Make it easier to find the information on copying and editing annotations

[CuzickA]

Notes from Google Doc with @smvelasquez

(MV) As I went along I realized that I could add new metagenotypes from scratch or add new phenotypes to an existing metagenotype
(AC 21/03/22) Yes, and it is also possible to copy and edit annotations to make curation quicker. Do you think the Help documentation is clear enough for these features?
(MV 21/03/22) Not really. I figured it out as I went along.
(AC 21/03/22) Can you suggest any new text in the Help document that could make this clearer? We have the section below, but it is not currently linked with a heading from the main Help Contents page.
(MV 25/03/22) Maybe “Copying and editing Metagenotypes” as a subheading inside Annotating Metagenotypes? Or add like a “Useful Tips/Hints” or some section like that to highlight that you can do this

@jseager7 it would be good to think of a way to make this clearer for new curators.

[jseager7]

Maybe “Copying and editing Metagenotypes” as a subheading inside Annotating Metagenotypes? Or add like a “Useful Tips/Hints” or some section like that to highlight that you can do this

This is a bit tricky: we can't describe a process of copying and editing metagenotypes, because there's no option to copy and edit the metagenotype itself, only its annotations.

I'm having trouble understanding the exact problem, based on the following comment:

As I went along I realized that I could add new metagenotypes from scratch or add new phenotypes to an existing metagenotype

If the problem is just that it's not obvious how to copy and edit annotations, then I don't think this page is the right place to cover that: this page is just about creating genotypes and metagenotypes.

I'm guessing that the problem is related to the fact that documentation isn't good at covering the whole annotation process for a particular feature type (e.g. gene, genotype, metagenotype). Currently, it's not clear how the user should make lots of annotations in an efficient way.

I was thinking it might be better if we restructured the documentation into sections that walk the user through the whole process for making each type of annotation – rather than this disjointed approach of 'make all your genotypes, then make all your metagenotypes, then apply your annotations in no particular order' – but then that doesn't match what a new curator sees on the Curation Summary page, which is just 'Pathogen genotype management', 'Host genotype management', and 'Metagenotype Management' (none of which are clearly related to any type of annotation).

If Advanced mode is enabled. then it's more obvious which annotations can be made from the Quick links section:

Unfortunately, Advanced mode can be very misleading because it's not properly configured for pathogen-host mode. For example, here's the thoroughly unhelpful message you see when you try to make a pathogen-host interaction phenotype annotation before creating a metagenotype:

(The 'Genotype management' link doesn't even exist in our version of Canto.)

So, I'm not really sure what to suggest. If curators are likely to think about curating a paper in terms of its results – that is, what will be curated as annotations in PHI-Canto – then having the documentation structured around annotations should help, but I guess the annotation process will really vary by publication: for example, a publication where every pathogen-host interaction has only one recorded phenotype won't require any copying of annotations in PHI-Canto.