i2b2 Ontology c_metadataxml Column

Tags: i2b2

A nullable column within the ontology table used to store extra information about the concept in xml format. Currently used to describe value metadata associated with a lab finding.

Formal Description

A fuller explanation is given in the accompanying document; see MetadataXML Column Format.. This requires careful reading. The use of this column has expanded from v1.5 to v1.6 of i2b2.

Example of use other than with a lab test

Interestingly, here is an example of its use applied to integer values other than lab results...

From: Larry Errecart [larry.errecart@ucdmc.ucdavis.edu]
Sent: 03 March 2011 20:22
To: Holden, Nick
Subject: Re: Integer values in i2b2 data other than lab users

We have blood pressure and BMI loaded and had to emulate the xml in the lab records to  enable the "set value" function.  
Here's our c_metadataxml entry for systolic:

<?xml version="1.0"?>
<ValueMetadata>
	<Version>3.02</Version>
	<CreationDateTime>12/15/2009 11:22:19</CreationDateTime>
	<TestID>SYSTOLIC</TestID>
	<TestName>SYSTOLIC</TestName>
	<DataType>PosInteger</DataType>
	<CodeType>GRP</CodeType>
	<Loinc>99999-9</Loinc>
	<Flagstouse>HL</Flagstouse>
	<Oktousevalues>Y</Oktousevalues>
	<MaxStringLength></MaxStringLength>
	<LowofLowValue>50</LowofLowValue>
	<HighofLowValue>90</HighofLowValue>
	<LowofHighValue>140</LowofHighValue>
	<HighofHighValue>230</HighofHighValue>
	<LowofToxicValue></LowofToxicValue>
	<HighofToxicValue></HighofToxicValue>
	<EnumValues></EnumValues>
	<CommentsDeterminingExclusion>
		<Com></Com>
	</CommentsDeterminingExclusion>
	<UnitValues>
		<NormalUnits>mm/Hg</NormalUnits>
		<EqualUnits> mm/Hg </EqualUnits>
		<ExcludingUnits></ExcludingUnits>
		<ConvertingUnits>
			<Units></Units>
			<MultiplyingFactor></MultiplyingFactor>
		</ConvertingUnits>
	</UnitValues>
	<Analysis>
		<Enums />
		<Counts />
		<New />
	</Analysis>
</ValueMetadata>

larry

An XML Schema

Here is a generated xml schema to describe the format: metadataxml schema. This may be useful in any programmatic manipulation of content before loading into the ontology table. However, it is probable any namespace declaration (or use of namespace qualification) within the contents would require removal before loading. The schema is provisional.

Editing within the workbench

It is possible to edit an ontology tree within the workbench provided the tree nodes are set to edit. I mention this here because this may be a way of editing the contents of this column using a GUI. At present I simply don't know. Some experimentation within the workbench is required here to set options etc to allow this to take place (any volunteers?). The use of the workbench for editing also presents a somewhat chicken-or-egg situation, as the ontology tree needs to be loaded before it is editable.

Example Ontology Data

See Ontology SQL Inserts. This file contains SQL inserts into the ontology table for pathology tests for the two i2b2 demo systems. It has been edited to reduce the size of the file, so is not a complete audit.

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