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

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

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

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

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

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

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

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?

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?

Mining Internet Biomedical Databases

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

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.

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.

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)

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.

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

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

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

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

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

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

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

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

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

ANSC644 Bioinformatics-Database Mining 25 Link

ANSC644 Bioinformatics-Database Mining 26

ANSC644 Bioinformatics-Database Mining 27

ANSC644 Bioinformatics-Database Mining 28

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}

ANSC644 Bioinformatics-Database Mining 30

ANSC644 Bioinformatics-Database Mining 31

ANSC644 Bioinformatics-Database Mining 32

ANSC644 Bioinformatics-Database Mining 33

ANSC644 Bioinformatics-Database Mining 34

ANSC644 Bioinformatics-Database Mining 35

ANSC644 Bioinformatics-Database Mining 36

ANSC644 Bioinformatics-Database Mining 37

ANSC644 Bioinformatics-Database Mining 38

ANSC644 Bioinformatics-Database Mining 39

ANSC644 Bioinformatics-Database Mining 40

ANSC644 Bioinformatics-Database Mining 41

ANSC644 Bioinformatics-Database Mining 42

ANSC644 Bioinformatics-Database Mining 43 PUBMED Tutorial

ANSC644 Bioinformatics-Database Mining 44 Pubcrawler

ANSC644 Bioinformatics-Database Mining 45

ANSC644 Bioinformatics-Database Mining 46

ANSC644 Bioinformatics-Database Mining 47

ANSC644 Bioinformatics-Database Mining 48