v2.0 docs update #186
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v2.0 docs update #186
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dogversioning
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Feb 27, 2024
| @@ -52,15 +51,12 @@ SELECT | |||
| id, | |||
| category_code, | |||
| category_code_system, | |||
| component, | |||
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the fields removed here were not flattened - i'll swing back around on the required/must support fields on these.
mikix
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Feb 27, 2024
dogversioning
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Feb 28, 2024
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| __Important detail on FHIR arrays__: When we flatten a FHIR element that | ||
| is specified as being potentially an array (like many instances of | ||
| CodeableConcept, for example), we create a seperate table from that | ||
| field. It can be joined back to the table it was extracted from by the | ||
| id field present in both tables. | ||
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| However - in your study design, you will need to handle cases where | ||
| multiple items may exist in these tables. It is common for multiple | ||
| code systems to be used for a single record. | ||
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| As an example, the Condition resource has a base level CodeableConcept | ||
| that _should_ contain a SNOMED code, but often has only an ICD9/10 code, | ||
| or a EHR vendor specific code. We handle this case in two ways: | ||
| - The __core__condition_codable_concepts_display__ table contains one | ||
| record per resource, where we specify a priority order and take the | ||
| first valid code we find, which is ok for cases where you aren't | ||
| very concerned about a specific coding and are just looking to get | ||
| an idea of what data you have | ||
| - The __core__condition_codable_concepts_all__ table contains | ||
| every code for every system found. This is useful when you are specifically | ||
| looking for data associated with a given clinical coding system, but | ||
| if you are not careful, you can cause a condition to be counted twice | ||
| by not specifying a coding system when joining this table with the | ||
| base condition table. | ||
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| Your approach to handling this is going to be dictated by the specific | ||
| clinical context you're working with. In cases where we don't specify | ||
| two table types for an array resource, you should assume that we are | ||
| following the second pattern and account for that in your queries. |
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Explicitly calling out this large text block i just added about the denormalized tables.
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| To document your study strucuture, you can use the `generate-md` command | ||
| to create markdown tables you can copy into your study docs. Note that, | ||
| as of this writing, you'll need to supply a description for each field by | ||
| hand. This output will be generated inside your study, in a file named | ||
| `{study name}_generated.md`. |
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also calling out the 'you need to define your own description, for now'
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This PR adds documentation around some V2 features, and a generator for creating markdown tables.
Checklist
docs/) needs to be updated