Rafael C Jimenez presents the Omics Discovery Index | OSFair2017 Workshop Workshop title: How FAIR friendly is your data catalogue? Workshop overview: This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users? DAY 3 - PARALLEL SESSION 6 & 7

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

6. Datasets search

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