Biology
Knowledge in biology is represented in different ways. Some are very general, like the concept of hemoglobin,
while others are very specific, like the chemical graph of caffeine. Databases generally have one level of
detail as the principle model of the biology it represents. And different databases may link to each other
but actually have a different model.
Biological entities
Genes
| |
Example |
Databases |
Represetation |
| Concept |
The concept cancer gene refers to something abstract. |
Wikipedia |
name |
| |
The human gene BRCA1. |
|
name, identifier |
| Sequence |
A specific nucleotide sequence of the human BRCA1 gene. |
NCBI RefSeq |
nucleotide sequence |
Proteins
| |
Example |
Databases |
Represetation |
| Concept |
The concept enzyme refers to something abstract. |
Wikipedia |
name |
| |
The human protein. |
|
name |
| Sequence |
A specific amino acid sequence of the human BRCA1 gene. |
UniProt |
amino acid sequence |
| Protein structure |
A crystal structure of a protein. |
PDB |
3D coordinate model |
Small compounds
| |
Example |
Databases |
Represetation |
| Concept |
The concept glucose. |
Wikipedia |
name |
| A chemical structure |
The chemical structure of the neutral formaldehyde. |
Wikidata |
chemical graph |
| A chemical structure |
Deprotonated acetic acid or heavy water. |
ChEBI |
chemical graph |