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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.

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beespace informatics building an interactive environment for functional analysis
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
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
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)
system architecture
System Architecture

BeeSpace

Concepts

Concepts

SEQ

Expressions

Expressions

Databases

Bees

Flies

Documents

Documents

SEQ

Community

Community

informatics researchers ii
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)
concept navigation in beespace

Behavioral

Molecular

Biologist

Biologist

Molecular

Biology

Literature

Brain Gene

Bee

Bee

Expression

Literature

Genome

Profiles

Flybase,

Brain Region

WormBase

Localization

Neuroscience

Literature

Neuro-

scientist

Concept Navigation in BeeSpace
beespace analysis environment
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
beespace v3 sample
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)
beespace semantic operations
BeeSpace Semantic Operations
  • Merge (S1,S2) into S3
  • Summarize (S) into Gene classify

Extract

S

R

Map

S

R