ANSC644 Bioinformatics
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Carl J. Schmidt
051 Townsend Hall
schmidtc@udel.edu
http://udgenome.ags.udel.edu/ANSC644
ANSC644 Bioinformatics-Database
Mining
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Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
ANSC644 Bioinformatics-Database
Mining
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Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
Computer
Science
Life
Science
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Mining
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Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
Computer
Science
Life
Science
Statistics
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Objectives:
 Introduce web accessible bioinformatics
programs
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Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist
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Mining
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Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist

What is available?
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Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist


What is available?
How do I use these tools?
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Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist



What is available?
How do I use these tools?
What do the results mean?
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Mining
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Mining Internet Biomedical
Databases
Database
 A computer accessible organized source of
information. Three types- differ in how
data is organized.
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Mining
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Database
 A computer accessible organized source of
information. Three types- differ in how
data is organized.
 Flatfile- ordered collection of files, typically
in a standard format.
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Mining
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Database
 A computer accessible organized source of
information. Three types- differ in how
data is organized.
 Flatfile- ordered collection of files, typically
in a standard format.
 Relational Database-Information is stored in
a collection of tables.
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Mining
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Database
 A computer accessible organized source of
information. Three types- differ in how
data is organized.
 Flatfile- ordered collection of files, typically
in a standard format.
 Relational Database-Information is stored in
a collection of tables.
 Object Oriented Database-Can handle
complex objects, beyond tables (images,
video files)
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Mining
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Database
 A computer accessible organized source of
information. Three types- differ in how data is
organized.
 Flatfile- ordered collection of files, typically in a
standard format.
 Relational Database-Information is stored in a
collection of tables.
 Object Oriented Database- Can handle complex
objects beyond tables such as images, video files
etc.
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Some Relationships for a Given Gene
GENE
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Some Relationships for a Given Gene
Sequence
GENE
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Some Relationships for a Given Gene
Sequence
Publications
GENE
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Some Relationships for a Given Gene
Sequence
Publications
GENE
Product
Publications
Structure
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Mining
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Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Product
Publications
Structure
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Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Expression Data
Product
Publications
Structure
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Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Mutation Data
Product
Publications
Expression Data
Structure
ANSC644 Bioinformatics-Database
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Phenotype
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Entrez
 Central Query Page for Biomedical
Information.
 Includes:


Literature
Sequences
– Nucleotide
– Protein
– Structures
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Online Mendelian Inheritance in Man
Much more
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Entrez
 Query interface
Pubmed - literature
Entrez
Query
Page
DBs
Nucleotide Sequences
Online Mendelian Inheritance
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Link
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Boolean operators
 The search engine understands:
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AND, OR, NOT
 This permits refining the search to focus on
topic of interest.
 If no operated added PUBMED uses AND
between terms.

Virus infection is {Virus AND infection}
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PUBMED Tutorial
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Pubcrawler
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