Genomic Annotation Compression for Selective Field Decompression

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Solution Overview

Problem

Existing genomic data compression algorithms lack selectivity, interoperability, and generality, leading to inefficient data management and frequent format conversions, and are unable to perform selective decompression and encryption of genomic annotation data.

Innovation Solution

A method and system for managing genomic annotation data compression by dividing data into chunks, applying different compressors based on attribute-specific characteristics, generating a unified file format with metadata and access control, and enabling selective decompression and encryption.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Ease of operation

If existing compression algorithms compress all fields together, then compression is simpler to implement, but selectivity is lost and individual field extraction requires full decompression

Engineering Contradiction:

Improvecompression implementation simplicityVSAvoidselective field extraction capability

Core Design Contradiction:

Ease of operationVSAdaptability or versatility

Solution Approach 1:

The patent divides the annotation data into multiple independent fields (e.g., chromosome, start position, end position, feature name, score, strand) that can be compressed separately using different compression algorithms. Each field is processed independently, allowing selective decompression of individual fields without requiring full decompression of all data.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent applies different compression algorithms to different fields based on their specific characteristics. For example, integer fields may use run-length encoding while string fields use dictionary-based compression. This localized optimization enables both efficient compression and selective extraction of specific field types.

Inventive Principle:

Principle #3Local quality

2Manufacturing precision

If multiple incompatible file formats are used for genomic annotation data, then each format can be optimized for specific data types, but interoperability is reduced and frequent format conversions are required

Engineering Contradiction:

Improvedata type optimizationVSAvoidinteroperability

Core Design Contradiction:

Manufacturing precisionVSAdaptability or versatility

Solution Approach 1:

The patent creates a unified file format that can accommodate multiple types of genomic annotation data (variant calls, gene expressions, Hi-C contact matrices, quantitative browser tracks) in a single standardized structure. This universal format eliminates the need for format conversions while maintaining the ability to optimize compression for each data type within the unified structure.

Inventive Principle:

Principle #6Universality (Multi-functionality)

Solution Approach 2:

The unified format combines elements from multiple existing formats (VCF, BED, WIG) into a single composite structure that preserves the strengths of each original format while adding interoperability. The format uses a hierarchical structure with common headers and type-specific sections that can be selectively processed.

Inventive Principle:

Principle #40Composite materials

3Productivity

If specialized compression methods based on disk-based array management tools are used, then compression efficiency improves for specific data types, but high-level features like metadata, linkages, and attribute-specific indexing are lost

Engineering Contradiction:

Improvecompression efficiencyVSAvoidhigh-level feature capability

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent implements a nested structure where compressed data chunks are organized within a hierarchical framework that preserves metadata, linkages, and indexing information. The compression algorithms operate on nested levels (fields within chunks within files), maintaining access to high-level features while achieving efficient compression at lower levels.

Inventive Principle:

Principle #7Nested doll (Nesting)

Solution Approach 2:

The patent introduces an intermediary layer between the compressed data and the user interface that manages metadata, linkages, and indexing. This intermediary maintains the semantic relationships and structural information while allowing efficient compressed storage and retrieval, bridging the gap between compression efficiency and feature richness.

Inventive Principle:

Principle #24Intermediary (Mediator)

Data Source

PatentUS12445148B2System and method for effective compression representation and decompression of diverse tabulated data

Publication Date: 2025.10.14 KONINKLIJKE PHILIPS NV

AI summary

A method for controlling compression of data includes accessing genomic annotation data in one of a plurality of first file formats, extracting attributes from the genomic annotation data, dividing the genomic annotation data into multiple chunks, and processing the extracted attributes and chunks into correlated information. The method also includes generating a file in a second file format that includes the correlated information and information indicative of the different compressors for the chunks and attributes indicated in the correlated information. The information indicative of the different compressors is processed into the second file format to allow selective decompression of the attributes and chunks indicated in correlated information. The method also includes generating access control policy information for the correlated information and integrating the access control policy information into the file of the second file format.