Updating quality tags on a large number of pathways

[Kristina Hanspers]

Hi all,

In my latest admin curation report I mentioned an issue that I think warrants its own thread. We have a large number of pathways with outdated quality tags, Analysis and Featured, because of a large number of edits by mostly one user, Eric Weitz. He has been in contact with the team and explained his intentions, so its not a random user. The edits are legitimate (updating pathway titles and adding/updating ontology tags), but the number of affected pathways makes it basically impossible to manually go through and update the tags on these, at least as part of the normal weekly curation protocol. 

What should we do with these? Below are some initial thoughts. I should also say that I have reviewed between 50-100 of these edits for human pathways, and they were all good.

1. Write a script to update the affected tags on pathways, for example only updating if the latest edit is by "Eweitz". Its a bit convoluted (first getting the tags, then compare revisions, then get pathway history to check against etc), but would work. 

2. Leave it as-is for now and slowly make the updates manually through the normal process. In some ways maybe this is the preferred option since it follows our protocol for quality control. For the species that are not updated much, the drawback is minor; basically these latest minor edits will not be reflected in the data release until we make the update. For more often updated species, the problem is that any additional edits after Eric's edits will also not be reflected in the data release until they are updated. 

3. Update the tags directly in the database?

Thoughts?

Kristina

[Martina Summer-Kutmon]

I think we should make sure this is updated before the next release. Tried to do some manually but that really takes forever. So I will check if I can write that script. 

Best, Tina

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Martina Summer-Kutmon, PhD
email: mku...@gmail.com

[Martina Summer-Kutmon]

Okay, I ran a script (after I found an error in the Java API...) and updated all tags that had the last edit by Eric. There are still a couple of pathways with not updated tags (15 or so) which probably had edits after Eric's edit. I will check those.

This is only for the analysis collection tag and not yet the featured pathway tag.

Best, Tina

[Martina Summer-Kutmon]

Okay, thanks to Egon all analysis collection curation tags are applied to the latest version. I will check the featured tag next - I think for that one, we could just let the script update all of them but not sure what people think.

Best, Tina