i2b2 - Documents

Please identify and upload documents useful for understanding an ontology and the structure of the CRC tables.

Ontology Cell:

Ontology Design. This is the published design document for the Ontology cell. It contains details of the Ontology table within the cell and is essential for understanding how a given ontology is stored. Needs careful pondering in association with the other documents concerning the CRC cell and the metadataxml column.

CRC Cell:

CRC Design. This is the published design document for the CRC cell. It contains details of the central observation_fact table and how the ontology is used via the concept_dimension table. Lots of other details too.

MetadataXML column:

MetadataXML Column Format. The Ontology table within the Ontology cell contains an optional column c_metadataxml. The design document for the Ontology Cell states in sum total:

c_metadataxml is an optional field to store extra information about the concept in xml
format. It is currently used to describe value metadata associated with a lab finding.

The attached document is a valuable addition. To my mind (Jeff), the use of this column extends beyond lab findings to any column which can contain a variable amount.

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