Download Mining Internet Biomedical Databases

Survey
yes no Was this document useful for you?
   Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

page
1
page
2
page
3
page
4
page
5
page
6
page
7
page
8
page
9
page
10
page
11
page
12
page
13
page
14
page
15
page
16
page
17
page
18
page
19
page
20
page
21
page
22
page
23
page
24
page
25
page
26
page
27
page
28
page
29
page
30
page
31
page
32
page
33
page
34
page
35
page
36
page
37
page
38
page
39
page
40
page
41
page
42
page
43
page
44
page
45
page
46
page
47
page
48
Document related concepts
no text concepts found
Transcript 
ANSC644 Bioinformatics




Carl J. Schmidt
051 Townsend Hall
schmidtc@udel.edu
http://udgenome.ags.udel.edu/ANSC644
ANSC644 Bioinformatics-Database
Mining
1
Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
ANSC644 Bioinformatics-Database
Mining
2
Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
Computer
Science
Life
Science
ANSC644 Bioinformatics-Database
Mining
3
Bioinformatics
 Application of computer science to aid the
life scientist in understanding biological
processes.
Computer
Science
Life
Science
Statistics
ANSC644 Bioinformatics-Database
Mining
4
Objectives:
 Introduce web accessible bioinformatics
programs
ANSC644 Bioinformatics-Database
Mining
5
Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist
ANSC644 Bioinformatics-Database
Mining
6
Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist

What is available?
ANSC644 Bioinformatics-Database
Mining
7
Objectives:
 Introduce web accessible bioinformatics
programs
 Perspective of the life scientist


What is available?
How do I use these tools?
ANSC644 Bioinformatics-Database
Mining
8
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?
ANSC644 Bioinformatics-Database
Mining
9
Mining Internet Biomedical
Databases
Database
 A computer accessible organized source of
information. Three types- differ in how
data is organized.
ANSC644 Bioinformatics-Database
Mining
11
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
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.
 Relational Database-Information is stored in
a collection of tables.
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.
 Object Oriented Database-Can handle
complex objects, beyond tables (images,
video files)
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 such as images, video files
etc.
ANSC644 Bioinformatics-Database
Mining
15
Some Relationships for a Given Gene
GENE
ANSC644 Bioinformatics-Database
Mining
16
Some Relationships for a Given Gene
Sequence
GENE
ANSC644 Bioinformatics-Database
Mining
17
Some Relationships for a Given Gene
Sequence
Publications
GENE
ANSC644 Bioinformatics-Database
Mining
18
Some Relationships for a Given Gene
Sequence
Publications
GENE
Product
Publications
Structure
ANSC644 Bioinformatics-Database
Mining
19
Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Product
Publications
Structure
ANSC644 Bioinformatics-Database
Mining
20
Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Expression Data
Product
Publications
Structure
ANSC644 Bioinformatics-Database
Mining
21
Some Relationships for a Given Gene
Homologs
Sequence
Publications
GENE
Mutation Data
Product
Publications
Expression Data
Structure
ANSC644 Bioinformatics-Database
Mining
Phenotype
22
Entrez
 Central Query Page for Biomedical
Information.
 Includes:


Literature
Sequences
– Nucleotide
– Protein
– Structures


Online Mendelian Inheritance in Man
Much more
ANSC644 Bioinformatics-Database
Mining
23
Entrez
 Query interface
Pubmed - literature
Entrez
Query
Page
DBs
Nucleotide Sequences
Online Mendelian Inheritance
ANSC644 Bioinformatics-Database
Mining
24
Link
ANSC644 Bioinformatics-Database
Mining
25
ANSC644 Bioinformatics-Database
Mining
26
ANSC644 Bioinformatics-Database
Mining
27
ANSC644 Bioinformatics-Database
Mining
28
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}
ANSC644 Bioinformatics-Database
Mining
29
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
PUBMED Tutorial
ANSC644 Bioinformatics-Database
Mining
43
Pubcrawler
ANSC644 Bioinformatics-Database
Mining
44
ANSC644 Bioinformatics-Database
Mining
45
ANSC644 Bioinformatics-Database
Mining
46
ANSC644 Bioinformatics-Database
Mining
47
ANSC644 Bioinformatics-Database
Mining
48
Related documents