Standardized Description of the Feature Extraction Process to Transform Raw Data Into Meaningful Information for Enhancing Data Reuse: Consensus Study. Lamer, A., Fruchart, M., Paris, N., Popoff, B., Payen, A., Balcaen, T., Gacquer, W., Bouzillé, G., Cuggia, M., Doutreligne, M., & Chazard, E. JMIR medical informatics, 10(10):e38936, October, 2022.
doi  abstract   bibtex   
BACKGROUND: Despite the many opportunities data reuse offers, its implementation presents many difficulties, and raw data cannot be reused directly. Information is not always directly available in the source database and needs to be computed afterwards with raw data for defining an algorithm. OBJECTIVE: The main purpose of this article is to present a standardized description of the steps and transformations required during the feature extraction process when conducting retrospective observational studies. A secondary objective is to identify how the features could be stored in the schema of a data warehouse. METHODS: This study involved the following 3 main steps: (1) the collection of relevant study cases related to feature extraction and based on the automatic and secondary use of data; (2) the standardized description of raw data, steps, and transformations, which were common to the study cases; and (3) the identification of an appropriate table to store the features in the Observation Medical Outcomes Partnership (OMOP) common data model (CDM). RESULTS: We interviewed 10 researchers from 3 French university hospitals and a national institution, who were involved in 8 retrospective and observational studies. Based on these studies, 2 states (track and feature) and 2 transformations (track definition and track aggregation) emerged. "Track" is a time-dependent signal or period of interest, defined by a statistical unit, a value, and 2 milestones (a start event and an end event). "Feature" is time-independent high-level information with dimensionality identical to the statistical unit of the study, defined by a label and a value. The time dimension has become implicit in the value or name of the variable. We propose the 2 tables "TRACK" and "FEATURE" to store variables obtained in feature extraction and extend the OMOP CDM. CONCLUSIONS: We propose a standardized description of the feature extraction process. The process combined the 2 steps of track definition and track aggregation. By dividing the feature extraction into these 2 steps, difficulty was managed during track definition. The standardization of tracks requires great expertise with regard to the data, but allows the application of an infinite number of complex transformations. On the contrary, track aggregation is a very simple operation with a finite number of possibilities. A complete description of these steps could enhance the reproducibility of retrospective studies.
@article{lamer_standardized_2022,
	title = {Standardized {Description} of the {Feature} {Extraction} {Process} to {Transform} {Raw} {Data} {Into} {Meaningful} {Information} for {Enhancing} {Data} {Reuse}: {Consensus} {Study}},
	volume = {10},
	issn = {2291-9694},
	shorttitle = {Standardized {Description} of the {Feature} {Extraction} {Process} to {Transform} {Raw} {Data} {Into} {Meaningful} {Information} for {Enhancing} {Data} {Reuse}},
	doi = {10.2196/38936},
	abstract = {BACKGROUND: Despite the many opportunities data reuse offers, its implementation presents many difficulties, and raw data cannot be reused directly. Information is not always directly available in the source database and needs to be computed afterwards with raw data for defining an algorithm.
OBJECTIVE: The main purpose of this article is to present a standardized description of the steps and transformations required during the feature extraction process when conducting retrospective observational studies. A secondary objective is to identify how the features could be stored in the schema of a data warehouse.
METHODS: This study involved the following 3 main steps: (1) the collection of relevant study cases related to feature extraction and based on the automatic and secondary use of data; (2) the standardized description of raw data, steps, and transformations, which were common to the study cases; and (3) the identification of an appropriate table to store the features in the Observation Medical Outcomes Partnership (OMOP) common data model (CDM).
RESULTS: We interviewed 10 researchers from 3 French university hospitals and a national institution, who were involved in 8 retrospective and observational studies. Based on these studies, 2 states (track and feature) and 2 transformations (track definition and track aggregation) emerged. "Track" is a time-dependent signal or period of interest, defined by a statistical unit, a value, and 2 milestones (a start event and an end event). "Feature" is time-independent high-level information with dimensionality identical to the statistical unit of the study, defined by a label and a value. The time dimension has become implicit in the value or name of the variable. We propose the 2 tables "TRACK" and "FEATURE" to store variables obtained in feature extraction and extend the OMOP CDM.
CONCLUSIONS: We propose a standardized description of the feature extraction process. The process combined the 2 steps of track definition and track aggregation. By dividing the feature extraction into these 2 steps, difficulty was managed during track definition. The standardization of tracks requires great expertise with regard to the data, but allows the application of an infinite number of complex transformations. On the contrary, track aggregation is a very simple operation with a finite number of possibilities. A complete description of these steps could enhance the reproducibility of retrospective studies.},
	language = {eng},
	number = {10},
	journal = {JMIR medical informatics},
	author = {Lamer, Antoine and Fruchart, Mathilde and Paris, Nicolas and Popoff, Benjamin and Payen, Anaïs and Balcaen, Thibaut and Gacquer, William and Bouzillé, Guillaume and Cuggia, Marc and Doutreligne, Matthieu and Chazard, Emmanuel},
	month = oct,
	year = {2022},
	pmid = {36251369},
	pmcid = {PMC9623460},
	keywords = {Observation Medical Outcomes Partnership, algorithm, data reuse, data warehouse, database, feature extraction},
	pages = {e38936},
}
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