Literature DB >> 31238109

HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model.

Jeremy L Warner1, Dmitry Dymshyts2, Christian G Reich3, Michael J Gurley4, Harry Hochheiser5, Zachary H Moldwin6, Rimma Belenkaya7, Andrew E Williams8, Peter C Yang9.   

Abstract

Systematic application of observational data to the understanding of impacts of cancer treatments requires detailed information models allowing meaningful comparisons between treatment regimens. Unfortunately, details of systemic therapies are scarce in registries and data warehouses, primarily due to the complex nature of the protocols and a lack of standardization. Since 2011, we have been creating a curated and semi-structured website of chemotherapy regimens, HemOnc.org. In coordination with the Observational Health Data Sciences and Informatics (OHDSI) Oncology Subgroup, we have transformed a substantial subset of this content into the OMOP common data model, with bindings to multiple external vocabularies, e.g., RxNorm and the National Cancer Institute Thesaurus. Currently, there are >73,000 concepts and >177,000 relationships in the full vocabulary. Content related to the definition and composition of chemotherapy regimens has been released within the ATHENA tool (athena.ohdsi.org) for widespread utilization by the OHDSI membership. Here, we describe the rationale, data model, and initial contents of the HemOnc vocabulary along with several use cases for which it may be valuable.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Knowledge engineering; Neoplasms; Ontologies

Year:  2019        PMID: 31238109      PMCID: PMC6697579          DOI: 10.1016/j.jbi.2019.103239

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  12 in total

1.  HemOnc.org: A Collaborative Online Knowledge Platform for Oncology Professionals.

Authors:  Jeremy L Warner; Andrew J Cowan; Aric C Hall; Peter C Yang
Journal:  J Oncol Pract       Date:  2015-03-03       Impact factor: 3.840

2.  Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens.

Authors:  Andrew M Malty; Sandeep K Jain; Peter C Yang; Krysten Harvey; Jeremy L Warner
Journal:  JCO Clin Cancer Inform       Date:  2018-05-11

3.  Temporal Annotation in the Clinical Domain.

Authors:  William F Styler; Steven Bethard; Sean Finan; Martha Palmer; Sameer Pradhan; Piet C de Groen; Brad Erickson; Timothy Miller; Chen Lin; Guergana Savova; James Pustejovsky
Journal:  Trans Assoc Comput Linguist       Date:  2014-04

Review 4.  Representing Knowledge Consistently Across Health Systems.

Authors:  S T Rosenbloom; R J Carroll; J L Warner; M E Matheny; J C Denny
Journal:  Yearb Med Inform       Date:  2017-09-11

5.  Patterns of adjuvant chemotherapy use in a population-based cohort of patients with resected stage II or III colon cancer.

Authors:  Thomas A Abrams; Rick Brightly; Jianbin Mao; Gregory Kirkner; Jeffrey A Meyerhardt; Deborah Schrag; Charles S Fuchs
Journal:  J Clin Oncol       Date:  2011-07-18       Impact factor: 44.544

6.  DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records.

Authors:  Guergana K Savova; Eugene Tseytlin; Sean Finan; Melissa Castine; Timothy Miller; Olga Medvedeva; David Harris; Harry Hochheiser; Chen Lin; Girish Chavan; Rebecca S Jacobson
Journal:  Cancer Res       Date:  2017-11-01       Impact factor: 12.701

7.  Discussions about clinical trials among patients with newly diagnosed lung and colorectal cancer.

Authors:  Kenneth L Kehl; Neeraj K Arora; Deborah Schrag; John Z Ayanian; Steven B Clauser; Carrie N Klabunde; Katherine L Kahn; Robert H Fletcher; Nancy L Keating
Journal:  J Natl Cancer Inst       Date:  2014-09-13       Impact factor: 13.506

8.  Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.

Authors:  George Hripcsak; Jon D Duke; Nigam H Shah; Christian G Reich; Vojtech Huser; Martijn J Schuemie; Marc A Suchard; Rae Woong Park; Ian Chi Kei Wong; Peter R Rijnbeek; Johan van der Lei; Nicole Pratt; G Niklas Norén; Yu-Chuan Li; Paul E Stang; David Madigan; Patrick B Ryan
Journal:  Stud Health Technol Inform       Date:  2015

9.  Real-world Data for Clinical Evidence Generation in Oncology.

Authors:  Sean Khozin; Gideon M Blumenthal; Richard Pazdur
Journal:  J Natl Cancer Inst       Date:  2017-11-01       Impact factor: 13.506

10.  Phase III study of capecitabine plus oxaliplatin compared with fluorouracil and leucovorin plus oxaliplatin in metastatic colorectal cancer: a final report of the AIO Colorectal Study Group.

Authors:  Rainer Porschen; Hendrik-Tobias Arkenau; Stephan Kubicka; Richard Greil; Thomas Seufferlein; Werner Freier; Albrecht Kretzschmar; Ullrich Graeven; Axel Grothey; Axel Hinke; Wolff Schmiegel; Hans-Joachim Schmoll
Journal:  J Clin Oncol       Date:  2007-06-04       Impact factor: 44.544

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  17 in total

1.  Patients Recently Treated for B-lymphoid Malignancies Show Increased Risk of Severe COVID-19.

Authors:  Samuel M Rubinstein; Divaya Bhutani; Ryan C Lynch; Jeremy L Warner; Michael A Thompson; Chih-Yuan Hsu; Yu Shyr; Shailesh Advani; Ruben A Mesa; Sanjay Mishra; Daniel P Mundt; Dimpy P Shah; R Alejandro Sica; Keith E Stockerl-Goldstein; Catherine Stratton; Matthias Weiss; Alicia Beeghly-Fadiel; Melissa Accordino; Sarit E Assouline; Joy Awosika; Ziad Bakouny; Babar Bashir; Stephanie Berg; Mehmet Asim Bilen; Cecilia A Castellano; Jacob C Cogan; Devendra Kc; Christopher R Friese; Shilpa Gupta; Daniel Hausrath; Clara Hwang; Nathalie A Johnson; Monika Joshi; Anup Kasi; Elizabeth J Klein; Vadim S Koshkin; Nicole M Kuderer; Daniel H Kwon; Chris Labaki; Tahir Latif; Eric Lau; Xuanyi Li; Gary H Lyman; Rana R McKay; Gayathri Nagaraj; Amanda Nizam; Taylor K Nonato; Adam J Olszewski; Hyma V Polimera; Andrew J Portuguese; Matthew M Puc; Pedram Razavi; Rachel Rosovski; Andrew Schmidt; Sumit A Shah; Aditi Shastri; Christopher Su; Pallawi Torka; Trisha M Wise-Draper; Leyre Zubiri
Journal:  Blood Cancer Discov       Date:  2022-05-05

2.  Application of Artificial Intelligence Methods to Pharmacy Data for Cancer Surveillance and Epidemiology Research: A Systematic Review.

Authors:  Andrew E Grothen; Bethany Tennant; Catherine Wang; Andrea Torres; Bonny Bloodgood Sheppard; Glenn Abastillas; Marina Matatova; Jeremy L Warner; Donna R Rivera
Journal:  JCO Clin Cancer Inform       Date:  2020-11

3.  Opportunities and Challenges for Analyzing Cancer Data at the Inter- and Intra-Institutional Levels.

Authors:  Julie Wu; Jordan Bryan; Samuel M Rubinstein; Lucy Wang; Michele Lenoue-Newton; Raed Zuhour; Mia Levy; Christine Micheel; Yaomin Xu; Suresh K Bhavnani; Lester Mackey; Jeremy L Warner
Journal:  JCO Precis Oncol       Date:  2020-06-25

4.  Chemotherapy Knowledge Base Management in the Era of Precision Oncology.

Authors:  Samuel M Rubinstein; Tarsheen Sethi; Neeta K Venepalli; Bishal Gyawali; Candice Schwartz; Donna R Rivera; Peter C Yang; Jeremy L Warner
Journal:  JCO Clin Cancer Inform       Date:  2021-01

5.  Extending the OMOP Common Data Model and Standardized Vocabularies to Support Observational Cancer Research.

Authors:  Rimma Belenkaya; Michael J Gurley; Asieh Golozar; Dmitry Dymshyts; Robert T Miller; Andrew E Williams; Shilpa Ratwani; Anastasios Siapos; Vladislav Korsik; Jeremy Warner; W Scott Campbell; Donna Rivera; Tatiana Banokina; Elizaveta Modina; Shantha Bethusamy; Henry Morgan Stewart; Meera Patel; Ruijun Chen; Thomas Falconer; Rae Woong Park; Seng Chan You; Hokyun Jeon; Soe Jeong Shin; Christian Reich
Journal:  JCO Clin Cancer Inform       Date:  2021-01

6.  Standardizing Chemotherapy Regimen Nomenclature: A Proposal and Evaluation of the HemOnc and National Cancer Institute Thesaurus Regimen Content.

Authors:  Samuel M Rubinstein; Peter C Yang; Andrew J Cowan; Jeremy L Warner
Journal:  JCO Clin Cancer Inform       Date:  2020-01

7.  OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

Authors:  Hayley M Dingerdissen; Frederic Bastian; K Vijay-Shanker; Marc Robinson-Rechavi; Amanda Bell; Nikhita Gogate; Samir Gupta; Evan Holmes; Robel Kahsay; Jonathon Keeney; Heather Kincaid; Charles Hadley King; David Liu; Daniel J Crichton; Raja Mazumder
Journal:  JCO Clin Cancer Inform       Date:  2020-03

8.  Clinical comparison between trial participants and potentially eligible patients using electronic health record data: A generalizability assessment method.

Authors:  James R Rogers; George Hripcsak; Ying Kuen Cheung; Chunhua Weng
Journal:  J Biomed Inform       Date:  2021-05-25       Impact factor: 8.000

9.  Deep phenotyping: Embracing complexity and temporality-Towards scalability, portability, and interoperability.

Authors:  Chunhua Weng; Nigam H Shah; George Hripcsak
Journal:  J Biomed Inform       Date:  2020-04-23       Impact factor: 6.317

Review 10.  A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants.

Authors:  Xuanyi Li; Jeremy L Warner
Journal:  Front Cell Dev Biol       Date:  2020-02-11
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