A metadata framework for electronic phenotypes
Creators
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Spotnitz, Matthew1
- Acharya, Nripendra1
- Cimino, James J.2
- Murphy, Shawn3
- Namjou-Khales, Bahram4
- Crimmins, Nancy4
- Walunas, Theresa5
- Liu, Cong1
- Crosslin, David6
- Benoit, Barbara3
- Rosenthal, Elisabeth7
- Pacheco, Jennifer8
- Ostropolets, Anna1
- Reyes Nieva, Harry1
- Patterson, Jason1
- Richter, Lauren1
- Callahan, Tiffany1
- Elhussein, Ahmed1
- Pang, Chao1
- Kiryluk, Krzysztof1
- Nestor, Jordan1
- Khan, Atlas1
- Mohan, Sumit1
- Minty, Evan9
- Chung, Wendy1
- Wei, Wei-Qi10
- Natarajan, Karthik1
- Weng, Chunhua1
- 1. Columbia University Medical Center
- 2. University of Alabama at Birmingham
- 3. Partners HealthCare
- 4. Cincinnati Children's Hospital Medical Center
- 5. Northwestern University
- 6. Tulane University
- 7. University of Washington
- 8. University of Northwestern
- 9. University of Calgary
- 10. Vanderbilt University Medical Center
Description
As many phenotyping algorithms are being created to support precision medicine or observational studies using electronic patient data, it is getting increasingly difficult to identify the right algorithm for the right task. A metadata framework promises to help curate phenotyping algorithms to facilitate more efficient and accurate retrieval. We recruited 20 researchers from two phenotyping communities, the eMERGE and the OHDSI communities, and used a mixed-methods approach to develop the metadata framework. Once we achieved a consensus of 39 metadata elements, we surveyed 47 new researchers from these communities to evaluate the utility of the metadata framework. Two researchers were also asked to use it to annotate eight type 2 diabetes mellitus phenotypes. The survey consisted of a series of multiple-choice questions, which allowed rating of the utility of each element on a scale of 1-5, and open-ended questions, which allowed for narrative responses. More than 90% of respondents rated metadata elements concerning phenotype definition and validation methods and metrics with a score of 4 or 5. Our thematic analysis of the respondents' feedback indicates that the strengths of the metadata framework were its ability to capture rich descriptions, explicitness, compliance with data standards, comprehensiveness in validation metrics, and ability to enable cross-phenotype searches. Limitations were its complexity for data collection and entailed costs.
Notes
Funding provided by: U.S. National Library of Medicine
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000092
Award Number: T15LM007079
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011172
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011175
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008680
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011176
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008685
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG006379
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011169
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011167
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008657
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011181
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG011166
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008672
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008666
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008680
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008684
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008701
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008673
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008676
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U01HG008664
Funding provided by: National Human Genome Research Institute
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000051
Award Number: U54MD007593
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