Biology Image Libraries : Biology Image Libraries Don Gilbert
Bioinformatics, Biology Department,
Indiana University
[email protected] Biology Large to Small,
Old to New in images
What is bioinformatics? : 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/bioinformatics.html
Natl. Library Medicine : Natl. Library Medicine www.nlm.nih.gov
Library includes Visible Human, Forensics and other image databases
Home to major US Bioinformatics Databases (NCBI)
Bioinformatics at Nat. Lib. Med. : Bioinformatics at Nat. Lib. Med. All Genes and Genomes of humans and others
BiologyLiterature and data searches
www.ncbi.nlm. nih.gov
Slide 5: Constellation of Bio-Data (SRS - Lion Bioscience)
Bioscience image resources : 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/bioimage.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
US Fish & Wildlife Image Library : US Fish & Wildlife Image Library Catalogs nature images
Browse by categories
Search Associated Data about contents
http://images. fws.gov/
NLM Visible Human : 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/
Gene expression via images : 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/
Genome Map (Daphnia water flea) : Genome Map (Daphnia water flea)
Bioscience image uses : Bioscience image uses Data -> Software -> 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)
Bioscience image uses : 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)
NIH Image Program : NIH Image Program Manipulate and analyze biology images
Measure areas, intensities, patterns
Free, widely used
http://rsb.info.nih.gov/ nih-image/
Anatomy of a biology database : Anatomy of a biology database
Anatomy of biology database 1 : 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
Anatomy of biology database 2 : 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
Anatomy of biology database 3 : 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
Biomedical Informatics Research Network (BIRN) : 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.
Brain Image Analysis Network : Biomedical Informatics Research Network:
Integrating Multi-Site Neuroimaging Data Acquisition,
Data Sharing and Brain Morphometric Processing Brain Image Analysis Network
Mouse BIRN : 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
Mouse BIRN Data Integration : Mouse BIRN Data Integration
Mouse BIRN Framework : Mouse BIRN Framework
Mouse BIRN Image Queries : Mouse BIRN Image Queries
Mouse BIRN 3D Atlas : Mouse BIRN 3D Atlas
Morphomentry BIRN : Morphomentry BIRN
BioMed Cyber Infrastructure : BioMed Cyber Infrastructure
Biology Image Collections ? : Biology Image Collections ? What are organization, access, quality and sustainability features of Biology image collections ?
US Fish&Wildlife, 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/~gilbertd/about/talks/
bioimagedbs06.ppt, bioimagedbs06.pdf My Bioinformatics @ IU : My Bioinformatics @ 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,
[email protected]