Figure suggestions

[jmh579]

The following suggestions refer to the first and second figures in the manuscript (1. fig:domains; 2. fig:apps).

• It would be nice to coordinate the color scheme between figures 1 and 2. The backgrounds for each domain in figure 1 could be made to match the corresponding groups of columns in figure 2, and both could use variations on the BrAPI logo colors (tints/shades) to add cohesion. See the figure 1 mockup below for a better idea of what I mean. I can keep working on this if it is of interest.
• It may be easier to interpret figure 2 with a more formal grouping scheme and/or a revised vertical ordering of applications. It looks like things are roughly grouped by phenotyping/genotyping, germplasm, database, etc. I suggest adding a column with this grouping designation and alphabetizing within groups or just alphabetizing the list overall.

@BrapiCoordinatorSelby do you have the original file for figure 2?

[BrapiCoordinatorSelby]

I have the original design files for figure 1 and 2 so I can easily make these edits.

regarding the vertical ordering, the table should match the order of the sections in the paper (some things may have moved around so I'll double check)
@mrouard suggested alphabetizing the sections of the paper. I can try it, but there are a few cases where I purposefully grouped similar tools for readability and flow. I'll mess around with it today

[BrapiCoordinatorSelby]

@jmh579 you can download the main table from here if you want to play with it https://github.com/plantbreeding/BrAPI-Manuscript2/blob/main/content/images/BrAPI_Application_Chart.xlsx
But I transfer that table into draw.io to make it an image and add the logos. those design files are not on github right now cuz they are just a bunch of intermediate steps to get from Excel to PNG.

[jmh579]

Thanks, @BrapiCoordinatorSelby!

I agree that grouping related tools makes sense for flow. What are your thoughts on alphabetizing within the 03 Success sub-sections (phenotyping, genotyping, germplasm management, etc)? We could reorder both the subsections and the figure. Maybe this would be the best of both worlds?

[BrapiCoordinatorSelby]

This is what the new ordering would look like going alphabetically by section.

HEADER.Phenotyping 
ClimMob 
Field_Book 
GridScore 
Image_Breed 
PHIS 
PIPPA 
Trait_Selector_BrAPP
HEADER.Genotyping 
DArT Sample Submission 
DArTView 
DivBrowse 
Flapjack 
GIGWA 
PHG 
HEADER.Germplasm_Management
AGENT 
FAIDARE 
FLORILEGE 
GLIS 
Helium 
MGIS 
HEADER.Data_Management 
BIMS 
BMS 
Breedbase 
Germinate 
DeltaBreed 
HEADER.Analytics 
G-Crunch 
Mr_Bean 
QBMS 
SCT 
ShinyBrAPPs 
HEADER.Infrastructure 
BrAPI2ISA 
BrAPIMapper 
MIRA 
Zendro 

I have a few small issues with this order ... but its over all doable.

• It seems odd to present ClimMob before Field Book and Gridscore. ClimMob is presented as an alternate way to collect data, contrasted with Field Book and Gridscore
• Mr.Bean directly depends on QBMS, odd to present QBMS second
• MIRA and BrAPI2ISA are highly related projects but they are now separated by BrAPIMapper

If we're good with these things, and no one sees any other issues, I think I'm good with this order. @jmh579 @mrouard any thoughts?

[mrouard]

Hi @BrapiCoordinatorSelby,

I was suggesting to alphabetize the tools within the section where they are grouped but from your comments; I understand the logic behind.

I am fine with the current order but if some tools are related, maybe they can be clustered by some logic. e.g. one sentence in the text to say how it is related. If they are more than related but dependent, it could be one section with merging the descriptions. (to be validated by contributors of course)

BrAPI2ISA and MIRA

Since the release of BrAPI 1.3, efforts have been made to incorporate support for the MIAPPE (Minimal Information About a Plant Phenotyping Experiment) standard into the specification, achieving full compatibility in BrAPI 2.0. Consequently, BrAPI now includes all attributes necessary for MIAPPE compliance, adhering to standardized descriptions in accordance with MIAPPE guidelines.In some communities and projects, phenotyping data and metadata are archived and published as structured ISA-Tab files, is user-friendly for non-technical experts due to its file-based approach, validated using the MIAPPE ISA configuration.

The BrAPI2ISA service functions as a converter between a BrAPI-compatible server and the ISA-Tab format, simplifying, automating, and facilitating the archiving of data, thereby enhancing data preservation and accessibility. The BrAPI2ISA tool is compatible with BrAPI 1.3 and welcomes community contributions to support the latest versions of BrAPI.

MIRA enables the automatic deployment of a BrAPI server on a MIAPPE-compliant dataset in ISA-Tab format, facilitating programmatic access to these datasets. It is deployable from a Docker image with the dataset mounted. This tool leverages the mapping between MIAPPE, ISA-Tab, and BrAPI, eliminating the need for parsing or manual mapping of datasets compliant with (meta-)data standards. By providing programmatic access through BrAPI, MIRA facilitates the integration of phenotyping datasets into web applications.

[jmh579]

Your logic makes sense, @BrapiCoordinatorSelby. Could we do it as you have listed but make the modifications you listed at the bottom?

I agree with @mrouard about combining sections, or at least explicitly discussing the connection between tools. Great idea! This may help with those exceptions to the alphabetic order