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General organization

There are 3 repositories behind this checklist:

  1. this COBIDAS_chckls repository where you are currently reading this. It contains:
  • the neurovault spreadsheet
  • the python script to turn that spreadsheet into a Repronim schema (basically a bunch hierarchically organized json files that link to each other).
  1. this fork of the ReproNim schema-standardization repository that hosts the schema representation of the checklist
  2. the cobidas-ui repository that does the actual rendering the checklist app by reading the schema hosted by the previous repository. There is a general explanation of how the app works in this issue. The prototype app for this checklist can be, for now, found here: https://cobidas-checklist.herokuapp.com/

You will need to fork and clone each of them if you want to work on the checklist on your own. If you want some stable versions of the repositories this table gives you link to the most recent ones.

Repositories Used version
COBIDAS checklist repository v0.0.1
schema-standardization repository v0.0.1
cobidas-ui repository v0.0.1

Spreadsheet work

So far most of the work is being done on spreadsheets hosted on this google drive folder and we try to keep a back up in the xlsx folder.

The MRI spreadsheet is accessible here

The MEEG spreadsheet is accessible here

The MRI part is the most advanced at this moment but we are looking for people to help with the MEEG part.

Spreadsheet content and organization

See the dedicated document

How is the Repronim schema organized

The first step to create the checklist involves taking a spreadsheet that contains all the items and turning that into a representation that can efficiently link the metadata about each item to the data imputed by the user. Basically it means turning your 'dumb' spreadsheet into an equivalent but 'smarter' representation of it: in this case a bunch hierarchically organized json files that link to each other.

In terms of choice of representation we are using the schema-standardization initiative from ReproNim to do this. On top of the inherent advantages of this schema representation:

  • its use simplifies the rendering of the checklist by using the schema-ui made for it,
  • this representation allows specification of user interface option that can simplify the user experience: it allows us to specify a branching logic that will prevent users to be presented with items that are not relevant to them (e.g answer PET related when they have only run an fMRI study).

The repronim schema is organized in a hierarchical manner with 3 levels.

  1. The lowest level is the item level where there is one question for each item with a expected format for the user interface: is this yes / no question (boolean), a multiple choice, a float or an integer...
  2. The second level is the activity level that contains a set of items. In the original repronim project this would constitute usually a questionnaire: like all the items of the Edinburgh handedness inventory would constitute one activity. In the COBIDAS case, it seems that we will most likely use this level to define some 'big' section of a method section (e.g preprocessing, design, participants...)
  3. The highest level is the activity_set or protocol level that originally define a set of activities to be included in a given study. At the moment this level is underused in the COBIDAS checklist but could be used to define activity sets for different use case: fMRI, MEEG, pre-registration...

So far we have a script to turn the neurovault list of required inputs into a schema that can then be render with the schema-ui.