OmicsDI enables users to search across multiple repositories rather than performing searches at each one (Perez-Riverol et al., 2017). One example use case is searching for human data across the main 3 human data repositories, The European Genome-phenome Archive (EGA), Database of Genotypes and Phenotypes (dbGAP), Japanese Genome-Phenotype Archive (JGA) which is not otherwise possible. It may also be useful for searching across ArrayExpress and Gene Expression Omnibus (GEO), the two main repositories that house functional genomics data. The index currently contains ~2.7 million datasets from 24 repositories. The databases currently indexed can be found on their website.
References
- Perez-Riverol, Y., Bai, M., da Veiga Leprevost, F., Squizzato, S., Park, Y. M., Haug, K., Carroll, A. J., Spalding, D., Paschall, J., Wang, M., del-Toro, N., Ternent, T., Zhang, P., Buso, N., Bandeira, N., Deutsch, E. W., Campbell, D. S., Beavis, R. C., Salek, R. M., … Hermjakob, H. (2017). Discovering and linking public omics data sets using the Omics Discovery Index. Nature Biotechnology, 35(5), 406–409. https://doi.org/10.1038/nbt.3790
Relevant tools and resources
Skip tool table| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| ArrayExpress | A repository of array based genomics data | ArrayExpress BioStudies Expression Atlas | Tool info Standards/Databases Training Publication |
| Database of Genotypes and Phenotypes (dbGAP) | The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans | dbGAP | Tool info Standards/Databases Training Publication |
| Gene Expression Omnibus (GEO) | A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing | Gene Expression Omnibus | Publication |
| Japanese Genome-Phenotype Archive (JGA) | A controlled access data repository for human data managed by the DDBJ. | JGA | Publication |
| OmicsDI | Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) | Tool info Standards/Databases Training Publication | |
| The European Genome-phenome Archive (EGA) | EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects | BioSample EGA Repositories | Tool info Standards/Databases Training Publication |
Editor
Australian BioCommons / University of Melbourne