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https://github.com/jmandel/json_ccda

Exploring conversation of Consolidated CDA to JSON for web apps
https://github.com/jmandel/json_ccda

Last synced: 19 days ago
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Exploring conversation of Consolidated CDA to JSON for web apps

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README 

        
Exploratory mapping of Consolidated CDA data to JSON, with a goal of preserving

CCDA's data model (but applying friendly names to properties whenever possible).



Inspired by popHealth's approach to mapping C32 (+ more Linked Data flavor)



## For automated setup, see https://github.com/jmandel/ansible-ccda



Manual Setup

```

$ git clone https://github.com/chb/json_ccda

$ cd json_ccda

$ npm install

$ cd smart-apps

$ npm install

```



Launching API server:

```

$ node launch.js

```



Launching App server:

```

$ cd son_ccda/smart-apps

$ node launch.js

```



Convert a CCD to JSON, without loading into DB:

```

$ node lib/ccda/import.js -f CCD.sample.xml -p 123  --stdout > sample_ccda.json

```



Convert and load into MongoDB:

```

$ node lib/ccda/import.js -f CCD.sample.xml -p 123 --mongo-db

```



Load a CCDA via HTTP POST:

```

$ curl -X POST -d @CCD.sample.xml http://localhost:3000/patients/123/documents/ccda

```



In Browser: `http://localhost:3000/patient/12345/



Testing:

```

$ ./node_modules/.bin/mocha -R spec

```

Lots of outstanding mapping questions, including:



* How to deal with negation indicators? (Would like separate 'AllergyNegation' items, rathern than just a flag)



* How to deal with nullFlavors? (Currently dropping for simple attributes; this

seems okay, otherwise JSON gets very cumbersome.  Will want to treat

nullFlavor differently in special cases, like problem codes that weren't

mappable to SNOMED / ICD10)



* How to effectively deal with elements that have multiple IDs (should be able

to lookup an item by any of its IDs; possibly just receiving a list of URIs

for that item).



* How to map document and entry IDs to stable URIs (considering using three

hierarchies in paralle: `documents`, `sections` and `entries` corresponding

fairly closely to these concepts in CCDA; except an `entry` will be

constrained.)



* How to assign IDs to sections (which have none in CCDA)



TODO:

* Get coding systems in DB (out of flat file)

* POST receiver to write JSON to DB (current output is files only)

* Example Mongo queries (e.g. "All patients w/ abnormal lab results since yesterday")



[x] Consider a separate 'links' collecition to offload  many:many relations.  Keep the fact documents cleaner.  But still need patient links for filtering without joins... (or can actually do this by convention + regix on _id:regex:^http:.../patient/123 (but implies we need a slash or huffman-coded pids. patient link is explicit -> better.)



[ ] Batch request mode to issue multiple individual-URI GETs in a swell foop.

[ ] Standalone and then integrated Validation of expected coding systems / constraints (explicit valuesets, snomed subsumptions, ucum, ?countries)

[ ] dates should be live DB dates and serialized in the REST server.

[ ] Use Mongolabs' syntax for queriese (across the board!)

[ ] use async.auto or similar to handle import.js flag interactions.

[ ] strip sourceIDs from the JS rep andn include only in links... ?

[ ] apply consistent units at import-time for vital signs? --> consider code + unit mapping in the import layer, or pushing out to apps



[ ]how to handle results that don't really belong to panels? all-in-one, or one-per? 



[ ] Add UCUM validation to physical quantities

[ ] Dynamically subclass ConceptDescriptor / SimpleCode to declare valid or obligatory valuesets.

  e.g. ["productName","0..1", 

        ".//h:manufacturedMaterial/h:code", 

        ConceptDescriptor.shall({valueSet: "1.2.3"})]



[ ] Sweep over the entire tree for validations to bulk-execute. 



[x] email struct doc WG to ask about IDs:  



    1.  Stable over time for an entry in a medicaiton list, or problem list, or vital sign?

    2.  Stable over time of an entry /changes/ (e.g. I upgrade asthma by adding a severity)?

    3.  Stable over time over change in status (inactive -> active) 

    4.  Are there current *actual* implementations that assign multiple identifiers to entries (meds, problems, labs; not people)

    



Data questions:



If normalizing displayNames, lincensing terms ?require the value come from the SDO?



* "doseQuantity, if present, SHOULD contain zero or one [0..1]

@unit="1", which SHALL be selected from ValueSet UCUM Units of

Measure (case sensitive) 2.16.840.1.113883.1.11.12839

DYNAMIC (CONF:8842)." -- how does one _select_ the value "1"? How is UCUM involved?



* what is manufacturerOrganization or a manufacturedProduct? No datatype in RIM or CDA or CCDA



(datatypes should be copied over from CDA spec!  This is a serious usability

issue --> easy errors)



* Severity free-text lives in a "text" element while medication free-text and immunization free-text are in a "code's" "original." 



BP centiles app: will have to leave out encounterType. (Semantics for vitals in CCDA are only implicit -- which encoutner did a given value come from? who was reponsible for it? etc.)



no consistent codes required for vital signs



What is the *meaning* of a vitals organizer?  does it imply that systolic and diastolic are matched, if they appear in the same organizer?



reported:

* What does it mean when a text has text _and_ a reference, and they both are non-emtpy and non-identical?



reported:

* ActReason code in examples is 2.16.840.1.113883.11.19725 ; but in the published table it is listed as 2.16.840.1.113883.5.8 .  Appears examples are wrong in the CCDA 1.1 spec + accompanying XML files.



reported:

* what is a Medication Activity's or Immunization Activity's "code" element?

  (CDA and RIM don't seem to say -- different from routeCode, or

approachSiteCode).