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Adaptation of OMOP in Veterinary Research

Comparative Informatics Veterinary Workshop: Session 2

Manlik Kwong BSEE, BSCS

Sr IT Advisor Tufts CTSI

Engineer/Scientist Tufts Institute for Clinical Research and Health Policy Studies

May 2022

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Topics�

  • CTSI One Health Alliance (COHA)
      • Bridging the gap between Veterinary and Human Informatics

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  • Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Overview

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  • Adaptation of OMOP CDM for Veterinary Research

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  • Use Case: Antibiotic Stewardship

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  • Use Case: Tufts Splenic Tumor Assessment Tool – T-STAT (t-stat.org)

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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CTSI One Health Alliance - COHA�

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  • Formed in 2016/2017 Tufts CTSI Renewal
  • 15 Veterinary Colleges that have partnered with Medical Colleges on a CTSA
  • URL: ctsaonehealthalliance.org
  • Workshops in 2018 and 2019 at Colorado State University, online workshop in 2020

Clinical and Translational Science Award One Health Alliance

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CTSI One Health Alliance – COHA Members�

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University of Minnesota

University of California, Davis

Colorado State University

University of Wisconsin

University of Missouri

University of Florida

North Carolina State University

University of Pennsylvania

Cornell University

Tufts University

Ohio State University

Purdue University

Kansas State University

University of Georgia

Auburn University

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Enabling One Health Research�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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  • How to bring together Veterinary and Human data for One Health studies
    • How to enable translation of veterinary research to human and vis versa
  • Common Data Model
  • Standard vocabularies and concepts

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CTSI One Health Alliance – TRANSLATOR Stack�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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  • TRanslational ANimal Shared CoLAboraTive Observational Research (TRANSLATOR - PMID: 31837763)
  • A Java/Web based Technology Platform
  • A Middleware Layer and reusable object component library

App1

App2

App3

COHA Research

Workbench Web-Application

Container

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OMOP Common Data Model�

  • Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM)
    • The OMOP is a public–private partnership, an initiative of the Foundation for the National Institutes of Health, a 501(c)(3) organization.
    • Focused on human care data
    • Patient Centric Design
    • Worldwide community supported
    • Estimated 11% global population has representation in an OMOP dataset
  • Enabled global collaborations in Study-a-thons and research across many networks and topics including COVID-19 (ex N3C)

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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OMOP Common Data Model�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Version 5.3

(ohdsi.org)

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OMOP Common Data Model�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Adaptation of OMOP for Veterinary Research�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Add support for species and breed concepts (primary)

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Adaptation of OMOP for Veterinary Research�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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OMOPv5+.person

OMOP Person

Table

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Adaptation of OMOP for Veterinary Research�

  • All other OMOP CDM tables unchanged
  • Vocabularies (consistent with Tufts CTSI’s OMOP Research Data Warehouse (TRDW)
      • SNOMED
      • LOINC
      • RxNORM
  • Daily ingestion of care sites, providers, patients, visits, treatments, labs, vitals, and invoice transactions
  • Presently (2000 – present) 391K patients; 1.27M visits; 4.4M drug exposures; 1.2M device exposures; 8.2M procedures; 6.4M observations; 9.7M measurements
  • Condition – diagnosis – from internal medicine discharge forms are being loaded/updated. Collaborative mapping standards are underway between Tufts, CSU, and UC Davis partners

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Veterinary Research Process�

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Use Case: Antibiotic Stewardship �(Fellman, Wayne, Chambers, Price, Kwong et al et al)

  • Cohort discovery and Analytics Use Case
  • Two Tufts DVM Student projects
      • Defined 61 Antibiotic Groups – MDR, Marbofloxacin oral, WHO, Beta lactam, etc by RxNORM codes
      • Defined 10 Risk group – prior surgery, ICU, O2 therapy, Hemodialysis, etc by SNOMED codes
      • Derived features:
        • Brachycephalic dog breeds
        • Acute Patient Physiologic and Laboratory Evaluation (APPLE) score (Glucose, Albumin, Lactate, Temperature, Creatinine, SpO2, T-Billi, Respiratory Rate, PVC, Urea, Age, Chloride)
        • Inpatient/outpatient criteria
      • Analytics and reporting using TRANSLATOR libraries/components

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Use Case: Antibiotic Stewardship �Publications

  • “Risk Factors for Antimicrobial Prescription in Dogs and Cats at a Tertiary Animal Hospital” [Emma Price VMD, et al – 2021 ACTS Translational Science]
  • “Development of a preliminary benchmark of patient days of antimicrobial therapy in cats and dogs at a tertiary veterinary hospital” [Emma Price VMD, et al –2022 ACTS Translational Science]
      • Characterize patient factors of hospitalized dogs and cats associated with the prescription of antimicrobials
  • “Factors associated with antimicrobial drug prescription among inpatient dogs and cats at an academic veterinary hospital” [Emma Price VMD, et al – 2022 SHEA Spring Conference]
      • Antimicrobial use in veterinary and human
      • Household sharing of resistant bacteria species
      • One Health perspective
      • 11,685 dogs (14,328 visits), 3,371 cats (4,088 visits)

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�Use Case: Tufts Splenic Tumor Assessment Tool (t-stat.org – Berg, Burgess, Price, King, Kwong et al PMID: 34061606)

  • Stand alone Veterinary OMOP CDM for Clinical Decision Support & Data Collection Use Case
  • Estimating the probability of malignancy in individual dogs with splenic masses
  • The calculation is based on a multivariable analysis of data from 422 dogs with splenic masses that were treated at our institution.
  • Web-based Calculator
  • Automated user/clinician reported outcomes via SMS Text based survey or online web-based survey

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Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Predicted Probability

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Prediction Details

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Use Case: Tufts Splenic Tumor Assessment Tool�

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Edit case or Download a pdf report for documentation

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Register contact method to submit follow-up outcomes data reporting

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Use Case: Tufts Splenic Tumor Assessment Tool�

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  • Automatically generated/sent after 5 days. Expires after 30 days
  • Series of individual yes/no questions (1 text answer question – “Other”)
    • SMS Survey file
    • 26 questions, answers mapped to OMOP concepts
    • Flow control based on answer
  • Captured and coded in OMOPv6+ survey_conduct database table and linked to case
  • Data intended to help improve future prediction models
  • Use Twilio SMS service (Twilio SendGrid E-mail service)

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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  • Auto owner/patient ID (GUID)
  • Clinical study visit type
  • Special Facility-Other (site)
  • T-STAT questions:
    • Serum total protein > SNOMED.37398462
    • CT Spleen > LOINC.3006580
    • Nucleated red blood cell count > SNOMED.37399327
    • Mass of spleen > SNOMED.45763557
    • Etc

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  • T-STAT answers:
    • Mild > SNOMED.45883535
    • Marked > SNOMED.46237456
    • Present > SNOMED.4181412
    • Absent > SNOMED.4132135

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Use Case: Tufts Splenic Tumor Assessment Tool�

Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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  • 26 SMS Text Questions
  • Q1: Did the data you entered in T-STAT pertain to an actual dog with a splenic mass?
  • Q2: Was the advice you gave the owner regarding pursuing splenectomy influenced by the T-STAT calculator result?
  • Q3: Did the owner consider the T-STAT result in deciding whether or not to pursue splenectomy?
  • Q4: Did the owner elect splenectomy?

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  • Q5: Final histopathologic diagnosis of Splenic Hematoma?
  • …[18 final diagnosis questions]
  • Q22: Final histopathologic diagnosis of Unspecified Round Cell Tumor?
  • Q23: Final histopathologic diagnosis of Extramedullary Hematopoiesis?

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  • Q26: Please enter other final histopathologic diagnosis description.

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Use Case: Tufts Splenic Tumor Assessment Tool�

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Number of visits/completed T-STAT calculations

Number of users registering their E-mail for online survey

Number of users registering their cell phone for SMS survey

Captured outcomes data linked to case input

(OMOP v6 database)

DATE

N Visits

N Email

N SMS

Survey Completed

Has Outcome

Other Benign or Non-neoplastic Conditions

Follicular lymphoma

Metastatic Adenocarcinoma

Hemangiosarcoma

Myelolipoma

Lymphoid Hyperplasia

Large cell lymphoma

Undifferentiated Neoplasms

Marginal zone lymphoma

Osteosarcoma

Lymphoma

Unspecified Round Cell Tumor

Extramedullary Hematopoiesis

Small cell lymphoma

Histiocytic Sarcoma

High-grade Fibrohistiocytic Nodule

Leiomyoma

Soft Tissue Sarcomas

Leiomyosarcoma

Other

1/1/2021

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

2/1/2021

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

3/1/2021

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

4/1/2021

18

1

2

2

2

0

0

0

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

5/1/2021

11

0

7

2

2

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

6/1/2021

218

6

2

4

4

1

0

0

1

0

1

0

0

0

0

0

0

0

0

0

0

0

0

1

1

7/1/2021

123

6

0

3

3

0

0

0

1

0

1

0

0

0

1

0

0

0

0

0

0

0

0

0

1

8/1/2021

89

2

0

2

2

0

0

0

1

0

1

0

0

0

0

0

0

0

0

0

0

0

0

0

0

9/1/2021

26

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

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�Conclusion�

  • OMOP CDM and the TRANSLATOR platform can be used in veterinary research – cohort discovery, analysis, preparatory to research, etc
  • It can also be used to support stand-alone studies and in the form of online applications for data capture and management
  • TRANSLATOR provides many re-usable components for Extract/Transform/Load (ETL) and application development operating on an OMOP CDM
  • Future Directions:
      • Continue enriching our OMOP CDM
      • Leverage our Human OMOP work in medical device and high-resolution data integration
      • Real-time, prospective study candidate/enrollment support
      • Support for operational needs

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Adaptation of OMOP in Veterinary Research | © Tufts Medicine 2022 | Private and confidential. Not for redistribution.

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Thank You

Manlik Kwong

mkwong@tuftsmedicalcenter.org

tuftsmedicine.org