CellSpace Knowledge Miner

1
CellSpace Knowledge Miner

• Ansuman Chattopadhyay, PhD
• Information Specialist in Molecular Biology and
  Genetics
• Health sciences Library system

2
What is CellSpace ?

• CellSpace is a bioinformatics tool-- a
  knowledge mining system that automatically
  detects, analyzes, and reports the logical
  relationships between four types of terms found
  in the research literature
• molecule proteins, genes, drugs
• function biological processes and disease states
• cell type
• organism

3
What is CellSpace ?
CellSpace Knowledge Miner
Literature Association
Cells Systems
Molecules
Functions
Organisms

• Molecules
• Molecules
• Drugs
• Genes
• Proteins

Molecules
Functions
Cells Systems

• Functions
• Biological
• Functions
• Disease
• States

Organisms
Cells Systems Cells, Sub-cellular
Components,Tissues and Organs
4
How CellSpace Works?
CellSpace computers analyze the National Library
of Medicine's MEDLINE database, performing
proprietary statistical correlation analyses
regarding the organisms, cell types, biological
processes, and molecules reported in 655
selected life science research journals. The
molecular relationships extracted from the
literature are then stored in the CellSpace
database, which can be queried via the CellSpace
user interface. The information is updated every
two weeks
5
What you can do with CellSpace?

• Start with a single protein (or other molecule)
  and
• find its functions, the diseases in which it is
  implicated,
• and related molecules.
• Start with a disease or biological function and
  find
• related molecules, or related functions.
• Start with two or more functions, and find the
  related
• molecules that they have in common

6
What you can do with CellSpace?

• Start with results from a high-throughput
  experiment
• (such as a cluster of co-regulated genes from
• microarray analysis), and easily find the
  functions
• that they share.
• Start with the results of proteomics
  experiments, and
• quickly screen the data to distinguish published
  
• interactions from novel ones.
• .View the literature that supports the
  connections
• found in CellSpace.

7
How to access CellSpace
CellSpace is available via the HSLS molecular
biology and genetics portal uides/genetics listed under Resource
Highlights. Access is limited to 8
simultaneous PC users (Mac OS is not supported)
from UPMC and the University of Pittsburgh
Oakland campus.
8
Access CellSpace
http//www.hsls.pitt.edu/guides/genetics
9
Access CellSpace
10
Access CellSpace
11
CellSpace graphical users interface
Result Find Dictionary or Query Result
Construct your query
12
What you can do with CellSpace?

• Start with a single protein (or other molecule)
  and
• find its functions, the diseases in which it is
  implicated,
• and related molecules.
• Start with a disease or biological function and
  find
• related molecules, or related functions.
• Start with two or more functions, and find the
  related
• molecules that they have in common

13
Start with a single protein and find its
functions, the diseases in which it is
implicated, and related molecules

• Find what other proteins are associated with
• epidermal growth factor receptor
• Find biological functions and disease states
  linked to
• EGF receptor

14
How to do query
Search the Dictionary for EGF receptor
1
2
3
Drag and Drop
15
How to do query
6
Click on query
Select Result Type
5
4
Select the term
16
Results
Results are presented with statistical likelihood
value
Click next for more results
17
Get references that supports the connections
found in CellSpace
7
18
Get references
Change to sort by date descending to get the
most recent article on top
8
9
19
Get the article abstract
10
20
Article abstract
21
Get the full text in PDF
22
PDF article
23
Find molecules related to EGF receptor where
each molecule is supported by references that
contain the term phosphotyrosine
Drag and Drop
1
24
Describe query
2
25
Do query
3
26
(No Transcript)
27
Find biological functions and disease states
linked to EGF receptor
Change the result type to Functions
28
(No Transcript)
29
Start with a disease or biological function and
find related molecules, or related functions
Find molecules related to apoptosis Find
molecules related to apoptosis in the context of
B-lymphocyte
30
Query steps
5
1
2
Drag and drop
3
4
Click to select
31
Query results
32
Find molecules related to apoptosis in the
context of B-lymphocyte
5
1
4
2
3
Change term type to cells and system
33
Query results
34
Browse articles
35
Browse articles
36
Start with results from a high-throughput
experiment (such as a cluster of co-regulated
genes from microarray analysis), and easily find
the functions that they share
37
(No Transcript)
38
Myc regulated genes
39
Find functions common to multiple down-regulated
genes
40
Query results
change Min Links to 8,7,6,5 etc.
41
(No Transcript)
42
Drag and drop
43
Show links
44
Show links
Click on links to see articles
45
Show links articles
46
Clear links to do further query
47
(No Transcript)
48
If you find Session has timed out
49
Save your search results
50
Save your search results
51
Then start it again