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📝 Review system thoeris

Reviewing thoeris : checklist

This is a guide to help you review an article of the wiki about the system thoeris. (If reading from you mail client, you can click on the link with the # above to go to the issue directly)

Link to all you issues : https://gitlab.pasteur.fr/mdm-lab/wiki/-/issues/?sort=updated_desc&state=opened&milestone_title=%3Atada%3A%20Hackaton%20%21&assignee_username%5B%5D=hshomar&first_page_size=20

The article for the system is there : https://defense-finder.pasteur.cloud/wiki/defense-systems/thoeris

[If it's slow, wait, it might fail (Time out from you browser), but you'll notice that :8080 has been inserted in the url, just remove it and reload the page. It's faster then to continue browsing from the website directly rather than opening another link, it's a bug we're aware of and we're tracking it]

You can find help here on how to edit : https://defense-finder.pasteur.cloud/wiki/help#_2-edit-a-page

Foud have further details here on what to do for each section : https://gitlab.pasteur.fr/mdm-lab/wiki/-/blob/main/helpers/system-template.md?ref_type=heads&plain=1

Please check that all the following criteria are met to consider that a page is complete and correct.

  • The article is correctly structured. It should contain :
    1. Header with the following fields (please pay attention to block indentation) --> /!\ This is not visible from the webpage, you need to edit it to see this part.
---
title: 
tableColumns: 
  article:
    doi: 
    abstract: 
  Sensor: 
  Activator: 
  Effector: 
  PFAM: 
contributors: 
  - Firstname Lastname
relevantAbstracts:
  - doi: my-doi
  - doi: my-doi2
---

  • The header contains all the required information. The information provided in the header is required to display the list of defense systems.

    • The mandatory fields are :
      • title:
      • tableColumns:
        • article:
          • doi:
          • abstract:
      • contributors
      • relevantAbstract
    • Optional fields are :
      • Sensor
      • Activator
      • Effector
      • PFAM
    1. The following paragraphs are in the correct order
      • Description
      • Molecular mechanisms
      • Example of genomic structure
      • Distribution of the system among prokaryotes
      • Structure (a plugin)
      • Experimental validation (a graph)
      • Relevant Abstract (Automatic)
      • References (Automatic)
    • Main title is correct. For a defense system, it should simply be the name of the system.
    • All the information is provided, correct and understandable. Rule of thumb : As a newcommer in the field, does the page provide the essential information in a clear way regarding the system ?
      • Short description of the system
      • Composition of the system
      • Mechanism of action if it is known
      • References to the literature to further explore the defense system,
      • inline references should have the following syntax : :ref{doi=my-doi}.
      • Distribution of the system among prokaryotes
      • Structure display
    • At least one relevant abstract is provided. (see frontmatter)
    • Old syntax is removed, eg:
      • There should not be any section ## Relevant abstract (with items and doi below), it's now automatic
      • Reference in the text shouldn't be (1) or (Toto et al) but :ref{doi=my-doi} It will be automatically replaced

You can create a Merge request at any time and continue working on it later

In your MR message, link it to this issue #273 (closed)

Edited by hshomar