Crete new documentation for WikiPathways reviewers that will replace the QA protocol. Documentation needs to describe how the new process of GH PRs work, the reviewers role, and the steps. This will eventually include a sandbox-style repo where reviewers can try things out.

• Slides
• Video
• Test repo

The bidirectional arrow between dimethylallylpyrophosphate and isopentenyl pyrophosphate in WP3917 has "Arrow" instead of "mim-conversion" one the start line type.

Tasks to be updated:

• https://academy.wikipathways.org/stages/task-recent-changes/
• https://academy.wikipathways.org/stages/task-under-construction/
• https://academy.wikipathways.org/stages/task-curated/

Even though the process for QA will change in the near future, minor updates now could still be useful, and could also be translated into other documentation later on.

Add an intro stage before "Advanced" track, since the transition from the previous track (Setting pathway information free) is abrupt and seems out of order.

See also edits made by Eric Weitz; perhaps combine with adding PW ontology?

QA tasks that are specific to new.wikipathways.org should be in a new track, which will eventually be expanded once the migration is complete.

Tasks:

• Send email in response to notifications in the new-users Slack channel. These are not really new users, but rather users who's pathways/edits have been included in the Approved collection for the first time (i.e. new to GitHub). Email template.

As discussed in the Curator's meeting, we need a full outline of when to use the different mim interaction types. This could be a table (for example) in the PathVisio "Book", which is then linked to (or recreated) in the Academy.

Add a step to email all new registered users (we used to do this by comment on Talk page but that doesn't work). Message should be:

• General onboarding tips
  - Let them know we are migrating to new platform

Add stage for illustrating adding Rhea IDs to metabolic conversions in Advanced Modeling track

From a curation report issue, how to best model protein families in pathways. Either use Pfam id on a single node representing the protein family, or list out all members of the protein family (if feasible).

Suggestion from Curators meeting (Freddie):

[paraphrased]
"The Academy doesn't describe explicitly how to transcribe a statement (sentence) in a paper or other source into a reaction in WikiPathways. This should be described in detail in either the first step of the blue path, or a new step".
Comment by KH: The language in subsequent steps describing modeling should be updated appropriately.

https://academy.wikipathways.org/path.html

From the Curator's meeting:

"One of the problems that people have with drawing pathways is still how to connect interactions." -> maybe this can be explained better with a short video.

Example: https://new.wikipathways.org/pathways/WP1539.html#gsc.tab=0 (see the Cited In section)

Tasks:

• Go through PMC listing to see if it looks like any particular pathways are highlighted, for example:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9530846/figure/fig5/
Mentions: WP1269 and WP447

• Then go to those pages on the new site and click on the edit icon for Cited In to add the new entry. Click 'Commit Changes’ and the site will rebuild.

Validation of some gpmls doesn't work, some of the problems include:

• interactions
• states (phosphorylation)

Note: This won't be fixed until the next version of gpml is ready

This is a list of updates/additions to the weekly QA protocol that could be useful (or are necessary) when the site is switched over to the Jekyll site.

For the transition period when both sites are live (Jekyll site is primary):

1. Idea: Add a step at the beginning of the QA track to:

• explain that pathway edits are reviewed on the "classic" wiki site, and not on the Jekyll site (to avoid confusion)
• ask curators to perform the Update Approval tags multiple times during the week, mainly minimize the delay for users to see their recent edit on the new site. Also this behavior is more similar to what will be expected of the weekly curators once everything works through Github.
• We could even switch the order of tasks so that the Update Approval tags task comes first.

When "classic" site is retired and edits happen directly at GitHub:

2. Updates to QA additional tasks:

• Test search: update for Jekyll site, or remove if not needed.
• Pathways for deletion: Update to reflect how delete works on Jekyll site, or remove if not needed.
• Instructions for passing the torch: update how to find who's next in the rotation

See paper on annotating omics databases with sex specific information (and in passing age and ethnicity is also mentioned).

ECO doesn't seem to have terms for this, I used the following keywords:

• female, male, gender, sex
• ethnicity, race, Caucasian, African
• age, time

There is one section on species:

I've tried to find other ontologies describing the above, but to no success... So, in order to structure this information in the future in the GPML2021 scheme, I think we should contact the ECO people and ask them to include terms for sex,age and ethnicity annotations.

http://academy.wikipathways.org/stages/walk-install-pv/ describes how to install the BridgeDB plugin, but not the database. It allows searching for Gene names, but protein names give an error if the database is not installed. See https://docs.google.com/document/d/14Qe54Eb-Yz3RfLLDnBV3tRNwX0PcJOX5OLUknSMINzU/edit for details on installation.

Add stage for illustrating phosphorylation to the Advanced Modeling track.

Should include when to use and also how to convert an interaction to a graphical line in the cases where an author didn't use a graphical line but should have.

Add better instructions for how to add ontology tags to new pathways

Some pathways have no quality tags at all, and are therefor difficult to find and are essentially orphaned pathways. The idea is to create a js task to look for these tasks, going back 60 days.

Hi guys,

One of our new colleagues at BiGCaT just discovered that the academy is not functioning properly.

If you click in this website on "launch editor", you get the following(If you click in the pop-up menu on download
):

It happens for more pages when you need to get the jnlp webversion of PV running....

I've checked the general drag and drop for jpml from local pathvisio, that works and provides me with this:

So people can still use the Academy (but it doesn't look so user friendly when at the first real practise you get an error message). I've contacted @nunogit about this as well .

Placeholder for updates to multiple steps, outlined in WikiPathways QA Protocol Overhaul doc.

The path.html page that contains the draw.io diagram can't be reloaded in Firefox. The page loads fine on the first try, but subsequent attempts to load the same page (in the same tab) results in a js error.

As noted by Freddie in the Weekly Curation report, the feed for Under Construction pathways is currently broken and just doesn't load any pathways. Here's what I've tested and my conclusions.

Here's the error from web service UI:

1. Under Construction list on classic shows 3 pathways, and removing these three does NOT fix the issue.
2. The list of Tutorial pathways shows 7 pathways, but a web service call returns 11 pathways. The 11 include the 7, plus another 4 that are in fact also tagged as Tutorial/Test (confirmed on classic).

So, there are probably other pathways on classic with the Under Construction tag, and maybe one of them is messing up the feed in the Academy. Potential solutions:

• Identify the full list of Under Construction from the database and fix the issue
  OR
• Remove the feed in the Academy and instead point directly to the Under Construction list.

Not sure how important this is to fix since its on the classic site. Worst case scenario is we will miss some legitimate pathways.

Instead of presenting curators with a long list of pathways that need help, add a task to the weekly curation where curators can sign up for a specific pathway that needs work. The task would describe the process and link to a spreadsheet where admins have already pre-selected a set of top-priority pathways representing a variety of processes and biology, where curators can self-assign one pathway.

See notes from Feb 8 Community Curation meeting.

We currently provide a counter for content tagged, e.g., "4 pathways remaining". In cases like Under Construction, it's often appropriate to complete the task and leave 4 pathways with the tag. It would be nice to improve the counter to also track pathways viewed (or yet to be reviewed), e.g., "3 of 4 remaining pathway to be reviewed".

Not sure how to implement this with current load/display/count logic...

E.g., for unconnected lines and missing xrefs. Display the counts so users can tell whether it's a quick fix or not.

Add short video showing how to add Ontology terms to: https://academy.wikipathways.org/stages/wp-add-ontology/. Based on comments by Chris that authors find it difficult to add ontology terms.

There are issues with the yellow part (Setting Pathway Information Free) in the academy (https://wikipathways.github.io/academy/path.html).

A file should open in this step: https://wikipathways.github.io/academy/stages/fig-met-1-second/ but that doesn't work. Should be rewritten to use PathVisio directly - but it is unclear which pathway should be opened.

@khanspers : the last step of the Academy now doesn't have a button to take them back to the overview page (iso the 'next button' at the bottom right), or to a celebratory page with confetti or something stating 'you're all done, congrats'.... What do you think ?
We could also do a page where they can claim a 'curation expert' diploma or something in the future as well (if we can link the academy to GitHub accounts?

Add stage for illustrating transport of proteins between compartments in the Advanced Modeling track

Add explanation of keyboard shortcut to relevant steps.

You can see it done for the demo code like this:
https://github.com/wikipathways/skilltree/blob/0543d4a5b4140876355c935b22fc530d6b2d385d/src/App.js#L2

@AlexanderPico @khanspers
which license should we use for the academy material?

From WP meeting notes 2022-04-27, it would be good to have some of the Jenkins reports be reviewed as part of the weekly curation report, as an extra task if there is time. It could go here: https://new.wikipathways.org/academy/stages/qaprotocol-extra/index.html

Should be able to build a table from the initial query where we gather the total count... maybe. We currently just grab 10 pathways as a time, so we might not have a lot of information about each pathway from just the count query. I guess we would need the pathway name and url at a minimum.

This could be a tab or toggle view switch: sequential images or table

The table should also include an interactive column where the user could indicate that they've viewed/fixed a particular pathway. Analogous to how "next pathway" currently works, but in the table view perhaps a simple 'X' or 'check mark' icon that then changes the style of (or hides) the row.

When you navigate to the Draw Conversion page, you get an error:

GET http://localhost:3000/src/stages/draw-conversion/glucose-solution.gpml 404 (Not Found)

The file does exist, but either the relative path is somehow wrong or else the dev server does not serve GPML.

Here's what the path is currently set:
https://github.com/wikipathways/skilltree/blob/0543d4a5b4140876355c935b22fc530d6b2d385d/src/Checker.js#L37