Type/Design/Method entity/field?

roll commented 9 years ago

Background Related to #21 issue.

Topic

Method - some trial implementation rules

Our ideal data model doesn't have a Method entity or field. It looks it's a vital part of a trial description. Example of method: Randomised - random number generation + admission order

Proposed solutions

we can have entity Method with m2m relation with Trial (as in Cochrane database)
we can have field Trial.method implemented as an array of strings

pwalsh commented 9 years ago

Similar comments here to those I made on #7. m2m seems wasteful if we are not expecting commonality - ie - that each trial just has its own text description(s) of method. Can you run some queries to see actually if there is any consistency here across trials?

BTW @roll this is great work, well done.

danfowler commented 9 years ago

@pwalsh @roll There are only 43 different method descriptions spread across 8851 studies, so I think it might be OK to do the m2m option.

pwalsh commented 9 years ago

Is there a further way to break down these strings into more structured data?

Example: @roll has an example which essentially is 'random'. If we look at these 43 manually, I'm curious if these are just textual variations on themes that could be enum-ed.

roll commented 9 years ago

@pwalsh But it's just one dataset. I think to make it more structured we have to have a very deep understanding of the domain and other dataset examples. To do not run into troubles further.

All of this looks like point 15 of http://www.who.int/ictrp/network/trds/en/ (Study type):

(from Design)

"RCT"
"CCT"

(from Method)

"Cluster randomisation (events)"
"Cluster randomisation (wards)"
"Cluster randomisation (families)"
"Cluster randomisation (homes)"
"Crossover"
"Blinding - open-label"
"Blinding - unclear"
"Blinding - double"
"Blinding - single"
"Cluster randomisation (mental health workers)"
"Blinding - triple"
"Blinding - multi-blind"
"Cluster randomisation (general practices)"
"Cluster randomisation (mental health centres)"
"Factorial"
"Unclear"
"Unclear - requires translation"
"Non blinded"
"Randomised- no further info"
"Block randomisation"
"Randomised - admission order"
"Randomised- tossing a coin"
"Randomised- drawing straws"
"Randomised - date of admission, odd or even"
"Randomised - consultation order"
"Randomised - random number generation"
"Randomised - number of admission, odd or even"
"Randomised - computer random number generation"
"Randomised - admission  and consultation order"
"Randomised - discharge order"
"Randomised - admission order, even or odd"
"Randomised - admission order and tossing a coin"
"Randomised - admission number, odd or even"
"Randomised - selection order"
"Randomised - random number generation + admission order"
"Randomised - random number generation table"
"Randomised - random number, odd or even"
"Randomised - admission order and random number generation"
"Randomised - case note numbers"
"Randomised - admission order + stratified"
"Randomised - block randomisation"
"Randomised - card"
"Quasi randomization"

roll commented 9 years ago

But here we see more structure - https://clinicaltrials.gov/ct2/show/results/NCT00922272?term=schizophrenia&rank=121&sect=X30156

Study Type - Interventional Study Design - Allocation: Randomized; Endpoint Classification: Safety/Efficacy Study; Intervention Model: Parallel Assignment; Masking: Double Blind (Subject, Caregiver, Investigator, Outcomes Assessor); Primary Purpose: Treatment

pwalsh commented 9 years ago

Those methods, I'm inclined to say we make a list of types, and have a method description field.

EG:

"Randomised - admission  and consultation order"
"Randomised - discharge order"

becomes:

method_type: "randomised" (enum or some other structure)
method_description: "admission and consultation order" or "discharge order"

WDYT?

pwalsh commented 9 years ago

method_type might become method_design or study_design if we want to align with other data sets... not sure.

roll commented 9 years ago

I see it in the same way on the dataset we have (about randomized/blinded/etc + type). Just a little bit afraid we don't see the whole picture.

It looks like - https://github.com/okfn/opentrials-cochrane-schizophrenia-data/issues/6#issuecomment-139465565 - it's kinda a reference for our problem. Here is some study types (1 type per study) and study designs (tags).

roll commented 9 years ago

Cochrane's RCT, CCT (from Dan):

http://handbook.cochrane.org/chapter_6/box_6_3_a_cochrane_definitions_and_criteria_for_randomized.htm

opentrials / cochrane-schizophrenia-data

Type/Design/Method entity/field? #6