OGI supports the development and maintenance of high-impact, publically-available resources emerging from genomics research projects in Ontario - these resources include technology platforms, databases, software, reagents and libraries. Our aim is to provide Ontario researchers with access to leading-edge, enabling technologies and to maintain domestic resources that can aid genomics research around the world.
Click here to learn about OGI's Technology Days, an effort to increase the visibility and usage of resources that have been developed by or in partnership with Ontario researchers.
Technology Platforms
The Centre for Applied Genomics (TCAG)
TCAG provides genomics services to researchers in academic, government, and private sectors all over the world. For more details, click here.
Databases
Autism Chromosome Rearrangement Database
This resource consists of hand-curated breakpoints and other genomic features relating to autism that derive from publicly available literature: databases and unpublished data. It undergoes continuous updating with data from in-house experiments and published research. It welcomes data and feedback from the research community.
Barcode of Life Data Systems (BOLD)
BOLD is an accessible database that aids in collection, management, analysis, dissemination, and searching of DNA barcodes. It is the definitive global DNA barcode database - created and maintained in Ontario, with researchers from over 25 countries contributing DNA samples. It already contains barcode sequences for over 50,000 species. Approximately three quarters of those have been added by Ontario researchers.
BOLD consists of three components: BOLD-MAS (a repository for DNA barcode records and analytical tools), BOLD-IDS (a species-identification tool that determines taxonomic assignment when possible based on submitted DNA sequences), and BOLD-ECS (for web developers and bioinformaticians to build tools and workflows than can become part of the BOLD framework).
Chromosome 7 Annotation Project
This resource comprises a collection of sequence, gene, and other annotations from all databases (e.g., Celera published, Ensembl, NCBI, RIKEN, and UCSC) as well as unpublished data.
Cystic Fibrosis Mutation Database
This database is a collection of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that acts as a resource for CF research everywhere. It currently contains more than 1,500 mutations and provides information about individual CFTR mutations and their related phenotypes. This database is augmented and maintained by a research team funded by Genome Canada through OGI.
Database of Genomic Variants (DGV)
DGV provides a comprehensive summary of structural variation resulting from alterations in the human genome. These changes involve segments of DNA larger than 1kb and insertions and deletions in the range 100bp-1kb. The DGV welcomes data on structural variation in the genome from scientific manuscripts.
Human Genome Segmental Duplication Database
This website contains information about segmental duplications in the human genome. The data come from analysis of the May 2004 Assembly of the Human Genome (also known as NCBI Build 35, or UCSC hg17).
Interologous Interaction Database (I2D)
I2D (formerly OPHID) is an on-line resource for exploring known and predicted mammalian and eukaryotic protein--protein interactions. It contains data for more than 430,000 protein interactions in humans and model organisms (fly, mouse, rat, worm, and yeast).
The Dynactome project has contributed more than 4,100 protein interactions to I2D, which has led to 8,880 more interactions through mapping to other organisms in the database. Further, by exploring texts, reviewing literature, and incorporating other high-throughput data sets, the project has given I2D a further 26,210 interactions and 56,810 interlogs.
Non-Human Segmental Duplication Database
This site contains information about segmental duplications in the genomes of chimpanzee, mouse, and rat.
StemBase
This is a publicly available database of Affymetrix DNA microarray and serial analysis of gene expression (SAGE) expression data from samples of human and mouse stem cells and their derivatives.
Structural Genomics Consortium (SGC) Materials and Methods
SGC is a not-for-profit organization that analyses the three-dimensional structure of proteins. It deposits structures (on average, 200 per year) in the Protein Data Bank (PDB), which releases them into the public domain and makes them freely accessible.
To access the PDB from the SGC homepage click on the "Structures" tab. From the "Structure Gallery" either search or scroll down for your protein of interest. The SGC entry will indicate the "PDB Code," which will transfer you to the PDB entry, and at the bottom of the page there will be a link to the SGC structure file with the same PDB code. Following this link provides basic background information on each target and the analysis of its structure. There is also a link to reagents for the structure, as well as one to a detailed description of the experimental materials and methods that generated the structure. For some protein structures, an associated iSee data pack provides an animated interpretation of the structure and tabs that include protocols. Alternatively, access the PDB and select the tabs for "Materials & Methods" and "Biology & Chemistry." There you will find purification and crystallization protocols, diffraction data, and other details about your selected structure.
Toronto Yeast Interaction Database and Toronto Yeast Pathway Database
These resources consolidate publicly available data and feature web-services interfaces that the Yeast Integrative Biology project maintains.
Software
Automated Splice Site Analyses
A web-based software tool for the prediction of the effects of sequence changes that alter mRNA splicing in human disease. This tool is used by researchers acroos Canada and worldwide, resulting in more than 130 citations to date.
eFISH (electronic fluorescence in situ hybridization)
eFISH is a BLAST-based program that facilitates the choice of appropriate clones for FISH and CGH experiments, as well as interpretation of results in which genomic DNA probes are used in hybridization-based experiments.
Network Analysis, Visualization & Graphing TORonto (NAViGaTOR)
NAViGaTOR is a software package for visualization and analysis of protein-protein interaction networks in two or three dimensions (2D or 3D, respectively). It is downloadable free of charge for academic and not-for-profit institutions.
WaterEngage
This on-line global community connects businesses, organizations, scientists, water activists, and young people. It informs and engages youths and the broader public on global water issues and their effects on health. It addresses many issues, including ways in which emerging nanotechnology and biotechnology applications can address waterborne and water-related diseases.
Reagents and Libraries
North American Conditional Mouse Mutagenesis (NorCOMM)
NorCOMM develops and distributes a library of lines of mouse embryonic stem (ES) cells that carry single conditional-knockout mutations across the mouse genome. ES cells that it develops become publicly available on a cost-recovery basis. NorCOMM also provides services across Canada in archiving, derivation, genotyping, and phenotyping of mouse ES cells.
