CellSpace Knowledge Miner

							CellSpace Knowledge Miner

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

1.   molecule: proteins, genes, drugs
2.   function: biological processes and disease states
3.   cell type
4.   organism
                                CellSpace Knowledge Miner
             What is CellSpace ?
Literature Association


                                                Molecules:
                +        +        +       +
 Molecules                                      • Molecules
                                                •Drugs
                +        +        +       +     •Genes
 Functions                                      •Proteins

  Cells &       +        +         _      _    Functions:
  Systems                                      • Biological
                                                 Functions
Organisms       +        +         _      _    • Disease
                                                 States
  Cells & Systems: Cells, Sub-cellular
  Components,Tissues and Organs
              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
          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
          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.
             How to access CellSpace


CellSpace is available via the HSLS molecular biology
 and genetics portal
<www.hsls.pitt.edu/guides/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.
http://www.hsls.pitt.edu/guides/genetics
                                   Access CellSpace
Access CellSpace
Access CellSpace
      CellSpace graphical users interface




    Result:
Find Dictionary or
                           Construct your query
  Query Result
          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
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
                   How to do query
1 Search the Dictionary for “EGF receptor”

            2




                     3    Drag and Drop
     How to do query
6   Click on query     Select Result Type
                                   5




                       4
                           Select the term
      Results



 Results are presented
with statistical likelihood
          value




             Click next for more
                   results
Get references that supports the connections
found in CellSpace
                     7
Get references
  Change to “sort by” date descending
  to get the most recent article on top

            8




                                9
Get the article abstract




                           10
Article abstract
Get the full text in PDF
PDF article
Find molecules related to “EGF receptor” where each
molecule is supported by references that contain the
              term “phosphotyrosine’




          1     Drag and Drop
Describe query

           2
    Do query

3
Find biological functions and disease states linked to
                    EGF receptor
                                  Change the “result type”
                                  to Functions
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
        5        Query steps

1
    2


                Drag and drop
            3

                                4
                                Click to select
Query results
         Find molecules related to apoptosis in the
                 context of B-lymphocyte
              5


         1                                            4
                        2

                            3


Change term type
to “cells and system”
Query results
Browse articles
Browse articles
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
Myc regulated genes
Find functions common to multiple down-
             regulated genes
Query results




                change Min # Links to
                8,7,6,5 etc.
Drag and drop
Show links
Show links




     Click on links to see articles
Show links articles
Clear links to do further query
If you find “Session has timed out”
Save your search results
Save your search results
Then start it again