mbio EDA: Add featured variables

[asizemore]

Featured variables in the EDA are variables that always live at the top of the variable picker in their own special box, so that it's easy for a user to see them (and star them) immediately. This view of featured variables is the same wherever the variable picker is seen - from the Subset to the Visualize to the Downloads tab.

The way we're doing it right now is that each study has it's own list of featured variables. From Danica: "I’m not sure if the way clinepi does it will work for mbio. We have an annotation property in the .owl for each study, which is called “is_featured”. we leave this blank for terms that are NOT featured, and fill in “yes” for variables that we want featured"

Doing this for mbio would address the goal of "pre-starring" variables that we think are interesting.

[asizemore]

Slack discussion on how to do this started here

[wbazant]

I'm going to feature one variable, EUPATH_0011996::Sample type, because it's my favourite variable, and I'll link the commit here so that it's clear how to do it.

If there's ever a variable V in studies S and S', such that V should be featured in S but not in S', then it's gonna be a problem because we have no technology allowing that. But otherwise you'll just be able to feature whatever variables you want!

[asizemore]

Thanks @wbazant !! Sounds like a great plan!

If there's ever a variable V in studies S and S', such that V should be featured in S but not in S', then it's gonna be a problem because we have no technology allowing that.

Ooh good to know, thank you. Tagging @dpbisme as an fyi

[asizemore]

I'm not seeing the featured var on any study. @dpbisme do you?

[asizemore]

Not crucial for beta release.

[asizemore]

reopening because it failed qa. Note that this is not crucial for the b59 beta release. Will pick back up after b59.

[asizemore]

Moving to b60 must haves

[danicahelb]

Annotation property is_featured needs to be filled out on a per-study basis

[asizemore]

As of b62, some studies have featured variables, but @dpbisme is hoping to add featured vars to all studies for b63

[danicahelb]

Dan's list of vars to be featured can be found here: https://epvb.slack.com/archives/CBLPK9ZD3/p1677987475497809

Anopheles albimanus

• Sample type
• Host life stage
• Study group

Bangladesh

• Age
• Sex
• Bifidobacterium
• Prevotella
• Faecalibacterium

Bee Microbiome

• Bee colony tetracycline
• Host life stage
• Social role
• Host body site

BONUS-CF

• CFTR mutation (F508del)
• Study group
• Fecal fat
• Calprotectin

CAMP

• Case or control participant
• Pathogen species
• Pathogen type

DailyBaby

• Age
• Delivery mode

DIABIMMUNE

• Type 1 diabetes diagnosed
• Insulin autoantibodies
• Country
• Study group
• Age

ECAM

• Delivery mode
• Antibiotics
• Courses of antibiotics

Eco-CF

• CFTR mutation (F508del)
• Clinical status
• Sample type
• Age

Experimental Cutaneous Leishmaniasis

• Treatment
• Study group

FARMM

• Sample type
• Diet

GEMS1 Case Control

• Age
• Age group at enrollment
• Case or control participant
• Country

HMP phase I (V1-V3)

• Host body habitat
• Host body site
• Sample type

HMP phase I (V3-V5)

• Host body habitat
• Host body site
• Sample type

HMP phase I (WGS)

• Host body habitat
• Host body site
• Sample type

Human Cutaneous Leishmaniasis

• Cured
• Skin type swabbed

MAL-ED 0-2yr

• Country
• Age

MAL-ED diarrhea

• Country
• Age
• Observation period

Malaysia helminth study

• City, village, or region
• Helminth

MORDOR phase I

• Treatment group

NICU NEC

• Necrotizing enterocolitis
• Age at study

PIH Uganda

• Hydrocephalus
• Paenibacillus

Preterm infant resistome I

• Age
• Weight
• Hospital room type

Preterm infant resistome II

• Age
• Weight
• Total antibiotic administered

Uganda maternal

• Age
• Delivery mode
• Previous pregnancies count