add participants.json with Levels as objects

[Remi-Gau]

closes #412

[Remi-Gau]

@surchs I may need your help on this

[sappelhoff]

We are getting this issue:

  	1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
		./participants.json
			Evidence: ['sex'].Levels['F'] should be string
		./participants.json
			Evidence: ['sex'].Levels['M'] should be string
		./participants.json
			Evidence: ['sex'].TermURL should match format "uri"

So we probably need to tell the (legacy JS) validator / the schema that levels as objects are fine (not only string)

And we furthermore need to add TermURLs for:

• age
• sex
• female
• male
• Hispanic
• MiddleEastern
• Caucasian/African/NativeSouthAmerican
• Caucasian
• Asian/Caucasian
• Asian
• Right
• Left
• Handedness
• dominant_hand
• gender

[surchs]

Hey folks! I think the variables listed by @sappelhoff fall into two levels with different answered by the TermURL:

• concepts (age, sex, handedness): "what is it ABOUT"
• values (27, female, left-handed): "what does it MEAN"

there are a ton of possible TermURLs for either, but I think it's a good idea to pick the TermURLs for values about the same concept from the same list. For example this could be a list:

• age: http://purl.obolibrary.org/obo/PATO_0000011
• gender: https://schema.org/gender (not standard yet)
  • female: https://schema.org/Female
  • male: https://schema.org/Male
• sex: http://purl.obolibrary.org/obo/PATO_0001894
• Ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0015
  • Hispanic: http://purl.obolibrary.org/obo/HANCESTRO_0014
  • MiddleEastern: http://purl.obolibrary.org/obo/HANCESTRO_0015
  • Caucasian/African/NativeSouthAmerican
  • Caucasian: http://purl.obolibrary.org/obo/HANCESTRO_0005
  • Asian/Caucasian
  • Asian: http://purl.obolibrary.org/obo/HANCESTRO_0005
• dominant_hand: http://purl.bioontology.org/ontology/SNOMEDCT/46669005
• Handedness: http://purl.bioontology.org/ontology/SNOMEDCT/57427004
  • Right: http://purl.bioontology.org/ontology/SNOMEDCT/46669005
  • Left: http://purl.bioontology.org/ontology/SNOMEDCT/46669005

What ontology to pick terms from is probably a bit beyond what BIDS can do in the examples / recommendations. But maybe we can provide some rule-of-thumb, i.e.: take from a list that is actively maintained, ideally widely used, ...

[sappelhoff]

I have removed "TermURL" here for now. If somebody knows what this means, please feel free to clarify.

[sappelhoff]

Okay:

• passes on master ✅
• adds correct TermURLs to many examples, exemplifying the new feature ✅
• I dropped everything that was unclear but wasn't really needed ✅
  • feel free to add later: for example what's the "D" sex?
  • or a TermURL for Caucasian/African/NativeSouthAmerican
• better done than perfect ✅

Will merge.

Thanks for the start @Remi-Gau and thanks for the support @surchs!

EDIT and of course thanks to @effigies for adding validator support.