Biological Databases and Ontologies


Prepared by: Nicola Mulder
Module name: Biological Databases and Ontologies
Contact hours (to be used as a guide): Total (15-20 hrs), Theory (30%), Practical (70%)


On completion of this module, students should be able to:

1. Find specific information from biological databases, such as literature references, genes or protein
2. Find information on how genes or proteins work in the context of the cell, for example in pathways or biological networks
3. Understand what an ontology is and become familiar with some of the key ontologies used in life sciences
4. Use ontologies to find genes or proteins involved in specific functions


The participants should be familiar with major biological concepts, such as DNA, genes, proteins, pathways, etc.


1. Websites: NCBI (, EBI (
2. Nucleic Acids Research Database Issue (January every year)


A) Theory lectures

1. Lecture 1 (<1 hour)
• What is a biological database?
• How is the data organized within databases
• How to search biological databases effectively and exporting of results/data

2. Lecture 2 (1-2 hours)
• Sequence databases, structure, examples and uses
• Other biological databases, e.g. chemicals, pathways, etc.
• Links between different databases
• Integrated databases, e.g. interaction networks, genome browsers/databases
• Which database to use

3. Lecture 3 (1 hour)
• Describe what an ontology is
• Describe the need for standards and ontologies in databases and research
• Provide some examples of biological ontologies and how they are annotated and used
• Discuss some example applications of ontologies and how they help in data retrieval, analysis and evaluation

B) Practical component

1. Practical on searching biological databases (follows lecture 1 & 2)
a. Search for specific genes or proteins from different search interfaces
b. Filter and export the results in different formats
c. Use links between databases to move between them
d. Provide more complex queries to see how participants are able to use the databases to answer specific questions or extract specific data

2. Practical on browsing ontologies and their annotations (follows lecture 3)
a. Query some of the ontologies (Ontology Lookup Service), e.g. the Gene Ontology (AmiGO or QuickGO) or phenotype ontology and look at the data they provide and the structure of the ontologies
b. Query specific genes or proteins within different ontologies, try to determine the source of and evidence for the annotations to ontology terms


Class exercises (no weight, not for marks)
Practical test (100% weight)

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