i2b2 Temporal Queries

i2b2 Proposal Aims

1. Implement sets of time points that can be queried by iterative use of simple time-based and Boolean operations

2. Implement temporal abstraction mechanisms to aggregate time points into intervals

3. Evaluate performance. Compare to temporal relations found by DBPs and previous pharmacovigilance work. Compare codified but incomplete EHR data to NLP from notes.

PM

ONT

WORK

Cell

CRC

Plugin

Server Side

Client Framework

Core Cell Viewers

Plugin Viewers

Client Side Web Browser

Ways to Extend i2b2

observation_factpatient_numencounter_numprovider_idconcept_cdstart_dateend_datevalue_num

patient_dimensionpatient_numbirth_datedeath_datesex_cdrace_cdethnicity_cdzip_cd

provider_dimensionprovider_idprovider_pathname_char

encounter_dimensionencounter_numpatient_numinout_cdlocation_cdlocation_pathstart_dateend_date

concept_dimensionconcept_cdconcept_pathname_char

query_masterquery_master_idnamerequest_xmluser_iddelete_flag

query_instancequery_instance_idquery_master_idstatus_type_idstart_dateend_date

query_result_instanceresult_instance_idquery_instance_idstatus_type_idresult_type_idset_size

patient_set_collectionpatient_set_coll_idresult_instance_idpatient_num

patient_enc_collectionpatient_enc_coll_idresult_instance_idpatient_numencounter_num

temporal_datetime_collectiontemporal_datetime_coll_idresult_instance_idpatient_numconcept_cdstart_dateend_datevalue_num

temporal_interval_collectiontemporal_interval_coll_idresult_instance_idpatient_numconcept_cdconcept2_cdinterval_type_cdinterval_size_numsequence_numstart_dateend_dateobservation_count_nummin_value_nummax_value_numavg_value_numstdev_value_nummedian_value_numupper_percentile_numupper_value_numlower_percentile_numlower_value_num

Data Tables New QueryResult Tables

Query History Tables

Query Result Tables

User Interface

Query Subpopulation

Patient A Patient B Patient C

Time

Set 2 –patients w/ elevated HbA1c

Patient A Patient C Patient D

Time

Set 1 –patients with diabetes

Patient A Patient B Patient C

Time

Set 3 –patients with diabetes AND elevated HbA1c

Patient A Patient C

“1 AND 2”

Graphical representation of a query subpopulation (Nigrin, 2000)

A Boolean combination between two retrieved patient subpopulations (Nigrin, 2000)

Types of Temporal Intervals

2006 2007 2008 2009

Based on Data(first-to-last)

Based on Data(3 months after)

Based on Bin(Seasons) Winter Spring Summer Fall

A1c 9.5 9.2 8.4 8.2 8.1 7.0 6.8 7.6

N = 8 Avg = 8.1

N = 2 Avg = 9.4

N = 2 Avg = 8.3 N = 2 Avg = 7.5 N = 0 Avg = N/A N = 4 Avg = 8.3

Based on Dates(1/1/07 – 12/31/07)

N = 4 Avg = 7.9