NIH BD2K bioCADDIE DataMed: Data Discovery Index
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This document summarizes the work of developing a Data Discovery Index prototype that helps users find and access shared biomedical data from various repositories. It ingests metadata from different standards and sources using ElasticSearch. It was presented at the Alan Turing Institute Symposium in April 2016. The project aims to organize data through an aggregator framework and portal. It involves mapping various metadata standards to have maximum coverage of use cases with minimal data elements. More information can be found at the listed websites.
NIH BD2K bioCADDIE DataMed: Data Discovery Index
- 1. Consultant, Honorary Academic Editor Associate Director, Principal Investigator ! Susanna-Assunta Sansone, PhD! ! ! Alan Turing Institute Symposium Oxford, 6-7 April, 2016
- 2. A Data Discovery Index prototype that:! • Helps users find and access shared data ! • Interoperates in the NIH Commons (biomedical digital assets) !
- 4. Repositories Metadata Ingestion ElasticSearch Terminology server User Interface Online datasets PublishersFunding Agencies Data producers DataSources Ingestion Indexing Searching prototype!
- 5. aggregator' A' B C A aggregator' Data'Discovery'Index' data' Organizing framework and portal for data Dashed lines: mapping of metadata standards, links to aggregators, data Aggregators: repositories or various indices Data: digital research objects Pilot projects*Core development team * There is work for everyone (and more) Designed as an element of the ecosystem!
- 6. Use cases- community-driven effort!
- 7. The ‘right’ level of metadata elements!! Examples of competency questions, derived from the use cases
- 8. The ‘appropriate’ metadata standards!! Mapping the landscape of standards and databases in the life sciences
- 9. mapped a variety of metadata standards and database schemas Generic schemas:! • schema.org! • DataCite! • RIF-CS! • DCAT! • PROV! • VOID! • Dublin Core ! • etc…! Life/biomedical schemas:! • BioProject! • BioSample! • MiNIML! • PRIDE-ml! • GA4GH metadata schema! • SRA xml! • CDISC SDM / BRIDGE model ! • etc…! We have aimed to have maximum coverage of use cases with minimal number of data elements We do foresee that not all questions can be answered in full From to!
- 10. Prototype, model, mappings, documentation and more at! https://biocaddie.org and https://github.com/biocaddie ! Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego