There are three main types of biological databases: primary, secondary, and tertiary. Primary databases contain directly submitted experimental data like sequences and metadata. Secondary databases contain processed and analyzed data from primary databases related to protein structure and function. Tertiary databases combine information from multiple sources and integrate results, such as databases on gene expression, metabolic pathways, and functional elements of the human genome.

1. Intro to Biological Databases
BIO 410
Elmhurst University

2. Examples
https://microbenotes.com/biological-databases-types-and-importance/

3. Three types of databases
 Primary
 Secondary
 Tertiary

4. Primary Databases
 Information (usually sequences and metadata) directly submitted by researchers
from experiments
 Nucleotide sequences
 GenBank: GenBank ® is the NIH genetic sequence database, an annotated collection of
all publicly available DNA sequences
 DDBJ (Japan) and EMBL (Europe)
 Protein sequences:
 Swiss-Prot, TrEMBL and PIR-PSD (now all subsumed into UniProt)

5. Secondary Databases
 Data that has resulted from post-processing and analysis of data in primary
databases, mostly related to protein structure and function
 UniProt: combined databases that contain a lot of protein information like structure and
function (we’ll explore this database later)
 PDB (protein structure)
 InterPro (also protein information)
 Other things to predict (domains, motifs)

6. Tertiary/Derived/Composite Databases
 Combine information from multiple databases and integrate results
 Gene expression (GEO)
 Gene ontology (GO)
 Metabolic Pathways (KEGG, PathDB)
 Functional elements of human genome (ENCODE)

7. Let’s explore a couple of these
 NCBI GenBank
 RefSeq
 PDB
 UniProt
 KEGG
 GO
 GEO
 ENCODE

8. Now let’s do a couple of tutorials