Preparation of v1.0 release

[strambc]

To do for v1.0 release

• [x] Add a section to the left-TOC entitled: "Allowable value lists" for all relevant fields

• • [ ] Units (##XYZ_unit, Time_unit, Intensity_unit)
• • [ ] Cell_Type, Sub-Cell_ROI_type, Extra-Cell_ROI_type etc.

• [ ] For all tables containing only an ID column and OptionalColumn(s) (i.e., bio, rna_bio, quality, rna_quality, trace, cell, subcell, extracell, mapping) : add the following statements:

• • [ ] .rst, "The table MUST contain at least 1 optional column.'
• • [ ] template, "#^Optional_column_1: [substitute with your column header; the presence of at least 1 optional column is MANDATORY if this table is submitted]
• • [ ] table/header: "Conditional requirement: this table MUST contain at least 1 Optional Column."

• [ ] Check all Mandatory, Conditionally Required and Optional table statuses (there are discrepancies between the summary table and the text entered in the .rst)

• [x] Add credit to Figure 1 (Sarah Aumfkolk)

• [x] Add credit to Figure 2 (VCF PDF)

• • [ ] remove "Fig.3" legend from figure

• [x] Something wrong with references to rna_bio and rna_quality references in the Summary table

• [x] Something wrong with the order of tables in the Summary table

• [x] Add a Section listed in the left-TOC entitled "How to use the Templates"

• • [ ] Add content to section

• [ ] Move examples at the end of each Table section (below Header and Columns)

• [ ] Add a note on top of each Example table stating explicitly that the columns in the table are example allowable columns but not mandatory

• [ ] On top of each table-header and table-column put a reference to relevant overview's paragraph to remind people about the meaning of the symbols

• [ ] On top of table.column add BOLD = REQUIRED

• [ ] Trace_ID in RNASPOT has to be mandatory

• [ ] All RNA, Table, Cell, SubCell, ExtraCell, and Trace will be set to RECOMMENDED

• [ ] MAKE the following fields MANDATORY

• • [ ] #lab_name, #experimenter_name, #experimenter_contact, #description

• [ ] Add a section "Examples and Available datasets"

• • [ ] Move available datasets links from miscellaneous to this section
• • [ ] Add references to 4DN data portal and IDR

• [ ] Rename "Miscellaneous" to "Additional Information"

[strambc]

• [ ] Optional_column has to have capital "O"

[strambc]

• [ ] Change cell description to include the possibility of reporting MESH structures for segmentation results

[RahiNav]

Completed some of the tasks mentioned. @strambc please take a look

[strambc]

Thank you. I have seen your changes. I have suggested some more. I will be able to be back on this job starting from next week. C

From: Rahi Navelkar @.> Date: Tuesday, June 25, 2024 at 04:16 To: 4dn-dcic/fish_omics_format @.> Cc: Strambio, Caterina @.>, Mention @.> Subject: Re: [4dn-dcic/fish_omics_format] Preparation of v1.0 release (Issue #38)

Completed some of the tasks mentioned. @strambchttps://github.com/strambc please take a look

— Reply to this email directly, view it on GitHubhttps://github.com/4dn-dcic/fish_omics_format/issues/38#issuecomment-2187240851, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA645GIK327TQKDYEFSB65LZJBWBHAVCNFSM6AAAAABJORPZCSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGI2DAOBVGE. You are receiving this because you were mentioned.Message ID: @.***>