Biological Database Classification

biological-database-classification.md

Biological Database Classification

The classification of biological databases follows a hierarchical system similar to information organization in other fields:

• Primary Databases: Contain raw experimental data directly submitted by researchers
• Secondary Databases: Contain processed, analyzed, and annotated data derived from primary databases
• Tertiary Databases: Integrate and synthesize information from multiple primary and secondary sources
• Mixed Databases: Incorporate aspects of multiple classification levels

Primary Databases

Database	Main Focus	Description
DDBJ	Nucleotide Sequences	DNA Data Bank of Japan, one of the three international nucleotide sequence databases
EMBL	Nucleotide Sequences	European Molecular Biology Laboratory nucleotide sequence database
GenBank	Nucleotide Sequences	NIH genetic sequence database, annotated collection of publicly available DNA sequences
GEO	Gene Expression	Gene Expression Omnibus, repository for high-throughput gene expression and related data
PDB	Protein Structures	Protein Data Bank, repository of 3D structural data of biological macromolecules
PubMed Central	Literature	Repository of biomedical and life sciences journal literature
RefSeq	Reference Sequences	NCBI Reference Sequence Database, collection of reference sequence standards
TrEMBL (UniProt)	Protein Sequences	Automatically annotated protein sequence database (part of UniProt)

Secondary Databases

Database	Main Focus	Description
BioGRID	Interaction Data	Biological General Repository for Interaction Datasets, contains curated protein, genetic, and chemical interactions
COMPARTMENTS	Protein Localization	Database of protein subcellular localization evidence
COG	Orthologous Groups	Clusters of Orthologous Groups, classification of proteins encoded in complete genomes
DIP	Protein Interactions	Database of Interacting Proteins, experimentally determined protein-protein interactions
DISEASES	Disease Associations	Integrates evidence on disease-gene associations from various sources
EggNOG	Orthologous Groups	Evolutionary genealogy of genes: Non-supervised Orthologous Groups, hierarchical classification of proteins
Gene Ontology	Functional Annotations	Controlled vocabulary of gene and gene product attributes across species
HPRD	Protein Reference	Human Protein Reference Database, curated proteomic information for human proteins
HUGO (HGNC)	Gene Nomenclature	HUGO Gene Nomenclature Committee, standardized nomenclature for human genes
Intact	Molecular Interactions	Database of molecular interaction data
InterPro	Protein Families	Integrates protein signatures from multiple databases to classify proteins
MINT	Molecular Interactions	Molecular INTeraction database, experimentally verified protein-protein interactions
OMIM	Human Disease Genes	Online Mendelian Inheritance in Man, catalog of human genes and genetic disorders
Pfam	Protein Families	Database of protein families represented by multiple sequence alignments and HMMs
proGenomes	Genome Classification	Database of prokaryotic genomes with taxonomic classification
ProteomeHD	Co-regulation Data	Contains co-regulation data for human proteins
SIMAP	Protein Similarity	Similarity Matrix of Proteins, precalculated similarity relationships between proteins
SMART	Protein Domains	Simple Modular Architecture Research Tool, identification and annotation of protein domains
SwissModel	Protein Structures	Database of annotated 3D protein structure homology models
TISSUES	Protein Expression	Database of protein expression patterns in tissues

Tertiary Databases

Database	Main Focus	Description
BioCyc	Pathways/Genomes	Collection of organism-specific Pathway/Genome Databases integrating genomic and metabolic pathway data
KEGG	Pathways and Systems	Kyoto Encyclopedia of Genes and Genomes, integrates genomic, chemical, and system functional information
Reactome	Biological Pathways	Curated and peer-reviewed database of reactions, pathways and biological processes
WikiPathways	Biological Pathways	Community-curated open pathway database

Mixed Databases

Database	Main Focus	Description
Ensembl	Genome Browser/Annotation	Genome browser that produces and maintains automatic annotation on selected eukaryotic genomes
FlyBase	Model Organism Database	Database of genetic, genomic, and functional data for Drosophila
SGD	Model Organism Database	Saccharomyces Genome Database, comprehensive resource for yeast biology
SwissProt (UniProt)	Protein Sequences	Manually annotated, high-quality protein sequence database (part of UniProt)
UniProt	Protein Sequences/Function	Universal Protein Resource, comprehensive resource of protein sequence and function
WormBase	Model Organism Database	Database for Caenorhabditis elegans and related nematodes

This classification reflects the nature of the data stored in each database, how it's processed, and its relationship to other data sources. Many databases have evolved over time to incorporate aspects of multiple categories as biological data becomes increasingly interconnected.

claude-background-on-analysis.md

I'll use sequential thinking to analyze each database more thoroughly and create a comprehensive table. Let me first use sequential thinking to ensure I have a systematic approach.

Let me try again with the sequential thinking tool:

I'll create a comprehensive table classifying the biological databases according to the primary/secondary/tertiary/mixed categorization system based on my research.

Based on my research using the web search tool and sequential thinking, I've created a comprehensive classification of the biological databases you listed. The table organizes them into primary, secondary, tertiary, and mixed categories, with descriptions of each database's focus and purpose.

Primary databases contain raw experimental data directly submitted by researchers, such as nucleotide sequences (GenBank, EMBL, DDBJ), protein structures (PDB), and gene expression data (GEO).

Secondary databases provide processed and analyzed information derived from primary data, including protein families (InterPro, Pfam), functional annotations (Gene Ontology), and interaction networks (BioGRID, DIP, MINT).

Tertiary databases integrate information across multiple sources to provide higher-level biological insights, particularly pathway and systems information (KEGG, BioCyc, WikiPathways).

Mixed databases span multiple categories, especially model organism databases (FlyBase, WormBase, SGD) and comprehensive resources like UniProt that include both primary sequence data and secondary annotations.

The classification table should serve as a useful reference for understanding the different types of biological databases in the EMBL ecosystem and how they relate to each other in the information hierarchy.