Lab models a set of lab tests.
See also the schema for Indivo Coded Values, Indivo Data Values Schema, and Indivo Provider Schema.
Schema:
<?xml version="1.0" encoding="ISO-8859-1" ?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://indivo.org/vocab/xml/documents#"
xmlns:indivo="http://indivo.org/vocab/xml/documents#"
elementFormDefault="qualified">
<xs:include schemaLocation="codes.xsd" />
<xs:include schemaLocation="provider.xsd" />
<xs:include schemaLocation="values.xsd" />
<!-- the base type for a lab test -->
<xs:complexType name="LabTest">
<xs:sequence>
<xs:element name="dateMeasured" type="xs:dateTime" minOccurs="1" maxOccurs="1" />
<!-- e.g. "hematocrit" -->
<xs:element name="name" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<!-- either preliminary, or final -->
<xs:element name="final" type="xs:boolean" minOccurs="1" maxOccurs="1" />
</xs:sequence>
</xs:complexType>
<!-- a type to represent a single-value lab test -->
<xs:complexType name="SingleResultLabTest">
<xs:complexContent>
<xs:extension base="indivo:LabTest">
<xs:sequence>
<!-- an abstract type, which will be subtyped in instance documents -->
<xs:element name="result" type="indivo:Result" minOccurs="1" maxOccurs="1" />
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<!-- a type to represent a single MIC lab test -->
<xs:complexType name="MicroWithCultureLabTest">
<xs:complexContent>
<xs:extension base="indivo:LabTest">
<xs:sequence>
<xs:element name="source" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<!-- a bunch of observations -->
<xs:element name="observation" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="time" type="xs:dateTime" minOccurs="1" maxOccurs="1" />
<xs:element name="microbialDensity" type="indivo:Concentration" minOccurs="0" maxOccurs="1" />
<xs:element name="organism" type="indivo:CodedValue" minOccurs="0" maxOccurs="1" />
<xs:element name="extendedDescription" type="xs:string" minOccurs="0" maxOccurs="1" />
<!-- aerobic, anaerobic, not specified, or not cultured altogether -->
<xs:element name="cultureCondition" type="xs:string" minOccurs="0" maxOccurs="1" />
<xs:element name="gram" type="xs:boolean" minOccurs="0" maxOccurs="1" />
<xs:element name="morphology" type="xs:string" minOccurs="0" maxOccurs="1" />
<xs:element name="organization" type="xs:string" minOccurs="0" maxOccurs="1" />
<xs:element name="comments" type="xs:string" minOccurs="0" maxOccurs="1" />
</xs:sequence>
<!-- an isolate is a group of organisms that look similar, while an identity is a clear identified microorg -->
<xs:attribute name="isolate" type="xs:string" use="required" />
<xs:attribute name="identity" type="xs:string" use="optional" />
</xs:complexType>
</xs:element>
<!-- a bunch of results (could be more than one if more than one bug -->
<xs:element name="result" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="organism" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<xs:element name="sensitivity" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element name="antibiotic" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<xs:element name="MIC" type="indivo:Concentration" minOccurs="0" maxOccurs="1" />
<!-- coded value for resistant/intermediate/not resistant -->
<xs:element name="interpretation" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<!-- more info -->
<xs:element name="comments" type="xs:string" minOccurs="0" maxOccurs="1" />
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="interpretation" type="xs:string" minOccurs="0" maxOccurs="1" />
<!-- additional comments that are not directly interpretation -->
<xs:element name="comments" type="xs:string" minOccurs="0" maxOccurs="1" />
</xs:sequence>
<xs:attribute name="isolate" type="xs:string" use="required" />
<xs:attribute name="identity" type="xs:string" use="optional" />
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<!-- a type to represent a panel of tests -->
<xs:complexType name="LabPanel">
<xs:sequence>
<!-- e.g. CBC -->
<xs:element name="name" type="indivo:CodedValue" minOccurs="1" maxOccurs="1" />
<!-- for now, no subpanels, but we could do it if we wanted to with a self-reference -->
<!-- a bunch of lab tests -->
<xs:element name="labTest" type="indivo:LabTest" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
</xs:complexType>
<xs:element name="Lab">
<xs:complexType>
<xs:sequence>
<xs:element name="dateMeasured" type="xs:dateTime" minOccurs="1" maxOccurs="1" />
<!-- e.g. "hematology" -->
<xs:element name="labType" type="xs:string" minOccurs="1" maxOccurs="1" />
<!-- the lab provider -->
<xs:element name="laboratory" type="indivo:LabProvider" minOccurs="0" maxOccurs="1" />
<!-- a bunch of panels -->
<xs:element name="labPanel" type="indivo:LabPanel" minOccurs="0" maxOccurs="unbounded" />
<!-- a bunch of additional tests not in any panel -->
<xs:element name="labTest" type="indivo:LabTest" minOccurs="0" maxOccurs="unbounded" />
<xs:element name="comments" type="xs:string" minOccurs="0" maxOccurs="1" />
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
Example:
<Lab xmlns="http://indivo.org/vocab/xml/documents#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dateMeasured>2009-07-16T12:00:00</dateMeasured>
<labType>hematology</labType>
<laboratory>
<name>Quest</name>
<address>300 Longwood Ave, Boston MA 02215</address>
</laboratory>
<labPanel>
<name type="http://codes.indivo.org/labs/panels#" abbrev="cbc" value="CBC">CBC</name>
<labTest xsi:type="SingleResultLabTest">
<dateMeasured>2009-07-16T12:23:00</dateMeasured>
<name type="http://codes.indivo.org/labs/tests#" abbrev="Hct" value="evf" />
<final>true</final>
<result xsi:type="ResultInRange">
<flag type="http://codes.indivo.org/hl7/abnormal-flags#" abbrev="A" value="abnormal" />
<valueAndUnit>
<value>49</value>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage" />
</valueAndUnit>
<normalRange>
<minimum>44</minimum>
<maximum>48</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage" />
</normalRange>
<nonCriticalRange>
<minimum>42</minimum>
<maximum>50</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage" />
</nonCriticalRange>
</result>
</labTest>
<labTest xsi:type="SingleResultLabTest">
<dateMeasured>2009-07-16T12:23:00</dateMeasured>
<name type="http://codes.indivo.org/labs/tests#" abbrev="hiv" value="HIV" />
<final>true</final>
<result xsi:type="ResultInSet">
<!-- there could be a flag here -->
<!-- <flag type="http://codes.indivo.org/hl7/abnormal-flags#" abbrev="A" value="abnormal" /> -->
<value>negative</value>
<!-- these options may not be listed, given that flag may be raised -->
<option normal="false">positive</option>
<option normal="true">negative</option>
<option normal="true" description="insufficient sample">inconclusive</option>
</result>
</labTest>
</labPanel>
<labTest xsi:type="SingleResultLabTest">
<dateMeasured>2009-07-16T12:23:00</dateMeasured>
<name type="http://codes.indivo.org/labs/tests#" abbrev="Hct" value="evf">evf</name>
<final>true</final>
<result xsi:type="ResultInRange">
<flag type="http://codes.indivo.org/hl7/abnormal-flags#" abbrev="A" value="abnormal" />
<valueAndUnit>
<value>49</value>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage">%</unit>
</valueAndUnit>
<normalRange>
<minimum>44</minimum>
<maximum>48</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage" />
</normalRange>
<nonCriticalRange>
<minimum>42</minimum>
<maximum>50</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="%" value="percentage" />
</nonCriticalRange>
</result>
</labTest>
<comments>was looking pretty sick</comments>
</Lab>
Another example, for a microbiology lab:
<Lab xmlns="http://indivo.org/vocab/xml/documents#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dateMeasured>2009-07-16T12:00:00</dateMeasured>
<!-- hematology, chemistry, immunology, body fluids -->
<labType>microbiology</labType>
<laboratory>
<name>Quest</name>
<address>300 Longwood Ave, Boston MA 02215</address>
</laboratory>
<labTest xsi:type="MicroWithCultureLabTest">
<dateMeasured>2010-06-10T12:23:00</dateMeasured>
<name type="http://codes.indivo.org/labs/tests#" abbrev="micro" value="MicroWithCultureLabTest" />
<!-- this flag means no further updates will be coming -->
<final>true</final>
<source type="http://codes.indivo.org/specimen sources#" abbrev="U FC" value="Urine - Foley Cath" />
<observation isolate="1">
<time>2009-07-16T13:10:00</time>
<!-- we get coded density + description OR extended description which is denorm of other fields -->
<microbialDensity>
<range>
<maximum>100000</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="cfuML" value="CFU per mL" />
</range>
</microbialDensity>
<!-- optional, might end up in <result> -->
<organism type="..." abbrev=".." value="...">E. coli</organism>
<extendedDescription>>100000 organisms/mL E. coli</extendedDescription>
<cultureCondition>anaerobic</cultureCondition>
<gram>false</gram>
<morphology>rods</morphology>
</observation>
<observation isolate="2">
<time>2009-07-16T13:10:00</time>
<microbialDensity>
<value>
<value>50000</value>
<unit type="http://codes.indivo.org/units#" abbrev="cfuML" value="CFU per mL" />
</value>
</microbialDensity>
<organism type="..." abbrev=".." value="...">Staphylococcus spp</organism>
<extendedDescription>50000 organisms/mL Staphylococcus spp</extendedDescription>
<cultureCondition>aerobic</cultureCondition>
<gram>true</gram>
<morphology>cocci</morphology>
<!-- optional fields -->
<organization>clusters</organization>
<comments>....</comments>
</observation>
<observation isolate="3">
<time>2009-07-16T13:10:00</time>
<extendedDescription>not sure what to think of this bug...</extendedDescription>
</observation>
<!-- possibility of splitting an observation of ONE isolate into multiple identities -->
<!-- possibility of identify the organism BEFORE the <result> with an additional <observation> -->
<!-- @identity is optional but is used when one isolate has more than one result -->
<result isolate="1">
<organism type="" abbrev="" value="">E. Coli</organism>
<!-- a result for an isolate MUST have a corresponding observation with density info -->
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMP" value="ampicillin" />
<MIC>
<value>
<value>32</value>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</value>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMPSULB" value="ampicillin/sulbactam" />
<MIC>
<value>
<value>16</value>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</value>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="I" value="intermediate" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="TMPSMX" value="Trimeth/Sulf" />
<MIC>
<value>
<value>1</value>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</value>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="S" value="sensitive" />
</sensitivity>
</result>
<result isolate="2" identity="1">
<organism type="" abbrev="" value="">S. aureus</organism>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMP" value="ampicillin" />
<MIC>
<range>
<minimum>32</minimum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
<comments>be careful when treating with AMP, call lab</comments>
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMPSULB" value="ampicillin/sulbactam" />
<MIC>
<range>
<minimum>32</minimum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="OXCLN" value="Oxacillin" />
<MIC>
<range>
<minimum>16</minimum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="VANC" value="Vancomycin" />
<MIC>
<range>
<maximum>2</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="S" value="Sensitive" />
</sensitivity>
<interpretation>MRSA</interpretation>
<comments>more stuff here</comments>
</result>
<result isolate="2" identity="2">
<organism>S. epidermidis</organism>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMP" value="ampicillin" />
<MIC>
<range>
<maximum>2</maximum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="S" value="Sensitive" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="AMPSULB" value="ampicillin/sulbactam" />
<MIC>
<range>
<minimum>32</minimum>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</range>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="OXCLN" value="Oxacillin" />
<MIC>
<value>
<value>16</value>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</value>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="resistant" />
</sensitivity>
<sensitivity>
<antibiotic type="http://codes.indivo.org/antibiotics#" abbrev="VANC" value="Vancomycin" />
<MIC>
<value>
<value>2</value>
<unit type="http://codes.indivo.org/units#" abbrev="ugML" value="mcg per mL" />
</value>
</MIC>
<interpretation type="http://codes.indivo.org/MIC interpretation#" abbrev="R" value="Resistant" />
</sensitivity>
<interpretation>Probable contaminant</interpretation>
</result>
</labTest>
</Lab>