:pencil: Review system abij
# Reviewing abij : checklist
This is a guide to help you review an article of the wiki about the system abij.
(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=hvaysset&first_page_size=20
The article for the system is there : https://defense-finder.pasteur.cloud/wiki/defense-systems/abij
[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.
```yaml
---
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`
2. 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 #196
issue