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- file: content/home
- part: FOREWORD
numbered: false
chapters:
# - file: content/recipes/introduction
- file: content/recipes/introduction/FAIR-cookbook-audience
title: Introduction
- file: content/recipes/introduction/priorization
title: Selecting projects for FAIRification # FCB055
- file: content/recipes/introduction/FAIRplus-values
title: Ethical values of FAIR
- file: content/recipes/glossary-fair-terms
title: Glossary
# title: Introduction
# numbered: true
# sections:
# - file: content/recipes/glossary-fair-terms
# - file: content/recipes/introduction/brief-FAIR-principles
# - file: content/recipes/introduction/what-is-IMI
# - file: content/recipes/introduction/FAIR-in-IMI-context
# - file: content/recipes/introduction/IMI-and-data-management-plans
# - file: content/recipes/introduction/IMI-Data-Access-Request-Process
# - file: content/recipes/introduction/data-sharing-models
- part: RECIPES
chapters:
- file: content/recipes/findability
title: Findability
numbered: true
sections:
- file: content/recipes/findability/identifiers
title: Unique, persistent identifiers #FCB006
- file: content/recipes/infrastructure/chemical-identities
title: InChI and SMILES identifiers for chemical structures #FCB007
- file: content/recipes/findability/identifiers-minids
title: Minting identifiers with Minid #FCB008
- file: content/recipes/findability/zenodo-deposition
title: Depositing in Zenodo generic repository #FCB009
- file: content/recipes/findability/checksum-create
title: Describe data by checksums #FCB052
- file: content/recipes/findability/checksum-validate
title: Validating data by checksums #FCB053
- file: content/recipes/findability/seo
title: Search engine optimization #FCB010
sections:
- file: content/recipes/findability/seo/bioschemas-data-page
title: Data page markup with Bioschemas #FCB011
- file: content/recipes/findability/seo/bioschemas-dataset
title: Dataset page markup with Schema.org #FCB012
- file: content/recipes/findability/seo/bioschemas-datacatalog
title: Data catalogue markup #FCB013
- file: content/recipes/accessibility
title: Accessibility
numbered: true
sections:
# - file: content/recipes/accessibility/anonymizing-patient-data
- file: content/recipes/accessibility/sftp
title: Transferring data with SFTP #FCB014
- file: content/recipes/accessibility/aspera
title: Downloading data with Aspera #FCB015
- file: content/recipes/interoperability
title: Interoperability
numbered: true
sections:
- file: content/recipes/interoperability/identifier-mapping
title: Interlinking data from different sources #FCB016
- file: content/recipes/interoperability/bridgedb-recipe
title: Identifier mapping with BridgeDb #FCB017
sections:
- file: content/recipes/interoperability/bridgedb/bridgedb-example.ipynb
title: Using BridgeDb web services #FCB018
- file: content/recipes/interoperability/introduction-terminologies-ontologies
title: Introduction to terminologies and ontologies #FCB019
- file: content/recipes/interoperability/selecting-ontologies
title: Selecting terminologies and ontologies #FCB020
- file: content/recipes/interoperability/ontology-new-term-request-recipe
title: Requesting new terms #FCB021
- file: content/recipes/interoperability/ontology-operations-tools
title: Ontology-related tools and services #FCB022
- file: content/recipes/interoperability/ontology-robot-recipe
title: Building an application ontology with ROBOT #FCB023
sections:
- file: content/recipes/interoperability/ontology-robot-recipe/competency-questions
title: Competency questions for the Ontology ROBOT use case
- file: content/recipes/interoperability/ontology-robot-recipe/MSIO-robot-build-process.ipynb
title: Application ontology for metabolomics #FCB024
- file: content/recipes/interoperability/creating-data-dictionary
title: Creating a data/variable dictionary #FCB025
- file: content/recipes/interoperability/creating-minimal-metadata-profiles
title: Creating a metadata profile #FCB026
sections:
- file: content/recipes/interoperability/transcriptomics-metadata
title: Metadata profile for transcriptomics #FCB027
- file: content/recipes/interoperability/covid19-sample-metadata-profile-shex-use-case
title: Metadata profile validation in RDF #FCB028
- file: content/recipes/interoperability/from-proprietary-to-open-standard-mzml-exemplar
title: Converting from proprietary to open format #FCB029
- file: content/recipes/interoperability/rdf-conversion
title: An inventory of tools for converting your data to RDF #FCB051
- file: content/recipes/interoperability/fastq-file-format-validators
title: File format validation, FASTQ example #FCB030
- file: content/recipes/interoperability/ETL-tools
title: Extraction, transformation, and loading process #FCB031
- file: content/recipes/reusability
title: Reusability
numbered: true
sections:
- file: content/recipes/reusability/ATI-licensing
title: Licensing #FCB032
- file: content/recipes/reusability/ATI_licensing_software
title: Software licenses #FCB033
- file: content/recipes/reusability/ATI_licensing_data
title: Data licenses #FCB034
# - file: content/recipes/reusability/license-selection
- file: content/recipes/reusability/expressing-data-use
title: Declaring data's permitted uses #FCB035
- file: content/recipes/reusability/provenance
title: Provenance information #FCB036
# - file: content/recipes/reusability/community-standards
- file: content/recipes/infrastructure
title: Infrastructure
numbered: true
sections:
- file: content/recipes/infrastructure/id-resolution
title: Identifier resolution services #FCB046
- file: content/recipes/infrastructure/data-catalog
title: Building a catalogue of datasets #FCB047
- file: content/recipes/infrastructure/data-catalog-deployment
title: Deploying the IMI data catalogue #FCB048
- file: content/recipes/infrastructure/vocabularies
title: Vocabulary management
sections:
- file: content/recipes/infrastructure/vocabularies/technical-and-architectural-selection-criteria-of-ontology-lookup-services
title: Portals and look-up services #FCB003
- file: content/recipes/infrastructure/vocabularies/Selecting_and_using_ontology_lookup_services
title: Selecting a look-up service #FCB004
- file: content/recipes/infrastructure/vocabularies/UC3_R13_local_ontology_services
title: Deploying the EBI OLS #FCB005
- file: content/recipes/assessing-fairness
title: Assessment
numbered: true
sections:
# - file: content/recipes/assessing-fairness/automatic-fair-assessment
- file: content/recipes/assessing-fairness/fair-assessment-fairevaluator
title: FAIR Evaluator tool #FCB049
- file: content/recipes/assessing-fairness/fair-assessment-fairshake
title: FAIRshake tool #FCB050
- file: content/recipes/applied-examples
title: Applied examples
numbered: true
sections:
- file: content/recipes/applied-examples/fair-data-matrix-recipe
title: Making omics data matrices FAIR #FCB037
# numbered: false
sections:
- file: content/recipes/applied-examples/fair-data-matrix/0-rose-metabolites-Python-data-handling.ipynb
title: Starting material #FCB038
- file: content/recipes/applied-examples/fair-data-matrix/1-rose-metabolites-Python-analysis.ipynb
title: Structuring data #FCB039
- file: content/recipes/applied-examples/fair-data-matrix/2-rose-metabolites-Python-RDF-querying-analysis.ipynb
title: Exploring data with SPARQL #FCB040
- file: content/recipes/applied-examples/fair-data-matrix/3-rose-metabolites-R-analysis.ipynb
title: Integrating data #FCB041
- file: content/recipes/applied-examples/etox
title: eTox - toxicity datasets #FCB042
- file: content/recipes/applied-examples/nd4bb
title: nd4bb - chemical activities datasets #FCB044
- file: content/recipes/applied-examples/oncotrack_raw/rawRecipe-oncotrack
title: Oncotrack - clinical cohort datasets #FCB044
- file: content/recipes/applied-examples/resolute_raw/resolute
title: ReSOLUTE - transcriptomics datasets #FCB045
- file: content/recipes/applied-examples/ehden-ohdsi
title: EHDEN-OHDSI #FCB054
numbered: false
# sections:
# - file: content/recipes/assessing-fairness/cmmi/Data-Management-Maturity-Model
# - file: content/recipes/assessing-fairness/cmmi/Datasets-Maturity-Model
# - file: content/recipes/assessing-fairness/cmmi/Data-Usage-Areas
# - file: content/recipes/assessing-fairness/fair-indicators
# sections:
# - file: content/recipes/assessing-fairness/cmmi/RDA-Indicators
# - file: content/recipes/assessing-fairness/cmmi/FAIRPlus-Indicators
# - file: content/recipes/assessing-fairness/manual-fair-assessment
# sections:
# - file: content/recipes/assessing-fairness/cmmi/evaluation-method
# - file: content/recipes/assessing-fairness/cmmi/rda-evaluation
- part: ABOUT
chapters:
- file: content/recipes/community
title: Community
numbered: true
sections:
# - file: content/recipes/boilerplate/governance
- file: content/recipes/boilerplate/people
title: Boards and contributors
- file: content/recipes/boilerplate/code_of_conduct
title: Code of conduct
- file: content/recipes/help
title: Contribute
numbered: true
sections:
- file: content/recipes/boilerplate/contributing
title: How to contribute
- file: content/recipes/help/how-to-create-recipe-with-gdoc
title: Add via GoogleDoc
- file: content/recipes/help/how-to-create-recipe-with-hackmd
title: Add via HackMD
- file: content/recipes/help/how-to-create-recipe-with-git
title: Add via Git
- file: content/recipes/help/recipe-template
title: Git recipe template
- file: content/recipes/help/tips-tricks
title: Tips and tricks
- file: content/recipes/help/myst
title: Markdown cheatsheet
- file: content/recipes/boilerplate
title: Platform
numbered: true
sections:
- file: content/recipes/introduction/the-turing-way
title: Leveraging the Turing Way Book
# - file: content/recipes/boilerplate/technology_stack
# title: Technology stack
# - file: content/recipes/boilerplate/license
# - file: content/recipes/boilerplate/project_information
# - file: content/recipes/boilerplate/roadmap
# - file: content/recipes/boilerplate/disclaimer