BeeSpace Informatics: Building an Interactive Environment for Functional Analysis

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BeeSpace InformaticsBuilding 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

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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

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Informatics Researchers I

• Bruce Schatz (faculty), systems
• ChengXiang Zhai (faculty), algorithms
• Todd Littell (staff), senior programmer
• Moushumi Sen Sarma (postdoc), biology usage
• Jim Buell (staff), user support
• Faculty Collaborators (joint authors)
• Saurabh Sinha (CS), Sheng Zhong (BIOENG)
• Jiawei Han (CS), Roxana Girju (LING)

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System Architecture

• BeeSpace

• Concepts

• Concepts

• SEQ

• Expressions

• Expressions

• Databases

• Bees

• Flies

• Documents

• Documents

• SEQ

• Community

• Community

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Informatics Researchers II

• 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)

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Concept Navigation in BeeSpace
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BeeSpace Analysis Environment

• SPACES and REGIONS
• Dynamic and Relative
• Space is collection of documents
• Region is collection of terms
• 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

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BeeSpace v3 Sample

• Refining and Merging Space Regions
• Cross bee species differential gene expression
  for behaviorial maturation into adult forager
• Functional Analysis for Similar Situation!
• Behavioral Maturation merge
• Cross-Species Comparisons merge
• Different Taxa (insect,fish,bird,rodent)

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BeeSpace Semantic Operations

• Extract

• S

• R

• Map

• R

• S

• Merge (S1,S2) into S3
• Summarize (S) into Gene classify