The FAIR Cookbook
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FOREWORD

  • Introduction
  • Introducing the FAIR Principles
  • Reflecting on the ethical values of FAIR
  • Introducing our FAIRification framework
  • Prioritizing projects for FAIRification
  • Framing FAIR and the notion of metadata
  • Understanding the relation between FAIR and Knowledge Graphs
  • Training for FAIRification with open or synthetic biomedical datasets
  • Raising Awareness in Public Knowledge Graphs for Life Sciences
  • Reflecting on Practical Considerations for CROs to play FAIR
  • Data Protection Impact Assessment and Data Privacy
  • Glossary

Recipes at a Glance

  • All Recipes In a Table

FAIR RECIPES

  • Findability
    • 1. Introducing unique, persistent identifiers
    • 2. Creating InChI & SMILES identifiers for chemical structures
    • 3. Creating InChIKeys for IUPAC names
    • 4. Minting identifiers with Globus Minid client
    • 5. Depositing to generic repositories - Zenodo use case
    • 6. Registering datasets with Wikidata
    • 7. Creating file checksums
    • 8. Validating checksums to verify file integrity
    • 9. Introducing Search Engine Optimization (SEO)
      • 9.9.1. Marking up Data pages with Schema.org & Bioschemas for SEO
      • 9.9.2. Marking up Dataset page with Schema.org & Bioschemas for SEO
      • 9.9.3. Marking up Data Catalogue page with Schema.org & Bioschemas for SEO
  • Accessibility
    • 1. Transferring data with SFTP protocol
    • 2. Downloading data with Aspera protocol
  • Interoperability
    • 1. Registering SwissLipids identifiers in Wikidata
    • 2. Interlinking data from different sources
    • 3. Mapping identifiers with BridgeDb
      • 3.11.1. Mapping identifiers using BridgeDb web services
    • 4. Introducing terminologies and ontologies
    • 5. Selecting terminologies and ontologies
    • 6. Requesting new terms from terminologies and ontologies
    • 7. Introducing ontology-related tools and services
    • 8. Building an application ontology with ROBOT
      • 8.11.1. Building an application ontology for metabolomics - MSIO
      • 8.11.2. Defining competency questions for the Ontology ROBOT use case
    • 9. Mapping Ontologies with OxO, EBI Ontology Xref Service
    • 10. Creating a data/variable dictionary
    • 11. Creating a metadata profile
      • 11.5.1. Outlining a metadata profile for transcriptomics
      • 11.5.2. Building a community compliant metadata profile - The Covid19 sample profile use case
      • 11.5.3. Outlining a metadata profile for Bioactivity data
      • 11.5.4. Creating a metadata profile for clinical trial protocols
    • 12. Converting from proprietary to open format
    • 13. Validating file format - FASTQ example
    • 14. Inventorying tools for converting data to RDF
    • 15. Surveying extraction, transformation, load (ETL) tools
    • 16. Expressing Clinical Genetic Information as FHIR JSON
      • 16.9.1. Converting VCF file to FHIR JSON
    • 17. Creating knowledge graphs from unstructured text
      • 17.12.1. unstructured text to graph as executable notebook
  • Reusability
    • 1. Licensing
    • 2. Licensing Software
    • 3. Licensing Data
    • 4. Declaring data permitted uses
    • 5. Introducing Provenance Information
  • Infrastructure
    • 1. Introducing identifier resolution services
    • 2. Creating resolvable identifiers
    • 3. Building a catalogue of datasets
    • 4. Introducing the DATS model
    • 5. Deploying a data catalogue - The IMI data catalogue example
    • 6. Vocabulary management
      • 6.1. Introducing vocabulary portals and lookup services
      • 6.2. Selecting an ontology lookup service
      • 6.3. Deploying EBI Ontology Loopkup Service
    • 7. Using OpenRefine and Karma for FAIRification
    • 8. Developing FAIR API for the Web
  • Assessment
    • 1. Assessing with FAIR Evaluator
    • 2. Assessing with FAIRshake

FAIR Maturity

  • Changing culture with the Dataset Maturity Model
    • Improving dataset maturity - MIAPPE-compliant submission to EMBL-EBI databases
    • Publishing plant phenotypic data
    • Moving through maturity levels with ISA
      • Minimal Data Maturity with ISA - ISA-Tab and free text
      • Enhanced Data Maturity with ISA - ISA-JSON and ontology markup
      • Moving to a semantically typed version - ISA-JSON-LD
      • Dissemination - Packaging ISA as a Research Object (RO)
    • Making an omics data matrix FAIR
      • FAIRifying Data Matrices - Step1 - Starting material
      • FAIRifying Data Matrices - Step2 - Structuring data
      • FAIRifying Data Matrices - Step3 - Exploring data with SPARQL
      • FAIRifying Data Matrices - Step4 - Integrating data
    • Making Computational Workflows FAIR

FAIRified Datasets

  • Applied examples
    • 1. IMI eTox - toxicity datasets
    • 2. IMI nd4bb - chemical activities datasets
    • 3. Readying IMI Oncotrack - clinical cohort datasets for deposition to EBI Biosamples
    • 4. Depositing IMI ReSOLUTE transcriptomics datasets to EBI repositories
    • 5. Enhancing discoverability of EHDEN OHDSI data with Schema.org markup
    • 6. Depositing IMI EUBOPEN High-Content Screening data to EBI BioImage Archive
    • 7. Depositing epifluorescence and confocal microscopy data to EBI BioImage Archive
    • 8. Mapping IMI APPROACH datasets to CDISC-SDTM standard

AFTERWORD

  • Lessons learned from the FAIR journey and project outlook

GLOSSARY

  • Glossary of terms and abbreviations

JOIN US

  • Community
    • Boards and contributors
    • Code of conduct
    • Platform
      • Leveraging the Turing Way Book
  • Contribute
    • 1. How to contribute
    • 2. Add via GoogleDoc
    • 3. Add via HackMD
    • 4. Add via Git
    • 5. Git recipe template
    • 6. Tips and tricks
    • 7. Markdown cheatsheet
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Glossary Findability
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Grant agreement 802750
  • Contact us
  • FAIRplus
  • Contributors
  • How to contribute
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Recommended in the IMI/IHI Project Guidelines and the Horizon Europe Work Programme for Health as the resource for FAIR Data Management guidelines and good practices for the Life Sciences.
The FAIR Cookbook is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.