1
VA Informatics and Computing Infrastructure

VINCI Organization

2

VHA

ORD

HSR&D

OI&T

BISL/CDW

VINCI

Veterans Affairs
• Establish a National Research Infrastructure

• Develop New Data Privacy & Security 

Capabilities

• Develop Remote Analysis Capability

• Prepare for Future Data Capabilities

• Partner With Other VA and Non-VA Entities

3

A Research / IT Partnership
Local VistA 

implementations

Corporate Data

Warehouse

Specialty VA 

data sources

VINCI

4
A Research / IT Partnership

5
6

VINCI Architecture
Data Extraction

• Research Study Team uploads cohort to a 

secure site or VINCI creates cohort per 

requirements

• Research Study Team completes the Data 

Selection Forms on correspondence site

• NDS approved data domains are extracted 

and provided

• Analysis performed by research project 

team staff

7
External Data

• Research Study Team may upload other 

data for analysis into project database or 

workspace

• Secure data upload process

• Optional direct database upload

• VINCI data managers work on behalf of 

research team to upload data from other 

data providers

8
 Data Processing/Analysis tools

• SQL Server as primary data store

• Multiple high performance servers

• Most data queries performed in SQL Server

• Accessible by all analysis software

• SSIS, SSRS, SSAS (SQL server integration, 

reporting, and analysis)

• High speed intra-server network will allow 

distributed queries

9
SAS

• High performance SAS server

 2 TB of RAM, 64 cores, 2 TB SSD

 Launch grid jobs

• SAS grid – very large data analysis work

 10 high performance servers

 Most advanced SAS implementation in VA

 Dedicated SAN

 Additional SAS modules

 SAS knowledge base SharePoint site

• Dedicated SAS administrator

10
Data Approvals
Data Access & Security

• Access groups created based on IRB and 

NDS approved research team

• Only research team members have access to 

the data

• Data stored on secure VINCI servers

• Regular data backup and archiving

• Workspace vs. collaboration site

• Project work can be performed in VINCI

• Export final result & publication

12
• Patient demographic information

• Vital signs

• Diagnoses and procedures from patient 

encounters

• Outpatient pharmacy data

• Laboratory values

• Immunizations

• Microbiology reports

• Text notes (including progress notes, discharge 

summaries, radiology reports)

• VA Decision Support System (DSS) in database

tables linked with other VINCI data or as the 

original SAS files

• VHA Medical SAS datasets
Using All You Have
REGION 1 REGION 2

REGION 4

REGION 3

RDW

V20

V19

V22 V18

V21

RDW

V1

V2

V4 V3

V5

RDW

V12

V15

V17 V16

V23

RDW

V6

V7

V8

V9

V10

V11

VINCI

CDW

16

VINCI
Data Standardization

MODERATE STAPHYLOCOCCUS AUREUS

E. COLI

> 100 CFU STAPHYLOCOCCUS AUREUS 

16 COLONIES SERRATIA SP 

GRAM NEG ORGANISM 

ANAEROBIC GRAM NEGATIVE RODS 

GRAM NEG BACILLI 

ENTEROCOCCUS FAECALIS - VANCOMYCIN RESISTANT 

ENTEROCOCCUS FAECIUM 

ENTEROCOCCUS SPP. 
INFLIXIMAB 100MG/VIL (PF) INJ

INFLIXIMAB 100MG/VIL PF INJ

INFLIXIMAB 100MG INJ

INFLIXIMAB 100MG VIAL

INFLIXIMAB 100MG 

INFLIXIMAB 100MG/20ML INJ

INFLIXIMAB 100MG/VIAL INJ

INFLIXIMAB 100MG/20ML VIAL

INFLIXIMAB 100MG IV

ZZINFLIXIMAB 100MG INJ

ZZINFLIXIMAB 100MG/20ML
Understand the 

Target Study 

Population

Understand the 

Care Workflow

Understand the 

Underlying Data

Log on and 

Manage 

Proposals

Filter

Proposal Phase

IRB / VA R&D

Transform

Approval Phase Approved Research

Apply For 

Funding

Awarded 

Funding

D.A.R.T.

No PHI 

or PII 

displayed

Data 

access 

audit

NDS and other 

stewards

Analyze

Extract (NLP)

Annotate Explore

Apply For 

Research 

Approval

Filter Explore

Approved 

study data 

displayed
 Why natural language processing?

• Increasing demands for more detailed clinical data

• Quality Measures

• Evidence-based medicine 

• Phenotyping for genomic-related analysis

• Biosurveillance

• The majority of EMR data is free text

22
training set Load and 

randomize 1 validation set

initial rule set

extract

concepts using 

current rule 

set

2

update / add to 

rule set

3

Use failure analysis 

to identify needed 

rule changes

Load and 

randomize 5 Repeat steps 3 

and 4 until recall 

and precision 

target levels are 

reached

4

training

Annotated

Document Corpus

relevant

concepts

irrelevant 

and 

missed

concepts

Compare extracted 

concepts with 

reference standard 

for accuracy

7

validation

relevant

concepts

irrelevant 

and 

missed

concepts

extract

concepts using

final rule

set

6

final

rule set
S

E

N

T

E

N

C

E

W

O

R

D

P

.

O

.

S

P

E

E

C

H

P

H

R

A

S

E

C

O

N

C

E

P

T

project-specific

concepts

word patterns output

pre-processing inference

post-processing

An NLP Pipeline
Pipeline Issues

Base modules have trouble with:

– Templates

– Incomplete Sentences

– Jargon
Pipeline Issues

Project-specific modules are:

– Limited by base module output

– Affected by propagation of errors from previous 

modules
Lookup Issues

• Target does not exist in database

• Lookup method insufficient to find target

Semantic bootstrapping

Structural cues
RxNorm

(UMLS)

Medication Name

Precision 61.86%

Recall 66.93%

F1 64.29%

SENTENCE

WORD

P.

O. SPEECH

PHRASE

CONCEPT
BASILISK

Seed

words

Extraction Patterns

Words used in Patterns

Corpus Corpus Corpus

Semantic Lexicon

Pattern Pool Candidate

Word Pool

best candidate words

extractions

best

patterns
RxNorm

(UMLS)

Basilisk 

word pool

RxNorm

only

RxNorm + 

Basilisk

1-pass 

Filtering

Precision 61.86% 66.74% 71.95%

Recall 66.93% 82.80% 82.80% 

F1 64.29% 73.91% 77.00%
Part 

1

Part 

2

Whole 

solution

Whole 

problem

31
• Craft very specific rules to handle specific 

situations

• Craft highly precise rules to determine 

which rules to apply in which situations

• Have general rules to apply elsewhere

32
 ----MICROBIOLOGY----

Accession: VA 123 Received: Oct 12, 2009

Collection sample: WOUND Collection date: Oct 12, 2009

Provider: Dr. General Hawk

Specimen: SWAB

CULTURE RESULTS: 1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S

33
 ----MICROBIOLOGY----

Accession: VA 123 Received: Oct 12, 2009

Collection sample: WOUND Collection date: Oct 12, 2009

Provider: Dr. General Hawk

Specimen: SWAB

CULTURE RESULTS: 1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S
 ----MICROBIOLOGY----

Accession: VA 123 Received: Oct 12, 2009

Collection sample: WOUND Collection date: Oct 12, 2009

Provider: Dr. General Hawk

Specimen: SWAB

CULTURE RESULTS: 1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S

35
 ----MICROBIOLOGY----

Accession: VA 123 Received: Oct 12, 2009

Collection sample: WOUND Collection date: Oct 12, 2009

Provider: Dr. General Hawk

Specimen: SWAB

CULTURE RESULTS: 1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S

Get numbered list 

of organisms

Look for 

Comments

36
 ----MICROBIOLOGY----

Accession: VA 123 Received: Oct 12, 2009

Collection sample: WOUND Collection date: Oct 12, 2009

Provider: Dr. General Hawk

Specimen: SWAB

CULTURE RESULTS: 1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S

Pull out susceptibility formatted like

DRUG = SUSCEPT.

Pull out 

susceptibility 

formatted in table

37
CULTURE RESULTS: 

1. MODERATE STAPHYLOCOCCUS AUREUS

Comment: CIPROFLOXACIN = S

ERYTHROMICIN = S

2. E. COLI

Comment: GENTAMICIN 500 synergy screen  RESISTANT

Confirmed sensitive to Penicillin

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. STAPHYLOCOCCUS AUREUS 

 : 2. ESCHERICHIA COLI

AMPICLN S

PENICLN S

38
CULTURE RESULTS: 

1. <ORGANISM>

Comment: <DRUG> = <SUSCEPTIBILITY>

<DRUG> = <SUSCEPTIBILITY>

2. <ORGANISM>

Comment: <DRUG> 500 synergy screen  <SUSCEPTIBILITY>

Confirmed <SUSCEPTIBILITY> to <DRUG> 

ANTIBIOTIC SUSCEPTIBILITY TESTS RESULTS:

1. <ORGANISM> 

 : 2. <ORGANISM>

<DRUG> <SUSCEPTIBILITY>

<DRUG> <SUSCEPTIBILITY>

39
Divide and Construct

Whole 

problem

Easy 

piece

Harder 

piece

Still

harder 

piece

Whole 

solution
• Break the problem down into pieces

• Determine which pieces are easiest to solve

• Use what you know about the pieces to find 

solutions

• Use solution from easier pieces to help solve 

harder pieces

Divide and Construct
DISCHARGE SUMMARY

ALLERGIES: Tylenol, Advil, Chocolate.

MEDICATIONS ON ADMISSION: diazapam 25 mg daily , 

aspirin 325 mg daily , Lasix 40 mg daily , Clariton

extended release 1 pill po prn.

HOSPITAL COURSE: The patient was admitted for a 

brain hemorrhage and was placed on Lasix. The patient 

became stable and was transferred to ICU for continued 

monitoring. While in the hospital, she acquired MRSA 

and was placed on antibiotics including vancomycin and 

penicillin. Patient should continue apirin daily and an oral 

dose of diazapam 25 mg for a total of 10 days.

Divide and Construct
DISCHARGE SUMMARY

ALLERGIES: Tylenol, Advil, Chocolate.

MEDICATIONS ON ADMISSION: diazapam 25 mg daily , 

aspirin 325 mg daily , Lasix 40 mg daily , Clariton

extended release 1 pill po prn.

HOSPITAL COURSE: The patient was admitted for a 

brain hemorrhage and was placed on Lasix. The patient 

became stable and was transferred to ICU for continued 

monitoring. While in the hospital, she acquired MRSA 

and was placed on antibiotics including vancomycin and 

penicillin. Patient should continue apirin daily and an oral 

dose of diazapam 25 mg for a total of 10 days.

Ignore this 

section

Has 

structure

No structure

Divide and Construct
DISCHARGE SUMMARY

ALLERGIES: Tylenol, Advil, Chocolate.

MEDICATIONS ON ADMISSION: diazapam 25 mg daily , 

aspirin 325 mg daily , Lasix 40 mg daily , Clariton

extended release 1 pill po prn.

HOSPITAL COURSE: The patient was admitted for a 

brain hemorrhage and was placed on Lasix. The patient 

became stable and was transferred to ICU for continued 

monitoring. While in the hospital, she acquired MRSA 

and was placed on antibiotics including vancomycin and 

penicillin. Patient should continue apirin daily and an oral 

dose of diazapam 25 mg for a total of 10 days.

Ignore this 

section

List

Narrative

Divide and Construct
What type 

of list?

DISCHARGE SUMMARY

ALLERGIES: Tylenol, Advil, Chocolate.

MEDICATIONS ON ADMISSION: diazapam 25 mg daily , 

aspirin 325 mg daily , Lasix 40 mg daily , Clariton

extended release 1 pill po prn.

HOSPITAL COURSE: The patient was admitted for a 

brain hemorrhage and was placed on Lasix. The patient 

became stable and was transferred to ICU for continued 

monitoring. While in the hospital, she acquired MRSA 

and was placed on antibiotics including vancomycin and 

penicillin. Patient should continue apirin daily and an oral 

dose of diazapam 25 mg for a total of 10 days.

Divide and Construct
DISCHARGE SUMMARY

ALLERGIES: Tylenol, Advil, Chocolate.

MEDICATIONS ON ADMISSION: diazapam 25 mg daily ,

aspirin 325 mg daily , Lasix 40 mg daily , Clariton

extended release 1 pill po prn.

HOSPITAL COURSE: The patient was admitted for a 

brain hemorrhage and was placed on Lasix. The patient 

became stable and was transferred to ICU for continued 

monitoring. While in the hospital, she acquired MRSA 

and was placed on antibiotics including vancomycin and 

penicillin. Patient should continue apirin daily and an oral 

dose of diazapam 25 mg for a total of 10 days.

List pieces

Divide and Construct

Part 

1

P 

Whole 

solution

Whole 

problem
Assumptions

• Some pieces must be easy

• The easy pieces have to be identified

• The easy pieces can aid in solving harder 

pieces
Conclusion

• NBS involved from the start and would love 

to re-engage NIST

• Opportunities include:

– Help in creating bridging architecture to next 

generation system including migration from M 

origins to a more modern architecture with 

ability to provide support from a whole new 

generation of developers using modern Web 

technology

48
Opportunities

– Incredible opportunity to study and create 

laboratory for usability and safety 

– Great opportunity to study healthcare security

– Excellent opportunity to evaluate and test 

standards
– Can evaluate and text logic used for business 

and clinical analytics and then test and release 

clinical software 

– Superb opportunity to utilize VA’s VINCI and 

other data as sandbox to evaluate big data using 

the 3.2 billion records available in the VINCI 

system and have access to not only data but also 

patient images
Dr. Robert Kolodner - VISTA

Dr. Scott DuVall – VISTA and VINCI

Acknowledgements