OMOP Preview

A brief introduction

Lihai Song

Backgroup

The current project called comparative effectiveness research through collaboration electronic reporting(CER2) is led by AAP. http://www2.aap.org/pros/epros/

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.

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.

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

OMOP resources

The overall previews and resources can be found http://omop.org/ The OMOP schema is based on Common Data Model(CDM).A well detailed information is provided here! http://omop.org/cdm

Vacabulary

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.

Vacabulary structure

The OMOP data provide demographic, drug,condition,obervation,procedure,provider,visit,cost etc. Here are the detailed information:

	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

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 http://www.fdbhealth.com/

Vacabulary 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

Vacabulary 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

Vacabulary 4

	Domain	Type	Vocabulary
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

LOINC tuturial is avaialbe here: https://loinc.org/slideshows/lab-loinc-tutorial

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 example

Suppose we want to know how the drug name 'Abilify' was mapped. We can get this informatino:

	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

Examples of OMOP

Suppose we wanted to identify those antipsychotic second generattion drugs. The goal is to find link using Rxnom and FDB ETC. We'll show in SAS.

Thank You!

Pediatric Research in Office Settings(ePros)

Pediatric Research Consortium (PeRC)

comparative effectiveness research through collaboration electronic reporting(CER2)