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ANSC644 Bioinformatics-Database Mining 1 ANSC644 Bioinformatics §Carl J. Schmidt §051 Townsend Hall §http://udgenome.ags.udel.edu/ANSC644.

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Presentation on theme: "ANSC644 Bioinformatics-Database Mining 1 ANSC644 Bioinformatics §Carl J. Schmidt §051 Townsend Hall §http://udgenome.ags.udel.edu/ANSC644."— Presentation transcript:

1 ANSC644 Bioinformatics-Database Mining 1 ANSC644 Bioinformatics §Carl J. Schmidt §051 Townsend Hall §http://udgenome.ags.udel.edu/ANSC644

2 ANSC644 Bioinformatics-Database Mining 2 Bioinformatics §Application of computer science to aid the life scientist in understanding biological processes.

3 ANSC644 Bioinformatics-Database Mining 3 Bioinformatics §Application of computer science to aid the life scientist in understanding biological processes. Computer Science Life Science

4 ANSC644 Bioinformatics-Database Mining 4 Bioinformatics §Application of computer science to aid the life scientist in understanding biological processes. Computer Science Life Science Statistics

5 ANSC644 Bioinformatics-Database Mining 5 Objectives: §Introduce web accessible bioinformatics programs

6 ANSC644 Bioinformatics-Database Mining 6 Objectives: §Introduce web accessible bioinformatics programs §Perspective of the life scientist

7 ANSC644 Bioinformatics-Database Mining 7 Objectives: §Introduce web accessible bioinformatics programs §Perspective of the life scientist l What is available?

8 ANSC644 Bioinformatics-Database Mining 8 Objectives: §Introduce web accessible bioinformatics programs §Perspective of the life scientist l What is available? l How do I use these tools?

9 ANSC644 Bioinformatics-Database Mining 9 Objectives: §Introduce web accessible bioinformatics programs §Perspective of the life scientist l What is available? l How do I use these tools? l What do the results mean?

10 Mining Internet Biomedical Databases

11 ANSC644 Bioinformatics-Database Mining 11 Database §A computer accessible organized source of information. Three types- differ in how data is organized.

12 ANSC644 Bioinformatics-Database Mining 12 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.

13 ANSC644 Bioinformatics-Database Mining 13 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.

14 ANSC644 Bioinformatics-Database Mining 14 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)

15 ANSC644 Bioinformatics-Database Mining 15 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.

16 ANSC644 Bioinformatics-Database Mining 16 GENE Some Relationships for a Given Gene

17 ANSC644 Bioinformatics-Database Mining 17 GENE Sequence Some Relationships for a Given Gene

18 ANSC644 Bioinformatics-Database Mining 18 GENE Publications Sequence Some Relationships for a Given Gene

19 ANSC644 Bioinformatics-Database Mining 19 GENE Publications Sequence Product PublicationsStructure Some Relationships for a Given Gene

20 ANSC644 Bioinformatics-Database Mining 20 GENE Publications Sequence Product PublicationsStructure Homologs Some Relationships for a Given Gene

21 ANSC644 Bioinformatics-Database Mining 21 GENE Publications Sequence Product PublicationsStructure Homologs Expression Data Some Relationships for a Given Gene

22 ANSC644 Bioinformatics-Database Mining 22 GENE Publications Sequence Product PublicationsStructure Homologs Expression Data Mutation Data Phenotype Some Relationships for a Given Gene

23 ANSC644 Bioinformatics-Database Mining 23 Entrez §Central Query Page for Biomedical Information. §Includes: l Literature l Sequences –Nucleotide –Protein –Structures l Online Mendelian Inheritance in Man l Much more

24 ANSC644 Bioinformatics-Database Mining 24 Entrez §Query interface Entrez Query Page Pubmed - literature Nucleotide Sequences Online Mendelian Inheritance DBs

25 ANSC644 Bioinformatics-Database Mining 25 Link

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29 ANSC644 Bioinformatics-Database Mining 29 Boolean operators §The search engine understands: l AND, OR, NOT §This permits refining the search to focus on topic of interest. §If no operated added PUBMED uses AND between terms. l Virus infection is {Virus AND infection}

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43 ANSC644 Bioinformatics-Database Mining 43 PUBMED Tutorial

44 ANSC644 Bioinformatics-Database Mining 44 Pubcrawler

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