_toc.yml

- file: content/home

- part: FOREWORD
  numbered: false
  chapters:
    - file: content/recipes/introduction/FAIR-cookbook-audience
      title: Introduction
    - file: content/recipes/introduction/brief-FAIR-principles
      title: Introducing the FAIR Principles
    - file: content/recipes/introduction/FAIRplus-values
      title: Reflecting on the ethical values of FAIR
    - file: content/recipes/introduction/fairification-process #FCB079
      title: Introducing our FAIRification framework
    - file: content/recipes/introduction/priorization #FCB055
      title: Prioritizing projects for FAIRification
    - file: content/recipes/introduction/metadata-fair #FCB068
      title: Framing FAIR and the notion of metadata
    - file: content/recipes/introduction/FAIR-and-knowledge-graphs #FCB070
      title: Understanding the relation between FAIR and Knowledge Graphs
    - file: content/recipes/introduction/training-datasets #FCB069
      title: Training for FAIRification with open or synthetic biomedical datasets
    - file: content/recipes/introduction/public-kg-resource-integration #FCB071
      title: Raising Awareness in Public Knowledge Graphs for Life Sciences
    - file: content/recipes/introduction/fair-cro #FCB056
      title: Reflecting on Practical Considerations for CROs to play FAIR
    - file: content/recipes/introduction/dpia #FCB074
      title: Data Protection Impact Assessment and Data Privacy
    - file: content/recipes/introduction/glossary-fair-terms
      title: Glossary


- part: Recipes at a Glance
  chapters:
    - file: content/search-wizard
      title: All Recipes In a Table


- part: FAIR RECIPES
  chapters:
    - file: content/recipes/findability 
      title: Findability
      numbered: true
      sections:
      - file: content/recipes/findability/identifiers
        title: Introducing unique, persistent identifiers #FCB006
      - file: content/recipes/infrastructure/chemical-identities
        title: Creating InChI & SMILES identifiers for chemical structures #FCB007
      - file: content/recipes/infrastructure/iupac-names
        title: Creating InChIKeys for IUPAC names #FCB080
      - file: content/recipes/findability/identifiers-minids
        title: Minting identifiers with Globus Minid client #FCB008
      - file: content/recipes/findability/zenodo-deposition
        title: Depositing to generic repositories - Zenodo use case #FCB009
      - file: content/recipes/findability/registeringDatasets
        title: Registering datasets with Wikidata #FCB060
      - file: content/recipes/findability/checksum-create
        title: Creating file checksums #FCB052
      - file: content/recipes/findability/checksum-validate
        title: Validating checksums to verify file integrity #FCB053
      - file: content/recipes/findability/seo
        title: Introducing Search Engine Optimization (SEO) #FCB010
        sections:
          - file: content/recipes/findability/seo/bioschemas-data-page
            title: Marking up Data pages with Schema.org & Bioschemas for SEO #FCB011
          - file: content/recipes/findability/seo/bioschemas-dataset
            title: Marking up Dataset page with Schema.org & Bioschemas for SEO #FCB012
          - file: content/recipes/findability/seo/bioschemas-datacatalog
            title: Marking up Data Catalogue page with Schema.org & Bioschemas for SEO #FCB013

    - file: content/recipes/accessibility
      title: Accessibility
      numbered: true
      sections:
        - file: content/recipes/accessibility/sftp
          title: Transferring data with SFTP protocol #FCB014
        - file: content/recipes/accessibility/aspera
          title: Downloading data with Aspera protocol #FCB015

    - file: content/recipes/interoperability
      title: Interoperability
      numbered: true
      sections:
          - file: content/recipes/interoperability/registering-swisslipids-identifiers
            title: Registering SwissLipids identifiers in Wikidata #FCB085
          - file: content/recipes/interoperability/identifier-mapping
            title: Interlinking data from different sources #FCB016
          - file: content/recipes/interoperability/bridgedb-recipe
            title: Mapping identifiers with BridgeDb #FCB017
            sections:
              - file: content/recipes/interoperability/bridgedb/bridgedb-example.ipynb
                title: Mapping identifiers using BridgeDb web services #FCB018
          - file: content/recipes/interoperability/introduction-terminologies-ontologies    
            title: Introducing 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 from terminologies and ontologies #FCB021
          - file: content/recipes/interoperability/ontology-operations-tools
            title: Introducing 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/MSIO-robot-build-process.ipynb
                title: Building an application ontology for metabolomics - MSIO  #FCB024
              - file: content/recipes/interoperability/ontology-robot-recipe/competency-questions
                title: Defining competency questions for the Ontology ROBOT use case
          - file: content/recipes/interoperability/ontology-alignment-oxo
            title: Mapping Ontologies with OxO, EBI Ontology Xref Service #FCB076
          - 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: Outlining a metadata profile for transcriptomics #FCB027
              - file: content/recipes/interoperability/covid19-sample-metadata-profile-shex-use-case
                title: Building a community compliant metadata profile - The Covid19 sample profile use case #FCB028
              - file: content/recipes/interoperability/bioactivity-profile
                title: Outlining a metadata profile for Bioactivity data #FCB057
              - file: content/recipes/interoperability/c4c-clinical-trials
                title: Creating a metadata profile for clinical trial protocols #FCB084PRE
          - file: content/recipes/interoperability/from-proprietary-to-open-standard-mzml-exemplar  
            title: Converting from proprietary to open format #FCB029
          - file: content/recipes/interoperability/fastq-file-format-validators
            title: Validating file format - FASTQ example #FCB030
          - file: content/recipes/interoperability/rdf-conversion 
            title: Inventorying tools for converting data to RDF #FCB051
          - file: content/recipes/interoperability/ETL-tools
            title: Surveying extraction, transformation, load (ETL) tools #FCB031
          - file: content/recipes/interoperability/VCF-to-FHIR-conversion
            title: Expressing Clinical Genetic Information as FHIR JSON #FCB058
            sections:
              - file: content/recipes/interoperability/vcf2fhir/FAIRcookbook-vcf2fhir.ipynb
                title: Converting VCF file to FHIR JSON #FCB059
          - file: content/recipes/interoperability/creating-knowledge-graph-from-unstructured-text
            title: Creating knowledge graphs from unstructured text #FCB081
            sections:
              - file: content/recipes/interoperability/nlp2kg/creating-knowledge-graph-from-text.ipynb
                title: unstructured text to graph as executable notebook


    - 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: Licensing Software #FCB033
        - file: content/recipes/reusability/ATI_licensing_data
          title: Licensing Data #FCB034
        - file: content/recipes/reusability/expressing-data-use 
          title: Declaring data permitted uses #FCB035
        - file: content/recipes/reusability/provenance
          title: Introducing Provenance Information #FCB036

    - file: content/recipes/infrastructure
      title: Infrastructure
      numbered: true
      sections:
          - file: content/recipes/infrastructure/id-resolution
            title: Introducing identifier resolution services #FCB046
          - file: content/recipes/infrastructure/gupri
            title: Creating resolvable identifiers #FCB077
          - file: content/recipes/infrastructure/data-catalog
            title: Building a catalogue of datasets #FCB047
          - file: content/recipes/infrastructure/dats-model
            title: Introducing the DATS model #FCB082
          - file: content/recipes/infrastructure/data-catalog-deployment
            title: Deploying a data catalogue - The IMI data catalogue example #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: Introducing vocabulary portals and lookup services #FCB003
              - file: content/recipes/infrastructure/vocabularies/Selecting_and_using_ontology_lookup_services
                title: Selecting an ontology lookup service #FCB004
              - file: content/recipes/infrastructure/vocabularies/UC3_R13_local_ontology_services
                title: Deploying EBI Ontology Loopkup Service #FCB005
          - file: content/recipes/infrastructure/openrefine-nvt
            title: Using OpenRefine and Karma for FAIRification #FCB075
          - file: content/recipes/infrastructure/fair-api #FCB073
            title: Developing FAIR API for the Web

    - file: content/recipes/assessing-fairness
      title: Assessment
      numbered: true
      sections:
            - file: content/recipes/assessing-fairness/fair-assessment-fairevaluator
              title: Assessing with FAIR Evaluator #FCB049
            - file: content/recipes/assessing-fairness/fair-assessment-fairshake
              title: Assessing with FAIRshake #FCB050

- part: FAIR Maturity
  chapters:
    - file: content/recipes/maturity
      title: Changing culture with the Dataset Maturity Model
      sections:
        - file: content/recipes/reusability/miappe #FCB061
          title: Improving dataset maturity - MIAPPE-compliant submission to EMBL-EBI databases
        - file: content/recipes/reusability/plant-pheno-data-publication #FCB083
          title: Publishing plant phenotypic data
        - file: content/recipes/maturity/isa-maturity-progression
          title: Moving through maturity levels with ISA
          sections:
            - file: content/recipes/maturity/create-a-simple-ISA-descriptor.ipynb #FCB063
              title: Minimal Data Maturity with ISA - ISA-Tab and free text
            - file: content/recipes/maturity/isa-api-programmatic-rebuild-of-BII-S-3.ipynb #FCB064
              title: Enhanced Data Maturity with ISA - ISA-JSON and ontology markup
            - file: content/recipes/maturity/isa-json-conversion-to-rdf-linked-data.ipynb #FCB065
              title: Moving to a semantically typed version - ISA-JSON-LD
            - file: content/recipes/maturity/isa-as-RO.ipynb #FCB066
              title: Dissemination - Packaging ISA as a Research Object (RO)
        - file: content/recipes/applied-examples/fair-data-matrix-recipe
          title: Making an omics data matrix FAIR #FCB037
          numbered: false
          sections:
            - file: content/recipes/applied-examples/fair-data-matrix/0-rose-metabolites-Python-data-handling.ipynb
              title: FAIRifying Data Matrices - Step1 - Starting material #FCB038
            - file: content/recipes/applied-examples/fair-data-matrix/1-rose-metabolites-Python-analysis.ipynb
              title: FAIRifying Data Matrices - Step2 - Structuring data #FCB039
            - file: content/recipes/applied-examples/fair-data-matrix/2-rose-metabolites-Python-RDF-querying-analysis.ipynb
              title: FAIRifying Data Matrices - Step3 - Exploring data with SPARQL #FCB040
            - file: content/recipes/applied-examples/fair-data-matrix/3-rose-metabolites-R-analysis.ipynb
              title: FAIRifying Data Matrices - Step4 - Integrating data #FCB041
        - file: content/recipes/applied-examples/fair-workflows
          title: Making Computational Workflows FAIR #FCB062



- part: FAIRified Datasets
  chapters:
    - file: content/recipes/applied-examples
      title: Applied examples
      numbered: true
      sections:
        - file: content/recipes/applied-examples/etox
          title: IMI eTox - toxicity datasets #FCB042
        - file: content/recipes/applied-examples/nd4bb
          title: IMI nd4bb - chemical activities datasets #FCB044
        - file: content/recipes/applied-examples/oncotrack_raw/rawRecipe-oncotrack
          title: Readying IMI Oncotrack - clinical cohort datasets for deposition to EBI Biosamples #FCB044
        - file: content/recipes/applied-examples/resolute_raw/resolute
          title: Depositing IMI ReSOLUTE transcriptomics datasets to EBI repositories #FCB045
        - file: content/recipes/applied-examples/ehden-ohdsi
          title: Enhancing discoverability of EHDEN OHDSI data with Schema.org markup #FCB054
        - file: content/recipes/applied-examples/eubopen-hcs-bioimage
          title: Depositing IMI EUBOPEN High-Content Screening data to EBI BioImage Archive #FCB067
        - file: content/recipes/applied-examples/approach-cdisc
          title: Mapping IMI APPROACH datasets to CDISC-SDTM standard #FCB078

- part: AFTERWORD
  chapters:
      - file: content/recipes/afterword/fair-reflections.md
        title: Lessons learned from the FAIR journey and project outlook
        numbered: false

- part: GLOSSARY
  chapters:
    - file: content/recipes/introduction/glossary-fair-terms
      title: Glossary of terms and abbreviations


- part: JOIN US
  chapters:
    - file: content/recipes/community
      title: Community
      numbered: false
      sections:
        - file: content/recipes/afterword/people
          title: Boards and contributors
        - file: content/recipes/afterword/code_of_conduct
          title: Code of conduct
        - file: content/recipes/afterword
          title: Platform
          numbered: false
          sections:
            - file: content/recipes/afterword/the-turing-way
              title: Leveraging the Turing Way Book

    - file: content/recipes/help
      title: Contribute
      numbered: true
      sections:
        - file: content/recipes/afterword/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