Biology Image Libraries

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Biology Image Libraries
Biology Large to Small, Old to New in images

• Don Gilbert
• Bioinformatics, Biology Department,
• Indiana University gilbertd_at_indiana.edu

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What is bioinformatics?

• Bioinformatics is the field of science in which
  biology, computer science, and information
  technology merge into a single discipline. The
  ultimate goal is to enable discovery of new
  biological insights...
• Bioinformatics has three important
  sub-disciplines
• development of new algorithms and statistics with
  which to assess relationships among members of
  large data sets
• analysis and interpretation of various types of
  data including DNA sequences gene and genome
  features and functions expression in cells, in
  development, and through evolution.
• development and implementation of tools that
  enable efficient access and management of
  different types of information.
• http//www.ncbi.nlm.nih.gov/About/primer/bioinform
  atics.html

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Natl. Library Medicine

• www.nlm.nih.gov
• Library includes Visible Human, Forensics and
  other image databases
• Home to major US Bioinformatics Databases (NCBI)

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Bioinformatics at Nat. Lib. Med.

• All Genes and Genomes of humans and others
• BiologyLiterature and data searches
• www.ncbi.nlm. nih.gov

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Constellation of Bio-Data (SRS - Lion Bioscience)
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Bioscience image resources

• Web Image Databases
• Collections of individual scientists (best
  science, limited funding)
• Institutions university, government libraries,
  longer-term
• Directory of Online Biology Images, Photos,
  Microscopy Illustrations. www.academicinfo.net/b
  ioimage.html
• CalPhotos, calphotos.berkeley.edu, nature image
  lib
• Image Research areas
• Biomedical anatomy (2D, 3D, atlases, diseases,
  growth stages)
• Other biology nature, organismal, molecular,
  gene expression plots, metabolic pathways
  linkage graphs
• Chemistry molecular models structure
  biochemical activity

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US Fish Wildlife Image Library

• Catalogs nature images
• Browse by categories
• Search Associated Data about contents
• http//images. fws.gov/

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NLM Visible Human

• Digital image dataset of complete human male and
  female cadavers in MRI, CT and anatomical modes
• ATLAS of Functional Human Anatomy and anatomical
  image
• www.nlm.nih.gov/research/visible/

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Gene expression via images

• Fruitfly embryos studied for gene expression
  during development stages
• Image patterns are analyzed for effects of genes
• High throughput analysis database can study 1000s
  of genes on many stages
• http//flyex.ams.sunysb.edu/FlyEx/

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Genome Map (Daphnia water flea)
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Bioscience image uses

• Data -gt Software -gt Visualize (typically not
  collected) versus Images as data (collected, e.g.
  anatomy pictures)
• Image collections integrated with other uses
• experiements with development, gene
  expression/function, evolution/species
  comparisions, ecology/environment,
  medicine/diseases,...
• Data from images (quantification) versus about
  images
• Image patterns, intensities, values
• "metadata" (e.g. size,date,author,source) and
• associated data (experimental conditions,
  activities related to image)
• Integration images experiment metadata
• search/compare/test images used with experiments
• image quantification (expression/action levels
  changes due to expt.)
• image analysis (what changed biological/med/chem
  mechanisms)

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Bioscience image uses

• Management Identifiers, image checksum,
  Dublin-core (author, date, )
• Manipulation visualizing data zooming to
  subsets annotating with experiment results
• Collecting images
• cameras microscopes in lab vs nature computer
  gen./collected high quality needs storage
• software hardware industry data standards
• Manipulating image data
• Commercial productivity tools for photos and
  video common
• Bio-image software packages (free and commercial)
  

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NIH Image Program

• Manipulate and analyze biology images
• Measure areas, intensities, patterns
• Free, widely used
• http//rsb.info.nih.gov/ nih-image/

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Anatomy of a biology database
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Anatomy of biology database 1

• Data components
• biosequences, literature, gene expression,
  pathways, maps, anatomy, species, ecology, stocks
• Metadata about primary data (ID, dates, sources,
  evidence)
• Architecture
• Backend (database, analyses piplelines)
• Relational database for management
• Flexible data schema changes are common
• Frontend (public views web, ftp)
• Browsing all data Search and retrieval of gene
  reports, maps
• Middleware ('glue' back and front)
• Internet-shared, standards-based, open-source
  preferred

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Anatomy of biology database 2

• Publication interface
• Detailed biological object views (sequences,
  genes, etc.)
• Queries simple and frequent, ad-hoc and general
• Graphic viewers
• Data exchange
• Data definitions schema (XML)
• Controlled vocabularies of science terms,
  ontologies
• Minimal information for collaboration, sharing

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Anatomy of biology database 3

• Analysis software
• Project uses sequence analyses, external
  database comparisons
• Pipeline for automated analyses, rerun as needed
• Public uses (e.g. BLAST search)
• Editing / data management interface
• Interactive document editing
• Batch data updates

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Biomedical Informatics Research Network (BIRN)

• National research network among several
  universities
• Human and Mouse Brain, Anatomy image databases
• Image analyses for bio-medical research
• Integrated databases, analyses pipelines
• Uses Grid computing (TeraGrid), high-speed
  network
• http//www.nbirn.net/
• Extracts of 2006 BIRN progress report by Mark
  Ellisman,Bruce Rosen, Steven Potkin and Arthur
  Toga.

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Brain Image Analysis Network
Biomedical Informatics Research
Network Integrating Multi-Site Neuroimaging Data
Acquisition, Data Sharing and Brain Morphometric
Processing
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Mouse BIRN

• Tools for structural and functional mouse brain
  data
• Digital Atlases
• Integrate Gene Expression Efforts
• Automated Image Processing
• Integrated Interface
• Focus on Neurodegenerative Diseases

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Mouse BIRN Data Integration
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Mouse BIRN Framework
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Mouse BIRN Image Queries
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Mouse BIRN 3D Atlas
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Morphomentry BIRN
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BioMed Cyber Infrastructure
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Biology Image Collections ?

• What are organization, access, quality and
  sustainability features of Biology image
  collections ?
• US FishWildlife, Visible Human, Fly Embryos,
  BIRN research
• Any unique aspects?
• What does a good biology image system contain?
• Contents, usage features, database components
• How would you create a biology image collection?
• Standard components?
• Biology-special ones?
• Slides at http//chipmunk.bio.indiana.edu/gilbert
  d/about/talks/
• bioimagedbs06.ppt, bioimagedbs06.pdf

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My Bioinformatics _at_ IU

• Genome database / information systems
• euGenes.org genome information for 8 model
  organisms
• insects.eugenes.org DroSpeGe, genomes of twelve
  Drosophila fruitflies
• wFleabase.org Daphnia water-flea genome
  database
• Generic Model Organism Database tools
  www.gmod.org
• Bio-info archiving and distribution
• IUBio Archive iubio.bio.indiana.edu public
  biology data / software archive
• Bio-Mirrors www.bio-mirror.net Sequence and
  related biology databank distribution

Don Gilbert, gilbertd_at_indiana.edu