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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.

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BeeSpace Informatics: Building an Interactive Environment for Functional Analysis

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  1. 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

  2. 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

  3. 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)

  4. System Architecture BeeSpace Concepts Concepts SEQ Expressions Expressions Databases Bees Flies Documents Documents SEQ Community Community

  5. 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)

  6. 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

  7. 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

  8. 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)

  9. BeeSpace Semantic Operations • Merge (S1,S2) into S3 • Summarize (S) into Gene classify Extract S R Map S R

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