bio image dbs06

Views:
 
     
 

Presentation Description

No description available.

Comments

Presentation Transcript

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]