Download THE INTERSPACE PROTOTYPE An Analysis Environment for

BeeSpace Informatics:
Building an Interactive Environment
for Functional Analysis
Bruce Schatz
Institute for Genomic Biology
University of Illinois at Urbana-Champaign
www.beespace.uiuc.edu
Third Annual Project Workshop
IGB, Urbana IL
May 21, 2007
Informational Science
Computational Science is the Third Branch of Science
(beyond Experimental and Theoretical)
Genes are Computed, Proteins are Computed,
Sequence “equivalences” are Computed.
Informational Science is coming to be accepted as
The Fourth Branch of Science
Based on Information Science technologies for
Functional Mining of Information Sources
Comparative Analysis within the
Dry Lab of Biological Knowledge
Informatics Researchers I
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Bruce Schatz (faculty), systems
ChengXiang Zhai (faculty), algorithms
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Todd Littell (staff), senior programmer
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Moushumi Sen Sarma (postdoc), biology usage
Jim Buell (staff), user support
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Faculty Collaborators (joint authors):
Saurabh Sinha (CS), Sheng Zhong (BIOENG)
Jiawei Han (CS), Roxana Girju (LING)
System Architecture
Informatics Researchers II
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Bioinformatics students:
Xu Ling
gene summarizer (cf. FlyBase)
Xin He
gene annotator (meta-analysis)
Computer Science students:
Jing Jiang
entity recognizer (relations)
Qiaozhu Mei extrinsic clusterer (priors)
Informatics students
Brant Chee
intrinsic clusterer (natural)
Yue Lu
question answerer (relations)
Concept Navigation in BeeSpace
Behavioral
Biologist
Bee
Literature
Molecular
Biology
Literature
Brain Gene
Expression
Profiles
Brain Region
Localization
Neuroscience
Literature
Neuroscientist
Molecular
Biologist
Bee
Genome
Flybase,
WormBase
BeeSpace Analysis Environment
SPACES and REGIONS
Dynamic and Relative
Space is collection of documents
Region is collection of terms
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Extract creates new Region from old Space
Map creates new Space from old Region
New from Old Spaces and Regions via merges
Summarize classifies Gene within Space
Annotate finds differential functional expression
BeeSpace v3 Sample
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Refining and Merging Space Regions
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Cross bee species differential gene expression
for behaviorial maturation into adult forager
Functional Analysis for Similar Situation!
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Behavioral Maturation
merge
Cross-Species Comparisons merge
Different Taxa (insect,fish,bird,rodent)
BeeSpace Semantic Operations
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Merge (S1,S2) into S3
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Summarize (S) into Gene classify