university of illinois at urbana-champaign institute for genomic biology beespace: an interactive...
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University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace: BeeSpace: An An Interactive Environment Interactive Environment
for Functional Analysis of Social Behaviorfor Functional Analysis of Social Behavior
BeeSpace: BeeSpace: An An Interactive Environment Interactive Environment
for Functional Analysis of Social Behaviorfor Functional Analysis of Social Behavior
Bruce Schatz, Principal InvestigatorGraduate School of Library & Information Science (GSLIS)
Department of Computer Science, Program in [email protected], www.canis.uiuc.edu
Theme for Genomics of Neural and Behavioral Plasticity
www.beespace.uiuc.edu
IGB Thematic Research Seminar, November 2, 2004
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
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University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace FIBR ProjectBeeSpace FIBR ProjectBeeSpace FIBR ProjectBeeSpace FIBR ProjectBeeSpace project is NSF FIBR flagshipFrontiers Integrative Biological Research, $5M for 5 years at University of Illinois
Nature-Nurture using honey bee as modelGenome technologies in wet lab and dry lab biology
Localized Gene Expression for Normal Social BehaviorGene Robinson, Entomology (behavioral expressions)Susan Fahrbach, Entomology (anatomical localization)Sandra Rodriguez-Zas, Animal Sciences (data analysis)
Interactive Information System for Functional AnalysisBruce Schatz, Library & Information Science (info systems)ChengXiang Zhai, Computer Science (text analysis)Chip Bruce, Library & Information Science (user support)
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Post-Genome InformaticsPost-Genome InformaticsPost-Genome InformaticsPost-Genome InformaticsClassical Organisms have extensive Genetic DescriptionsThere will be NO more classical organisms beyondMice and Men other than Worms and Flies, Yeasts and
Weeds.
So must use comparative genomics to classical organisms,Via sequence homologies and literature analysis.
Automatic annotation of genes to standard classifications,Such as Gene Ontology via sequence homology.
Automatic analysis of functions to scientific literature,Such as concept spaces via text mining.
Descriptions in Literature MUST be used for future interactive environments for functional analysis!
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Informational ScienceInformational ScienceInformational ScienceInformational ScienceComputational Science is widely accepted as theThird 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 theFourth Branch of Science
Based on Information Science technologies forFunctional Mining of Information Sources
Comparative Analysis within theDry Lab of Biological Knowledge
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Conceptual Navigation in Conceptual Navigation in BeeSpaceBeeSpaceConceptual Navigation in Conceptual Navigation in BeeSpaceBeeSpace
NeuroscienceLiterature
MolecularBiology
Literature
BeeLiterature
Flybase,WormBase
BeeGenome
Brain RegionLocalization
Brain GeneExpression
Profiles
BehavioralBiologist
MolecularBiologist
Neuro-scientist
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Biology: The Model OrganismBiology: The Model OrganismBiology: The Model OrganismBiology: The Model OrganismThe Western Honey Bee, Apis melliferahas become a primary model for social behavior
Complex social behavior in controllable urban environmentNormal Behavior – honey bees live in the wildControllable Environment – hives can be modified
Small size manageable with current genomic technologyCapture bees on-the-fly during normal behaviorRecord gene expressions for whole-brain or brain-region
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Informatics: From Bases to Informatics: From Bases to SpacesSpacesInformatics: From Bases to Informatics: From Bases to SpacesSpacesdata Bases support genome datae.g. FlyBase has sequences and mapsGenes annotated by GeneOntology and linked to literature
BeeBase (Christine Elsik, Texas A&M)Uses computed homologies to annotate genes
information Spaces support biomedical literaturee.g. BeeSpace uses automatically generated conceptual relationships to navigate functions
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace Software EnvironmentBeeSpace Software EnvironmentBeeSpace Software EnvironmentBeeSpace Software EnvironmentWill build a Concept Space of Biomedical Literature for Functional Analysis of Bee Genes
-Partition Literature into Community Collections-Extract and Index Concepts within Collections-Navigate Concepts within Documents-Follow Links from Documents into Databases
Locate Candidate Genes in Related Literatures then follow links into Genome Databases
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace Software BeeSpace Software ImplementationImplementationBeeSpace Software BeeSpace Software ImplementationImplementation
Natural Language Processing
Identify noun phrasesRecognize biological entities
Statistical Information Retrieval Compute statistical contextsSupport conceptual navigation
Network Information SystemConcept switch across community collectionsSemantic Links into biological databases
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace Information SourcesBeeSpace Information SourcesBeeSpace Information SourcesBeeSpace Information Sources
Biomedical Literature- Medline (medicine)- Biosis (biology)- Agricola, CAB Abstracts, Agris (agriculture)
Model Organisms (heredity)-Gene Descriptions (FlyBase, WormBase)
Natural Histories (environment)-BeeKeeping Books (Cornell Library, Harvard Press)
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Worm Community System (1991)Worm Community System (1991)Worm Community System (1991)Worm Community System (1991)
WCS Information SourcesLiterature Biosis, Medline, newsletters, meetings
Data Genes, Maps, Sequences, strains, cells
WCS Interactive EnvironmentBrowsing search, navigationFiltering selection, analysisSharing linking, publishing
WCS: 250 users at 50 labs across Internet (1991)
Flagship in NSF National Collaboratory program
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Medical Concept Spaces (1998)Medical Concept Spaces (1998)Medical Concept Spaces (1998)Medical Concept Spaces (1998)
Obtain discipline-scale collection Medline from NLM, 10M bibliographic abstractshuman classification: Medical Subject Headings
Partition discipline into Community Repositories
4 core terms per abstract for MeSH classification32K nodes with core terms (classification tree)
Community is all abstracts classified by core term
40M abstracts containing 280M conceptscomputation took 2 days on NCSA Origin 2000
Simulating World of Medical Communities10K repositories with > 1K abstracts (1K w/ > 10K)
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Navigation in MedSpaceNavigation in MedSpaceNavigation in MedSpaceNavigation in MedSpaceFor a patient with Rheumatoid Arthritis
Find a drug that reduces the pain (analgesic)but does not cause stomach (gastrointestinal) bleeding
Choose DomainChoose DomainChoose DomainChoose Domain
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Concept SearchConcept SearchConcept SearchConcept Search
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Concept NavigationConcept NavigationConcept NavigationConcept Navigation
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Retrieve DocumentRetrieve DocumentRetrieve DocumentRetrieve Document
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Biomedical SessionBiomedical SessionBiomedical SessionBiomedical Session
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Categories and ConceptsCategories and ConceptsCategories and ConceptsCategories and Concepts
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Concept SwitchingConcept SwitchingConcept SwitchingConcept Switching
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Document RetrievalDocument RetrievalDocument RetrievalDocument Retrieval
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Biological Concept Spaces (2005)Biological Concept Spaces (2005)Biological Concept Spaces (2005)Biological Concept Spaces (2005)Compute concept spaces for All of BiologyBioSpace across entire biomedical literature
50M abstracts across 50K repositories
Use Gene Ontology to partition literature into biological communities for functional analysis
GO same scale as MeSH but adequate coverage?GO light on social behavior (biological process)
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
Interactive Functional AnalysisInteractive Functional AnalysisInteractive Functional AnalysisInteractive Functional AnalysisBeeSpace will enable users to navigate a uniform space of
diverse databases and literature sources for hypothesis development and testing, with a software system that goes beyond a searchable database, using statistical literature analyses to discover functional relationships between genes and behavior.
Genes to BehaviorsBehaviors to GenesConcepts to ConceptsClusters to ClustersNavigation across Sources
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
BeeSpace Information SourcesBeeSpace Information SourcesBeeSpace Information SourcesBeeSpace Information SourcesGeneral for All Spaces:
Scientific Literature-Medline, Biosis, Agricola, Agris, CAB Abstracts-partitioned by organisms and by functions
Model Organisms -Gene Descriptions (FlyBase, WormBase, MGI, SCD, TAIR)
Special Sources for BeeSpace:-Natural History Books (Cornell Library, Harvard Press)
University of Illinois at Urbana-ChampaignINSTITUTE FOR GENOMIC BIOLOGY
XSpace Information SourcesXSpace Information SourcesXSpace Information SourcesXSpace Information SourcesOrganize Genome Databases (XBase)Compute Gene Descriptions from Model OrganismsPartition Scientific Literature for Organism XCompute XSpace using Semantic Indexing Technology
Boost the Functional Analysis from Special SourcesCollecting Useful Data about Natural Historiese.g. CowSpace Leverage in AIPL Databases