ANSC644 Bioinformatics-Database Mining 1 ANSC644 Bioinformatics §Carl J. Schmidt §051 Townsend...

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ANSC644 Bioinformatics-Da tabase Mining 1 ANSC644 Bioinformatics Carl J. Schmidt 051 Townsend Hall [email protected] http:// udgenome.ags.udel.edu/ANSC644

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ANSC644 Bioinformatics

Carl J. Schmidt051 Townsend [email protected]://udgenome.ags.udel.edu/ANSC644

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Bioinformatics

Application of computer science to aid the life scientist in understanding biological processes.

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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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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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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 Internet Biomedical Databases

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Database

A computer accessible organized source of information. Three types- differ in how data is organized.

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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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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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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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DatabaseA 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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GENE

Some Relationships for a Given Gene

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GENE

Sequence

Some Relationships for a Given Gene

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GENEPublications

Sequence

Some Relationships for a Given Gene

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GENEPublications

Sequence

Product

Publications Structure

Some Relationships for a Given Gene

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GENEPublications

Sequence

Product

Publications Structure

Homologs

Some Relationships for a Given Gene

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GENEPublications

Sequence

Product

Publications Structure

Homologs

Expression Data

Some Relationships for a Given Gene

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GENEPublications

Sequence

Product

Publications Structure

Homologs

Expression Data

Mutation Data

Phenotype

Some Relationships for a Given Gene

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EntrezCentral Query Page for Biomedical

Information.Includes:

Literature Sequences

– Nucleotide

– Protein

– Structures

Online Mendelian Inheritance in Man Much more

http://www.ncbi.nlm.nih.gov/Entrez/
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EntrezQuery interface

Entrez Query Page

Pubmed - literature

Nucleotide Sequences

Online Mendelian Inheritance

DBs

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Link

http://www.ncbi.nlm.nih.gov/Entrez/
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Boolean operators

The search engine understands: 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

http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html
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Pubcrawler

http://pubcrawler.gen.tcd.ie/about.html
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