OSFair2017 Workshop | OmicsDI: Omics discovery index
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The document discusses the aims of the Omics Discovery Index (OmicsDI), which strives to facilitate the discovery of high-quality 'omics' datasets across various biological fields. It details the infrastructure for registering and integrating data repositories, outlining mandatory and recommended metadata fields for dataset submissions. Additionally, it presents resources for dataset search capabilities, statistical analysis, and metadata enrichment processes.
OSFair2017 Workshop | OmicsDI: Omics discovery index
- 1. www.elixir-europe.org @ELIXIREurope /company/elixir-europe OmicsDI Omics discovery index Rafael C Jimenez
- 2. How we can find a publication?
- 3. How we can find a dataset?
- 4. Aims • Facilitate discovery of high-quality ‘omics’ datasets (genomics, proteomics, transcriptomics and metabolomics). • Provide added value not just integration • Provide the infrastructure to register and integrate data repositories and their datasets.
- 5. http://www.omicsdi.org 15 repositories 90,880 datasets 3,840 diseases 2,781 tissues 4,605 species
- 7. Similarity visualization Metadata SimilarityBiological Similarity
- 9. Dataset metadata format Mandatory Fields: • Dataset Id • Dataset Title • Publication date • Submitter information (Name, Affiliation) • Original URL Recommended Fields: • Description/Abstract • Sample and Data Protocols • PubMed Id • Organism, Tissue, Disease. Additional Fields: • Protein Id (Ensembl or Uniprot) • Metabolite Id (ChEMBL) • More… https://github.com/BD2K-DDI/specifications/blob/master/docs/schema/fileds.md
- 10. OmicsDI XMLDatabases EBI Search Indexer INDEXING ENGINE EBI CLUSTER RESTWS SEARCH ENGINE End points: • Statistics • Datasets RESTFUL WS DATABASE WEB APP SEARCH STATISTICS TAGGING DDIApp Enrichment Annotation
- 11. Metadata processing • Input data Validation https://github.com/BD2K-DDI/xml-validator • Metadata enrichment https://github.com/BD2K-DDI/ddi-annotation • Identifier mapping ie. DOI to puimde IDs • Ontologies mapping ie. Text to NCBI taxonomy • Ontology enrichment ie. Disease synonymous and parent terms (annotator) • Analysis of dataset entries ie. Overlap of biological entries between datasets
- 12. Thanks for your attention