Data Discovery Index Ecosystem by NIH Core Team
Explore the BioCADDIE project led by the NIH Core Team, focusing on biomedical and healthcare data discovery, indexing, and FAIR principles. Learn about creating a prototype data discovery index, metadata mapping, and open community participation. The project emphasizes findability, accessibility, interoperability, and reusability of shared data. Join the endeavor to enhance data organization and accessibility for research and innovation in the field of healthcare.
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Presentation Transcript
biomedical and healthCAre Data Discovery Index Ecosystem NIH Core Team Ron Margolis (Lead) Ian Fore (Science Officer) Dawei Lin & Alison Yao (Program Officers) Jennie Larkin (ADDS office liaison) RDA BOF on Data Search 3/1/16 NIH grant 1U24 AI117966-01 to the University of California, San Diego
Aims Pubmed for Data FAIR: Findability, Accessibility, Interoperability, Reusability 1. Help users find shared data 2. Build a prototype data discovery index 3. Evaluate requirements for next phase White Paper finalized 3/8/2015 (can be found at biocaddie.org)
The Concepts of DDI Organizing framework and portal for data Data? Discovery? Index? A? A dashed lines: mapping of metadata, standards, links to aggregators aggregator? aggregator? C B aggregators: various indices whose metadata are or can be mapped into Commons metadata data? Data Digital objects From Lucila Ohno Machado 3
Open Community Participation Identifiers Identifiers Metadata Metadata Working Groups Pilot Projects/RFAs to the Community Supplements
Data Indexing Pipeline Configuration file developed by curator Extraction of metadata/data from data resource or dataset via ingestion module Cache information for further processing Process metadata/data via sequential set of processing modules e.g. ID conversion, keyword extraction, data normalization Mapping of metadata/data to metadata model(s) Export to target endpoint(s)via export modules Search via ElasticSearch APIs 1. 2. 3. 4. 5. 6. From Jeff Grethe
Acknowledgements Lucila Ohno Machado (PI) The bioCADDIE team NIH Staff The bioCADDIE ESP Working Group experts Collaborators
A DDI Example for PDB { "dataItem": { "ID": "4IAQ", "title": "Crystal structure of the chimeric protein of 5-HT1B-BRIL in complex with dihydroergotamine (PSI Community Target)", "description": "5-hydroxytryptamine receptor 1B", "keywords": [ "Signaling Protein , "GPCR Dock" ], "dataTypes": [ "dataItem", "citation", "materialEntity", "organism", "identifiers" ] }, "materialEntity": [ { "name": "TYROSINE", "role": "chemical component", "formula": "C9 H11 N O3", "weight": "181.191", "type": "L-peptide linking" }, . . Identifier Metadata
