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  • FAIR Cookbook

FOREWORD

  • Introduction
  • What are the FAIR principles?
  • Ethical values of FAIR
  • Metadata and FAIR
  • Datasets to train on FAIRification
  • FAIR and Knowledge Graphs
  • Public Knowledge Graphs for Life Sciences
  • Selecting projects for FAIRification
  • Practical Considerations for a CRO to do FAIR
  • Glossary

FAIR RECIPES

  • Findability
    • 1. Unique, persistent identifiers
    • 2. InChI and SMILES identifiers for chemical structures
    • 3. Minting identifiers with Minid
    • 4. Depositing in Zenodo generic repository
    • 5. Registering Datasets in Wikidata
    • 6. Describe data by checksums
    • 7. Validating data by checksums
    • 8. Search engine optimization
      • 8.9.1. Data page markup with Bioschemas
      • 8.9.2. Dataset page markup with Schema.org
      • 8.9.3. Data catalogue markup
  • Accessibility
    • 1. Transferring data with SFTP
    • 2. Downloading data with Aspera
  • Interoperability
    • 1. Interlinking data from different sources
    • 2. Identifier mapping with BridgeDb
      • 2.11.1. Using BridgeDb web services
    • 3. Introduction to terminologies and ontologies
    • 4. Selecting terminologies and ontologies
    • 5. Requesting new terms
    • 6. Ontology-related tools and services
    • 7. Building an application ontology with ROBOT
      • 7.11.1. Competency questions for the Ontology ROBOT use case
      • 7.11.2. Application ontology for metabolomics
    • 8. Creating a data/variable dictionary
    • 9. Creating a metadata profile
      • 9.4.1. Metadata profile for transcriptomics
      • 9.4.2. Metadata profile validation in RDF
      • 9.4.3. Bioactivity data profile
    • 10. Converting from proprietary to open format
    • 11. An inventory of tools for converting your data to RDF
    • 12. File format validation, FASTQ example
    • 13. Extraction, transformation, and loading process
    • 14. Clinical Genetic Information as FHIR JSON
      • 14.9.1. Converting VCF file to FHIR JSON
  • Reusability
    • 1. Licensing
    • 2. Software licenses
    • 3. Data licenses
    • 4. Declaring data's permitted uses
    • 5. Provenance information
  • Infrastructure
    • 1. Identifier resolution services
    • 2. Building a catalogue of datasets
    • 3. Deploying the IMI data catalogue
    • 4. Vocabulary management
      • 4.1. Portals and look-up services
      • 4.2. Selecting a look-up service
      • 4.3. Deploying the EBI OLS
    • 5. Using OpenRefine and Karma for FAIRification
  • Assessment
    • 1. FAIR Evaluator tool
    • 2. FAIRshake tool

FAIR Maturity

  • A Model To Gauge Dataset Maturity
    • Improving dataset maturity - the MIAPPE use case
    • Moving through maturity levels with ISA
      • Creating a basic ISA document
      • Making a community compliant - ISA in JSON
      • Moving to a semantically typed version - ISA in RDF
      • Packaging ISA as a Research Object (RO)
    • Making omics data matrices FAIR
      • 1. Starting material
      • 2. Structuring data
      • 3. Exploring data with SPARQL
      • 4. Integrating data
    • Making Computational Workflows FAIR

FAIRified Datasets

  • Applied examples
    • 1. IMI eTox - toxicity datasets
    • 2. IMI nd4bb - chemical activities datasets
    • 3. IMI Oncotrack - clinical cohort datasets
    • 4. IMI ReSOLUTE - transcriptomics datasets
    • 5. IMI EHDEN-OHDSI
    • 6. IMI EUBOPEN FAIR High-Content Screening data deposition

AFTERWORD

  • 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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Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y

A

  • Access Rights
  • Accessibility

B

  • BYOD

C

  • CDE
  • CDISC
  • CMMI
  • Controlled Terminology

D

  • DAA
  • DAG
  • Data Catalogue
  • Data Dictionary
  • Data Enclave
  • DCAT
  • Descriptive Metadata

E

  • ECHA
  • EMA
  • ETL

F

  • FAIR
  • FAIR assessment
  • FDA
  • FHIR
  • FIP

G

  • GDPR
  • GO-FAIR
  • GraphQL
  • Gremlin
  • GUPRID

H

  • HIPAA
  • HL7 FHIR
  • HTTP

I

  • ID
  • IMI
  • Interoperability

J

  • JSON

K

  • KG
  • KPI

L

  • LD
  • Licensing

M

  • MDR
  • Metadata
  • MIC
  • MTA

N

  • Neo4J
  • NO-SQL

O

  • ODRL
  • OMOP-CDM
  • Ontology
  • OpenAPI

P

  • PID
  • Property Graph
  • PROV
  • Provenance Metadata

Q

  • QMS
  • QUDT

R

  • RDA
  • RDBMS
  • RDF
  • Reification
  • Reusability
  • RO
  • ROI
  • RRID
  • RWD
  • RWE

S

  • SEO
  • SHACL
  • ShEX
  • SPARQL
  • Structural Metadata
  • Swagger API

T

  • Turtle

U

  • URI

V

  • ValueSet

W

  • Wikidata

X

  • XML

Y

  • YML
  • Yummydata

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The FAIR Cookbook is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.