Download Document

Introduction to Practical 1
Biological databases
1
Overview of L1
BIOINFORMATICS ~ biology + computers
 Data (databases)
 Query and Analysis of Data (software/tools)
….more on this in your upcoming lectures….
2
Biological databases
 Structured storage of many kinds of data,
including:
•
•
•
•
•
•
Sequence (eg chromosomal DNA, mRNA, protein)
Structures
Literature (eg PubMed)
Diseases
Biomolecular interactions
Etc etc etc etc
3
Databases, continued:
• Databases can come and go.
• There can be:
 Multiple databases for a single kind of data (eg
protein sequence, pathways, etc)
 New databases for “new” kinds of data
• Every database has its own peculiarities
And so….
4
A good biologist
 Acquires a general set of skills for FINDING and
USING databases
 “poke around”
 “look”
 “think”
 Can critically assess the quality of a search (in terms of
specificity, true positives (relevant hits) and false
positives (irrelevant hits), as well as the contents of
databases
5
P1: a gentle introduction to databases
LEARNING GOALS:
• Know how to perform simple queries of several databases
• Gain some familiarity with the contents of selected databases
• Learn to identify distinct elements of database records
• Use database cross references to link to other databases
• Know multiple approaches to find biological data on the
internet
6
The exercise
Section A) Take an introductory look at selected databases
Section B) Find additional databases using the Nucleic Acids
Research Database Issue
7
Section A: An introductory look at biological
databases
Follow the instructions in the exercise to look at:
• Protein: database of protein sequences
• Gene: Whole genome annotation
• OMIM: genes and diseases
• KEGG Pathway: metabolic and signalling pathways
• PDB: three-dimensional biomolecular structures
8
Section B: the Nucleic Acids
Research database issue – identifying useful
databases
• Hundreds of DBs out there, and more coming all the
time
• Various ways to find them:
 Google etc
 PubMed (eg p53 database)
 Catalogs of the databases
9
An example of a database catalogue:
Nucleic Acids Research Database Issue
•
Special supplementary issue of the Nucleic Acids Research journal
•
Collection of all DBs published in NAR & selected DBs relevant to biologists
•
•
not complete, but contains most of the popular DBs
•
Hotlinks & brief summaries provided for each DB
Catalog List: Categorize the DBs based on different type of info
• eg, sequence, structure, signaling, plant, metabolics, disease
10
From: http://nar.oxfordjournals.org/content/39/suppl_1/D1/suppl/DC1
Capture your answers
Eg:
 Capture your answers electronically by writing them in
the exercise Ms Word document provide for each
practical  Start a new Word document or Excel
document…
You work will be discussed before the end of the
practical
11
Begin your exercise work now
12