Analysis Environments For Scientific Communities From Bases to Spaces
description
Transcript of Analysis Environments For Scientific Communities From Bases to Spaces
![Page 1: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/1.jpg)
Analysis EnvironmentsAnalysis Environments For Scientific CommunitiesFor Scientific Communities
From Bases to SpacesFrom Bases to Spaces
Bruce R. SchatzInstitute for Genomic Biology
University of Illinois at [email protected],www.beespace.uiuc.edu
Baker Center for BioinformaticsIowa State University
October 6, 2006
![Page 2: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/2.jpg)
What are Analysis Environments
Functional Analysis Find the underlying Mechanisms Of Genes, Behaviors, Diseases
Comparative Analysis Top-down data mining (vs Bottom-up) Multiple Sources especially literature
![Page 3: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/3.jpg)
Building Analysis Environments
Manual by Humans Interaction user navigation Classification collection indexing
Automatic by Computers Federation search bridges Integration results links
![Page 4: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/4.jpg)
Trends in Analysis Environments
Central versus Distributed Viewpoints
The 90s Pre-Genome Entrez (NIH NCBI) versus WCS (NSF Arizona)
The 00s Post-Genome GO (NIH curators) versus BeeSpace (NSF Illinois)
![Page 5: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/5.jpg)
Pre-Genome Environments
Focused on Syntax pre-Web
WCS (Worm Community System) Search words across sources Follow links across sources Words automatic, Links manual
Towards Integrated Searching
![Page 6: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/6.jpg)
Post-Genome Environments
Focused on Semantics post-Web
BeeSpace (Honey Bee Inter Space) Navigate concepts across sources Integrate data across sources Concepts automatic, Links automatic
Towards Conceptual Navigation
![Page 7: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/7.jpg)
Worm Community System WCS Information:Literature BIOSIS, MEDLINE, newsletters,
meetingsData Genes, Maps, Sequences, strains, cells
WCS FunctionalityBrowsing search, navigationFiltering selection, analysisSharing linking, publishing
WCS: 250 users at 50 labs across Internet (1991)
![Page 8: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/8.jpg)
WCSMolecular
![Page 9: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/9.jpg)
WCS Cellular
![Page 10: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/10.jpg)
WCS invokes
gm
![Page 11: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/11.jpg)
WCS vis-à-vis acedb
![Page 12: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/12.jpg)
from Objects to Concepts from Syntax to Semantics Infrastructure is Interaction with Abstraction
Internet is packet transmission across computersInterspace is concept navigation across repositories
Towards the Interspace
![Page 13: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/13.jpg)
THE THIRD WAVE OF NET EVOLUTION
PACKETS
OBJECTS
CONCEPTS
![Page 14: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/14.jpg)
Technology
Engineering
Electrical
FORMAL
INFORMAL
(manual)
(automatic)
IEEE
communities
groups
individuals
LEVELS OF INDEXES
![Page 15: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/15.jpg)
Post-Genome Informatics IComparative Analysis within the
Dry Lab of Biological Knowledge
Classical Organisms have Genetic Descriptions.There will be NO more classical organisms beyondMice and Men, Worms and Flies, Yeasts and Weeds.
Must use comparative genomics on classical organismsVia sequence homologies and literature analysis.
![Page 16: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/16.jpg)
Post-Genome Informatics IIFunctional Analysis within the
Dry Lab of Biological Knowledge
Automatic annotation of genes to standard classifications, e.g. Gene Ontology via homology on computed protein sequences.
Automatic analysis of functions to scientific literature, e.g. concept spaces via text extractions. Thus must use functions in literature descriptions.
![Page 17: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/17.jpg)
Informatics: From Bases to Spacesdata Bases support genome datae.g. FlyBase has sequences and mapsGenes annotated by GeneOntology and
linked to biological literature
information Spaces support biological literaturee.g. BeeSpace uses automatically generated conceptual relationships to navigate functions
![Page 18: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/18.jpg)
BeeSpace FIBR ProjectBeeSpace project is NSF FIBR flagshipFrontiers Integrative Biological Research, $5M for 5 years at University of Illinois
Analyzing Nature and Nurture in Societal Roles using honey bee as model
(Functional Analysis of Social Behavior)
Genomic technologies in wet lab and dry lab BeeBee [Biology] gene expressions SpaceSpace [Informatics] concept navigations
![Page 19: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/19.jpg)
![Page 20: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/20.jpg)
System Architecture
![Page 21: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/21.jpg)
Concept Navigation in BeeSpace
NeuroscienceLiterature
MolecularBiology
Literature
BeeLiterature
Flybase,WormBase
BeeGenome
Brain RegionLocalization
Brain GeneExpression
Profiles
BehavioralBiologist
MolecularBiologist
Neuro-scientist
![Page 22: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/22.jpg)
V1 BeeSpace Community Collections
Organism Honey Bee / Fruit Fly Song Bird / Soy Bean
Behavior Social / Territorial Foraging / Nesting
Development Behavioral Maturation Insect Development Insect Communication
Structure Fly Genetics / Fly Biochemistry Fly Physiology / Insect Neurophysiology
![Page 23: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/23.jpg)
CONCEPT SWITCHING “Concept” versus “Term”
set of “semantically” equivalent terms Concept switching
region to region (set to set) match
term
Semantic region
Concept SpaceConcept Space
![Page 24: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/24.jpg)
![Page 25: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/25.jpg)
![Page 26: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/26.jpg)
![Page 27: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/27.jpg)
![Page 28: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/28.jpg)
![Page 29: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/29.jpg)
BeeSpace Analysis Environment Build 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
![Page 30: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/30.jpg)
Well Characterized Gene
![Page 31: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/31.jpg)
Poorly Characterized Gene
![Page 32: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/32.jpg)
Gene Summarization, BeeSpace V2
![Page 33: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/33.jpg)
![Page 34: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/34.jpg)
Collaboration across Users
![Page 35: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/35.jpg)
![Page 36: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/36.jpg)
![Page 37: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/37.jpg)
![Page 38: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/38.jpg)
![Page 39: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/39.jpg)
![Page 40: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/40.jpg)
![Page 41: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/41.jpg)
Category Browse (Collection)
![Page 42: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/42.jpg)
![Page 43: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/43.jpg)
![Page 44: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/44.jpg)
Category Browse (Search)
![Page 45: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/45.jpg)
![Page 46: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/46.jpg)
![Page 47: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/47.jpg)
PlantSpace Examples
![Page 48: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/48.jpg)
![Page 49: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/49.jpg)
![Page 50: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/50.jpg)
![Page 51: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/51.jpg)
![Page 52: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/52.jpg)
![Page 53: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/53.jpg)
![Page 54: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/54.jpg)
![Page 55: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/55.jpg)
![Page 56: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/56.jpg)
Interactive 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 beyond a searchable database, using literature analyses to discover functional relationships between genes and behavior.
Genes to BehaviorsBehaviors to GenesConcepts to ConceptsClusters to ClustersNavigation across Sources
![Page 57: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/57.jpg)
BeeSpace Information SourcesGeneral for All Spaces: Scientific Literature-Medline, Biosis, CAB Abstracts Genome Databases-GenBank, ProteinDataBank, ArrayExpress
Special for BeeSpace: Model Organisms (heredity)-Gene Descriptions (FlyBase, WormBase) Natural Histories (environment)-BeeKeeping Books (Cornell, Harvard)
![Page 58: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/58.jpg)
XSpace Information SourcesOrganize Genome Databases (XBase)Compute Gene Descriptions from Model OrganismsPartition Scientific Literature for Organism XCompute XSpace using Semantic Indexing
Boost the Functional Analysis from Special SourcesCollecting Useful Data about Natural Historiese.g. CowSpace Leverage in AIPL Databases
![Page 59: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/59.jpg)
Towards SoySpace Organize Genome Databases (SoyBase) Partition Scientific Literature for SoyBean Gene Descriptions from Models (TAIR) Natural Histories from Population Databases
Key to Functional Analysis is Special Sources Collecting Appropriate Text about Genes Extracting Adequate Data about Histories Leverage is National Archives of germplasm
and Historical Records for soybean crops
![Page 60: Analysis Environments For Scientific Communities From Bases to Spaces](https://reader035.fdocuments.in/reader035/viewer/2022062501/56816806550346895ddd8941/html5/thumbnails/60.jpg)
Towards the InterspaceThe Analysis Environment technology is
GENERAL!
BirdSpace? BeeSpace?PigSpace? CowSpace? BehaviorSpace? BrainSpace?SoySpace? PlantSpace?
BioSpace… Interspace