to create a valid C2M2 datapackage for submission to CFDE, please replace it with the current https://osf.io/c63aw/ (listed in the section https://info.cfde.cloud/documentation/C2M2#resources ).
2. In the section https://info.cfde.cloud/documentation/C2M2#submission-prep-script : remove python from "python prepare_C2M2_submission.py". https://info.cfde.cloud/documentation/C2M2#general-steps step 6 lists the full command.
3. Reference tables (not part of the submission package): If not already somewhere, for our internal record, perhaps we can include a link to the Reference tables (which links to https://osf.io/m3a85/) as in the image below from the github.com/nih-cfde repo. We will have to change these if there were such an indication from the higher CFDE leadership.
4. In the section general steps: https://info.cfde.cloud/documentation/C2M2#general-steps: some URLs may need fixing:

• The first item is actually numbered 0. The link in "C2M2 Table wiki" is linked to github page. Do you want to link it to https://info.cfde.cloud/documentation/C2M2#c2m2-tables .
• The link for "Download the script": There seem to be more recent one (though I didn't check if it is indeed different): https://osf.io/7qdz4 as listed on the page https://osf.io/bq6k9/.
• Should we include step 5 (OPTIONAL: run the frictionless validator script) mentioned on the page https://github.com/nih-cfde/published-documentation/wiki/Building-a-datapackage. This step helped me quite a bit during 2020-21-22. I think it is better to list the frictionless commands the user needs to run (something similar to that listed on: https://github.com/nih-cfde/published-documentation/wiki/Quickstart#optional-frictionless) either here or elsewhere (e.g., the Tutorials or https://info.cfde.cloud/documentation/C2M2#resources sections).
• Just for completeness, add the submission step as well with link to the submission page.

[sxie04]

Hi @mano-at-sdsc I tried to address most of your comments in the latest deployment, with the exception of the 0-numbering at Submission Prep Script General Steps because this section is pulled directly from the original Wiki documentation.

[mano-at-sdsc]

Thank you very much, @sxie04 .

[mano-at-sdsc]

Hi @sxie04, Please see if this minor issue needs fixing: The ones which don't have _ in the file name. On pages https://info.cfde.cloud/documentation/C2M2/TableInfo:-file.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-project.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-biosample.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-collection.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-compound.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-dcc.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-disease.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-gene.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-phenotype.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-protein.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-subject.tsv
https://info.cfde.cloud/documentation/C2M2/TableInfo:-substance.tsv

e.g., the bold text appears as TableInfo%3A file.tsv [contains %3A, which appear as : colon].