OMOP Preview

A brief introduction

Lihai Song

Backgroup

The current project called comparative effectiveness research through collaboration electronic reporting(CER2) is led by AAP.

  • Pediatric Research in Office Settings(ePros)-OMOP
  • Pediatric Research Consortium (PeRC)-EPIC
  • Boston Medical Center-I2B2
  • MetroHealth of Cleverland-EPIC

There are different EHR systems over 1.3 Million patients seen in primary care network!

Work flow

Data integration across system have been a challenge. The goal is to find a way to aggregat data to a format that can be easily portable and standardize to all researchers. For example, lab results without LOINC code must be convereted to keep consistency across all systems. Error: Embedded data could not be displayed. http://www2.aap.org/pros/epros/

Observational Medical Outcomes Partnership(OMOP)

The OMOP was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products.

  1. Conduct methodological research to empirically evaluate the performance of various analytical methods on their ability to identify true associations and avoid false findings
  2. Develop tools and capabilities for transforming, characterizing, and analyzing disparate data sources across the health care delivery spectrum
  3. Establish a shared resource so that the broader research community can collaboratively advance the science

OMOP resources

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The overall previews and resources can be found http://omop.org/.

OMOP resources CDM

Error: Embedded data could not be displayed. http://omop.org/cdm. The OMOP schema is based on Common Data Model(CDM).

Vocabulary

The Standard Vocabulary is a foundational tool developed by the OMOP team to enable transparent and consistent content across disparate observational databases, and serves to support the OMOP research community in conducting efficient and reproducible observational research.

  • Demographic
  • Drug
  • Condition
  • Obervation(Height weight BP)
  • procedure
  • Drug
  • Provider
  • Other

Those resources can be varied by projects.

Vocabulary structure

Here are the detailed information about the vocabulary:

Domain Type Vocabulary Restricted
1 Demographic Standard terminology HL7 Administrative Sex
2 OMB Ethnicity
3 CDC Race
4 Drug Standard terminology RxNorm
5 WHO ATC
6 VA Class
7 NDF-RT
8 FDB ETC Yes
9 Mapped coding scheme Cerner Multum
10 NDC
11 FDA SPL
12 FDB Drug Product Yes

Vocabulary 2

Domain Type Vocabulary Restricted
13 FDB Indication Yes
14 Medi-Span GPI Yes
15 Multilex Yes
16 NLM MeSH
17 VA Product
18 Condition Standard terminology, classification SNOMED-CT
19 MEDRA Yes
20 Mapped coding scheme ICD-10-CM
21 ICD-9-CM
22 OXMIS
23 Read
24 Procedure Standard classification SNOMED-CT

Note about FDB ETC

The FDB ETC enhensed theraphical categoris which was provided by First Databank, which creates and maintains sidely used drug database products,software for drug database integration, and drug reference products.

http://en.wikipedia.org/wiki/First_DataBank

About FDB ETC

Vocabulary 3

Domain Type Vocabulary Restricted
25 Standard terminology ICD-9-Procedure
26 HCPCS
27 CPT-4 Yes
28 Mapped coding scheme ICD-10-PCS
29 Cohort Analysis SMQ Yes
30 OMOP DOI
31 OMOP HOI
32 Observation Standard terminology, classification SNOMED-CT
33 LOINC
34 UCUM
35 Standard classification LOINC Multidimentional Classification
36 Provider Standard terminology NUCC

Vocabulary 4

Domain Type Vocabulary Restricted
37 CMS Speciality
38 Visit Standard terminology OMOP Visit
39 CMS Place of Service
40 Cost Standard classification MDC
41 Standard terminology Revenue Code
42 DRG
43 APC
44 Concept Type Standard terminology OMOP Condition Occurance Type
45 OMOP Procedure Occurance Type
46 OMOP Observation Type
47 OMOP Drug Exposure Type
48 OMOP Death Type

Actual vocabulary data information

vocabulary_id vocabulary_name vocabulary_id.1 vocabulary_name.1
1 0 IMEDS Vocabulary v4.4 2014-04-11 17 Read
2 1 SNOMED-CT 18 OXMIS
3 2 ICD-9-CM 21 WHO ATC
4 3 ICD-9-Procedure 24 IMEDS Visit
5 5 HCPCS 28 VA Product
6 6 LOINC 32 VA Class
7 7 NDF-RT 33 Cohort
8 8 RxNorm 34 ICD-10-CM
9 9 NDC 35 ICD-10-PCS
10 10 GPI 36 IMEDS Drug Exposure Type
11 11 UCUM 37 IMEDS Condition Occurrence Type
12 12 HL7 Administrative Sex 38 IMEDS Procedure Occurrence Type
13 13 CDC Race 39 IMEDS Observation Type
14 14 CMS Place of Service 40 DRG
15 16 Multum 41 MDC

Actual vocabulary data information(continue)

vocabulary_id vocabulary_name vocabulary_id.1 vocabulary_name.1
31 42 APC 54 CCS
32 43 Revenue Code 55 OPCS-4
33 44 Ethnicity 56 Gemscript
34 45 IMEDS Death Type 57 HES Specialty
35 46 NLM Mesh 4 CPT-4
36 47 NUCC 20 FDB ETC
37 48 CMS Specialty 19 FDB Indication/Contraindication
38 49 LOINC Multidimensional Classification 15 MedDRA
39 50 FDA SPL 22 Multilex
40 53 FDB Genseqno 31 SMQ

LOINC

Logical Observation Identifiers Names and Codes (LOINC) is a database and universal standard for identifying medical laboratory observations. It was developed and is maintained by the Regenstrief Institute, a US non-profit medical research organization, in 1994. LOINC was created in response to the demand for an electronic database for clinical care and management and is publicly available at no cost.

Information regrading LOINC

Mapping example

A example of mapping from ndc code to rxnorm etc

source_code source_vocabulary_id source_code_description target_concept_id target_vocabulary_id
1 54738095016 9 Ribavirin 200 MG Oral Tablet 19061194 8
2 00185064401 9 Phentermine Hydrochloride 18.8 MG Oral Capsule 735394 8
3 00185065430 9 Phentermine Hydrochloride 37.5 MG Oral Tablet 19131610 8
4 51079030601 9 POLYETHYLENE GLYCOL 3350 142 MG/ML Oral Solution 40167259 8
5 51129355902 9 Benazepril hydrochloride 5 MG Oral Tablet 40171682 8
6 50732091501 9 Verapamil hydrochloride 180 MG Extended Release Tablet 40171863 8
7 51079068220 9 Verapamil hydrochloride 80 MG Oral Tablet 40171917 8
8 51129396102 9 Benazepril hydrochloride 10 MG Oral Tablet 40171661 8

Mapping Atypical Antipsychotic

Suppose we want to know how the drug name 'Abilify' was mapped.

source_code source_vocabulary_id source_code_description target_concept_id target_vocabulary_id
1 68071079315 9 aripiprazole 10 MG Oral Tablet [Abilify] 19098477 8
2 59148001007 9 aripiprazole 20 MG Oral Tablet [Abilify] 19098479 8
3 59148000816 9 aripiprazole 10 MG Oral Tablet [Abilify] 19098477 8
4 58016094036 9 aripiprazole 10 MG Oral Tablet [Abilify] 19098477 8
5 58016094069 9 aripiprazole 10 MG Oral Tablet [Abilify] 19098477 8
6 51129293301 9 aripiprazole 5 MG Oral Tablet [Abilify] 19102836 8
7 58016094026 9 aripiprazole 10 MG Oral Tablet [Abilify] 19098477 8
8 58016005401 9 aripiprazole 5 MG Oral Tablet [Abilify] 19102836 8

This will be what We can get from this information.

Examples of OMOP

Suppose we wanted to identify those antipsychotic second generattion drugs. The goal is to find link using Rxnom and FDB ETC.

Let's go to SAS and see the real data and look at more examples about Hierarchy of the FDB Enhanced Therapeutic Class.

Thank You!

  • Pediatric Research in Office Settings(ePros)
  • Pediatric Research Consortium (PeRC)
  • comparative effectiveness research through collaboration electronic reporting(CER2)

Resources are available from the link!