jmandel

<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>

jmandel

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:<http://www.w3.org/2001/XMLSchema#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX umls:<http://bioportal.bioontology.org/ontologies/umls/>
PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
select distinct ?xl ?bodyPartLabel {
  ?x rdfs:subClassOf* ?y.
  ?y <http://purl.bioontology.org/ontology/SNOMEDCT/has_finding_site> ?z. 
  ?z rdfs:subClassOf* ?bodyPart.
  ?x skos:prefLabel ?xl.

jmandel

At yesterday's Health 2.0 conference, Farzad Mostashari asked why SMART isn't using CCD export (as specified by Meaningful Use) to extract data from EMR systems. This is a great question, in part because it separates out two important aspects of SMART:

1. Getting data out of today's EHRs
2. Presenting those data to apps in a natural, convenient, developer-friendly way. -- and focuses on #1. (I don't think many would argue that CCD is fit for #2. And to be clear: for developers building a SMART app, the details of #1 are almost irrelevant. SMART app developers get one clear-cut API to work with, and consistent SMART data elements)

Well! ONC is certainly headed in the right direction by requiring more specific, demanding export formats as part of meaningful use. Having a baseline level of consistently structured data is the right aspiration! And MU s

jmandel

        client = get_smart_client(smart_oauth_header)

        # Represent the list as an RDF graph
        med_lists = client.records_X_medication_lists_GET()
   
        lists_q = """
            PREFIX dcterms:<http://purl.org/dc/terms/>
            PREFIX sp:<http://smartplatforms.org/terms#>
            PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            select ?l ?s ?sname ?d 

jmandel

import sys
import urllib
import urllib2

REPOSITORY = "http://localhost:8080/openrdf-sesame/repositories/test/statements"

head="""INSERT DATA {
  GRAPH <http://one-graph-to-break-them-all> { """
    
tail="""  }

jmandel

@prefix : <http://smartplatforms.org/terms#> .
@prefix dcterms:<http://purl.org/dc/terms/>.

# We start with a mixed bag:
#  some problems have local code only
#  some problems have snomed code only
#  some problems have both

<http://pboth>  a :Problem;
  :code <http://some.refrence.to/icd9#982.1>;

jmandel

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
  xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  xmlns:sp="http://smartplatforms.org/terms#"
  xmlns:dcterms="http://purl.org/dc/terms/"
  xmlns:v="http://www.w3.org/2006/vcard/ns#"
  xmlns:foaf="http://xmlns.com/foaf/0.1/"
  xmlns:spcode="http://smartplatforms.org/terms/codes/">

   <sp:Demographics>

jmandel

It's a mistake to abstract Coding Systems from Data Models

JCM, 12/27/2011

How models are "supposed to work"

In theory, clinical modellers erect an abstraction barrier to keep the details of coding systems out of their data models. According to this theory:

1. "Data Models" describe classes or types of data, along with the properties that class members can/should/must assign. For instance, let's take a model for "Prescription" specifying that each Prescription has a required start date, optional end date, and a required "drug" field.

2. "Coding Systems" are separately-maintained sets of values that a data model can "bind" to a given property. These are often large, multi-purpose systems maintained by teams of analysts working for a major healthcare organization, government, or SDO. For instance:

jmandel

{
   "@context": {
      "@coerce": {
         "ex:contains": "@iri"
      },
      "dc": "http://purl.org/dc/elements/1.1/",
      "ex": "http://example.org/vocab#",
      "xsd": "http://www.w3.org/2001/XMLSchema#"
   },
   "@subject": [

jmandel

QUERY:
BASE <http://smartplatforms.org/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
CONSTRUCT {
    ?root_subject <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://smartplatforms.org/cemterms#OrderMedAmb>.
    ?root_subject <http://smartplatforms.org/cemterms#orderNumber> ?orderNumber_object.
    ?orderNumber_object <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type_object.
    ?orderNumber_object <http://smartplatforms.org/terms#string> ?string_object.
    ?root_subject <http://smartplatforms.org/cemterms#counterSigned> ?counterSigned_object.
    ?counterSigned_object <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type_object_2.