Genetic Test Results Ingestion System for Format Normalization
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Solution Overview
Problem
Genetic test results from healthcare providers are often stored in unstructured or semi-structured formats, leading to inefficiencies in storage and analysis, as they are not searchable and lack standardized labels, making population-level analytics challenging.
Innovation Solution
A genetic test results ingestion application processes and stores genetic test results in a structured format by applying optical character recognition (OCR) to unstructured formats and using lexing and parsing rules to standardize semi-structured formats, enabling efficient storage and analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If genetic test results are stored in unstructured or semi-structured formats, then data can be received from various genetic laboratories, but storage resources are burdened and data are not searchable
Solution Approach 1:
The patent transforms genetic test results from unstructured/semi-structured formats to a standardized structured format by changing the data organization parameters. This includes converting free-text descriptions to coded elements, transforming variable layouts to fixed schemas, and reorganizing data hierarchies to match the standardized format requirements, thereby reducing storage burden while maintaining compatibility
Solution Approach 2:
The system creates a standardized copy of genetic test results data from various source formats. Instead of storing multiple format variations, the patent extracts essential information from incoming unstructured/semi-structured data and reconstructs it in a unified structured format, eliminating redundant storage while preserving data integrity
2Adaptability or versatility
If genetic test results are stored in different formats from different genetic laboratories, then data from multiple sources can be accommodated, but population level analytics cannot be performed
Solution Approach 1:
The patent applies parameter changes by standardizing variable names, data types, and structural organization across all incoming genetic test results. This transformation enables consistent data aggregation from multiple laboratories, making population-level analytics feasible while maintaining the ability to accept diverse source formats
Solution Approach 2:
The system implements a universal standardized format that serves multiple functions: it accommodates data from various genetic laboratories with different formats, enables searchable access, and supports population-level analytics. This multi-functional approach resolves the contradiction between format diversity and analytical capability
3Stability of the object's composition
If genetic test results are stored in unstructured format, then original data format is preserved, but data are not searchable and lack semantic annotation
Solution Approach 1:
The patent creates a structured copy of the original unstructured genetic test results data. The standardized format preserves the essential information content while adding searchability and semantic annotation through consistent field names, data types, and hierarchical organization, without requiring modification of the source data
Solution Approach 2:
The standardized structured format acts as an intermediary representation between the original unstructured data from genetic laboratories and the analytics/search systems. This intermediate structured form maintains fidelity to the source data while enabling enhanced functionality through searchability and semantic clarity
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This solution enhances storage efficiency and facilitates population-level analytics by converting genetic test results into a standardized, searchable format, reducing storage burdens and improving data accessibility for healthcare providers.
Implementation Method 1
The genetic test results ingestion application applies an optical character recognition (OCR) process to the genetic test results such that the genetic test results are formatted in the semi-structured format
Data Source
AI summary
A computer-executable application receives genetic test results for a genetic test a patient has undergone, an identifier for the genetic test, and an identifier for the genetic laboratory that performed the genetic test. The application identifies a format type of the genetic test results. When the format type is unstructured, the application performs an optical character recognition process to the genetic test results such that the format type of the genetic test results is semi-structured. When the format type is semi-structured, the application identifies a set of lexing and parsing rules assigned to the genetic test. The application generates processed genetic test results by applying the set of lexing and parsing rules to the genetic test results and stores the processed genetic test results in a data store. When the format type is structured, the application stores the genetic test results as the processed genetic test results in the data store.