Skip to content

Instantly share code, notes, and snippets.

Avatar

Josh Mandel jmandel

View GitHub Profile
View example.xml
<example xsi:type="QSI_TS"><!-- intersection, because it is a QSI -->
<!-- every other Tuesday -->
<term xsi:type='PIVL_TS' alignment='DW'>
<phase lowClosed='true' highClosed='false'>
<low value='20001202'/>
<high value='20001203'/>
</phase>
<period value='2' unit='wk'/>
</term>
View example.md
<problem code="363346000" codeSystem="[sct]" displayName="Cancer">
  <qualifier>
    <code code="363698007"  displayName="finding site"/>
    <value code="39607008" displayName="Lung"/>
  </qualifier>
  <qualifier>
    <code code="408729009" displayName="finding status"/>
    <value code="415684004" displayName="suspected"/>
  </qualifier>
View 0-i2b2-source.ttl
@prefix : <http://i2b2.org/terms#> .
[] a :Observation;
:code "ICD9:724.5"; # backache
:date "2012-04-14";
:modifier [
:code "SNOMED:24484000" # severe
].
@jmandel
jmandel / sparql-got-statins.md
Last active Dec 17, 2015
SPARQL Queries from drug --> disease, mechanism
View sparql-got-statins.md
prefix rxnorm: <http://purl.bioontology.org/ontology/RXNORM/> 
prefix skos: <http://www.w3.org/2004/02/skos/core#> 
prefix umls: <http://bioportal.bioontology.org/ontologies/umls/> 
prefix ndfrt: <http://purl.bioontology.org/ontology/NDFRT/> 
SELECT distinct ?d ?label 
WHERE { 
 FILTER (?d = rxnorm:153843 ||
         ?d = rxnorm:312961 ||
         ?d = rxnorm:866514 ||
@jmandel
jmandel / diagnostic-report.ttl
Last active Dec 18, 2015
FHIR RDF proposals / examples
View diagnostic-report.ttl
@prefix : <http://hl7/org/fhir/DiagnosticReport#> .
@prefix fhir: <http://hl7/org/fhir/> .
@prefix Narrative: <http://hl7/org/fhir/Narrative#> .
@prefix Observation: <http://hl7/org/fhir/Observation#> .
@prefix Quantity: <http://hl7/org/fhir/Quantity#> .
@prefix Resource: <http://hl7/org/fhir/Resource#> .
@prefix Reference: <http://hl7/org/fhir/Reference#> .
@prefix Range: <http://hl7/org/fhir/Range#> .
@prefix Codeable: <http://hl7/org/fhir/Codeable#> .
@prefix Coding: <http://hl7/org/fhir/Coding#> .
View browser.md

The browser field is provided by a module author as a hint to javascript bundlers or component tools when preparing modules for client side use.

terms

Below are common terms used in the rest of the document

server

This is a non-dom based javascript execution environment. It usually only contains the base javascript language spec libraries and objects along with modules to communicate with OS features (available through commonjs require).

client

@jmandel
jmandel / bb-plus-demo.md
Last active Dec 18, 2015
BlueButton+ Pull Demo
View bb-plus-demo.md

Hi BB+ Pull!

I wanted to share links to the demo we showed on the previous call. To try it out:

  1. Visit Blood Pressure App
  2. Choose "Good Health Clinic". (this register a new client_id then redirects for authorization.)
  3. Log in as demo/demo to Authorize access

More details below :-)

@jmandel
jmandel / explanation.md
Last active Dec 20, 2015
Generating value set for C-CDA Language Codes
View explanation.md

Picking Language Codes for MU2 Consolidated CDA

Here you'll find:

  • An English-language description of how to choose language codes for MU2 C-CDA
  • An AWK script that generates the complete list of languages in the value set
  • The value set itself, with two tab-separated columns (Code, Language)

Here's the algorithm:

@jmandel
jmandel / bundle.xml
Created Sep 5, 2013
FHIR bundle for a SMART patient record
View bundle.xml
<?xml version="1.0" encoding="UTF-8"?>
<feed xmlns="http://www.w3.org/2005/Atom">
<title>SMART patient bundle for transactional posting</title>
<id>urn:uuid:9ba0e98e-47a3-42d1-ae1a-55cd1057da44</id>
<updated>2013-09-04T18:28:06.243926</updated>
<entry xmlns="http://www.w3.org/2005/Atom">
<title>SMART Patient-level resource</title>
<id>cid:patient-2081539</id>
<updated>2013-09-04T18:28:06.243926</updated>
View three-requests-answered.txt
$ sh three-requests.sh
Response 2: 500
Response 1: 200
Response 3: 200
You can’t perform that action at this time.