Data Models & Global Constants

Relevant source files

The following files were used as context for generating this wiki page:

• src/constants/datafields/genome_sequence.ts
• src/lib/forms/(protein-tools)/msa-snp-analysis/msa-snp-analysis-form-schema.ts
• src/lib/forms/(viral-tools)/subspecies-classification/subspecies-classification-form-schema.ts
• src/lib/forms/(viral-tools)/sars-cov2-genome-analysis/sars-cov2-genome-analysis-form-schema.ts
• src/lib/services/service-info.ts
• src/styles/theme-content.ts
• src/app/allTermSearchResults.tsx

Introduction

The Data Models & Global Constants within the DXKB project define the structural foundations for biological data representation, service parameters, and application-wide configurations. These models ensure consistency across various bioinformatics tools, including genome assembly, variation analysis, and taxonomic classification, by providing strongly typed schemas and standardized field definitions.

These constants encompass everything from biological entity attributes (genomes, sequences, and features) to UI-specific content mapping for different project themes (zinc, dxkb, or bvbrc). By centralizing these definitions, the system maintains a unified interface for complex scientific data interactions and API communications.

Biological Data Models

Genome Sequence Fields

The project defines a standardized structure for genomic sequence metadata, categorized into logical groups such as General Info, Sequence Info, Taxonomy Info, and Additional Info.

Field	Label	Group	Description
genome_id	Genome ID	General Info	Unique identifier for the genome.
accession	Accession	Sequence Info	NCBI NucCore accession number.
sequence_type	Sequence Type	Sequence Info	Type of sequence (e.g., chromosome, plasmid).
gc_content	GC Content %	Sequence Info	Percentage of Guanine and Cytosine.
length	Length (bp)	Sequence Info	Total length of the sequence in base pairs.

Sources: src/constants/datafields/genome_sequence.ts:1-105

Search Result Data Types

The system processes various biological entities during search operations, each requiring specific metadata formatting for the user interface.

The search system supports specialized types including taxonomy, genome, strain, genome_feature, epitope, and protein_structure.
Sources: src/app/allTermSearchResults.tsx:112-280

Service Parameter Models

MSA & SNP Analysis Schema

The Multiple Sequence Alignment (MSA) and SNP analysis module utilizes a strict Zod schema to validate input sources, reference types, and alignment strategies.

Parameter	Type	Valid Values
input_status	Enum	unaligned, aligned
alphabet	Enum	dna, protein
aligner	Enum	Mafft, Muscle
ref_type	Enum	none, first, feature_id, genome_id, string

Sources: src/lib/forms/(protein-tools)/msa-snp-analysis/msa-snp-analysis-form-schema.ts:4-44

Subspecies Classification Options

Global constants define a fixed list of virus types supported for subspecies classification, mapped to legacy API values from the BV-BRC project.

export const subspeciesVirusTypeOptions = [
  { value: "MASTADENOA", label: "Adenoviridae - Human mastadenovirus A" },
  { value: "DENGUE", label: "Flaviviridae - Dengue virus" },
  { value: "HCV", label: "Flaviviridae - Hepatitis C virus" },
  { value: "INFLUENZAH5", label: "Orthomyxoviridae - Influenza A H5" },
  { value: "MPOX", label: "Poxviridae - Monkeypox virus" },
];

Sources: src/lib/forms/(viral-tools)/subspecies-classification/subspecies-classification-form-schema.ts:13-40

Global UI and Theme Constants

Theme Content Mapping

The application supports multiple themes (DXKB, BV-BRC, and generic variants) using a centralized mapping system to control site naming, funding statements, and welcome subtitles.

Content Definitions:

• DXKB: "Disease X Knowledge Base" - Funded via Federal funds awarded to the University of Chicago.
• BV-BRC: "Bacterial and Viral Bioinformatics Resource Center" - Funded by NIAID/NIH under Grant No. U24AI183849.
  Sources: src/styles/theme-content.ts:4-58

Service Metadata & Documentation

Global constants are used to populate informational popups throughout the service forms, providing technical context for users.

Read Input Metadata

Documentation constants define the standard handling for different read libraries:

• Paired-end reads: Expected as file pairs (Read 1 and Read 2) where each read occurs in the same Nth position as its mate.
• SRA Accession: Numerical identifiers used to pull data directly from the NCBI Sequence Read Archive.
  Sources: src/lib/services/service-info.ts:7-36

Summary

Data Models and Global Constants in DXKB facilitate the rigorous validation and standardized representation required for bioinformatics workflows. By utilizing Zod schemas for service parameters and structured field definitions for biological entities, the project ensures data integrity from user input through to API submission and result rendering. Additionally, the thematic constant system allows the platform to serve multiple organizational identities while maintaining a shared codebase.