FAIR Sequencing Data Repository based on iRODS Felipe O. Gutierrez - - PowerPoint PPT Presentation

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FAIR Sequencing Data Repository based on iRODS Felipe O. Gutierrez - - PowerPoint PPT Presentation

Mar 21, 2024 37 likes •219 views

FAIR Sequencing Data Repository based on iRODS Felipe O. Gutierrez AMC - Academic Medical Center - Amsterdam, Netherlands A.C.Camargo Cancer Center - So Paulo, Brazil F. Oliveira Aldo Sjoerd Diogo A.H.C. van Silvia D. P.F.G. De J.T.

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SLIDE 1

Felipe O. Gutierrez

AMC - Academic Medical Center - Amsterdam, Netherlands A.C.Camargo Cancer Center - São Paulo, Brazil

FAIR Sequencing Data Repository based on iRODS

Silvia D. Olabarriaga

  • F. Oliveira

Gutierrez P.F.G. De Geest Diogo Ferreira Patrão A.H.C. van Kampen J.T. van den Berg Aldo Jongejan Sjoerd Repping

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SLIDE 2

Problem

  • Inadequate RDM (Research Data Management) solution for NGS data (Next

Generation Sequencing):

○ Individual storage and backup ○ Dispersed datasets ○ Disconnected from metadata ○ Not FAIR

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Considerations

Fit within organization

  • ICT culture
  • Research culture
  • Sustainability vision

Adhere to international community best practices Reuse and extend existing solutions

3 Freeman, 1983

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Fit into AMC Vision for RDM

Based on NFU Data4Lifesciences WP2

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An NGS repository that is:

  • Part of an ecosystem
  • Controlled by AMC
  • Distributed
  • Scalable
  • FAIR compliant
  • Easy to use
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SLIDE 5

System Design

  • iRODS 4.1.10

○ Middleware ○ Data virtualization

  • Virtuoso 7.2

○ Triplestore ○ Supports ontologies

  • User interfaces:

○ Metalnx web ○ Davrods 4.1 ○ iCommands

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System Architecture

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Stewardship: Ontologies

  • EDAM

Ontology for bioinformatics

  • perations, types of data, data

identifiers, data formats, and topics

  • OMIABIS

Ontologized Minimum Information About Biobank data Sharing (MIABIS)

  • OBI

Ontology for Biomedical Investigations

  • EFO

Experimental Factor Ontology

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Workflow: Data Ingestion

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Workflow: (meta)data Registration

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Workflow: (meta)data Retrieval

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Access and Security

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Status

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Report file

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nmon read KB/s

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nmon write KB/s

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nmon IOPs

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Qualitative & Quantitative questions

  • (meta)data preparation? Clear, doable, easy, ...
  • (meta)data upload? Type, size, quantity, integrity, ...
  • Rule processing? Report file clear and easy, system delay feedback, ...
  • (meta)data retrieval? Findable, Accessible, Organized, Interoperable,

Reusable, ..

  • Concurrent users, variation on the number and size of files.

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SLIDE 18

Acknowledgements

KEBB:

  • Barbera van Schaik
  • Allard van Altena

ADICT: Hans van den Berg UvA ICTS: Joyce Nijkamp Medical Library: Lieuwe Kool Clinical Research Unit: Rudy Scholte Reproductive medicine: Sjoerd Repping Genetic Metabolic Diseases: Frédéric Vaz Immunogenomics: Niek de Vries