# Table of Contents
1. [Main FAIRification Objectives](#Main%20FAIRification%20Objectives)
2. [Graphical Overview of the FAIRification Recipe Objectives](#Graphical%20Overview%20of%20the%20FAIRification%20Recipe%20Objectives)
3. [FAIRification Objectives, Inputs and Outputs](#FAIRification%20Objectives,%20Inputs%20and%20Outputs)
4. [Capability & Maturity Table](#Capability%20&%20Maturity%20Table)
5. [Table of Data Standards](#Table%20of%20Data%20Standards)
6. [Executable Code in Notebook](#Executable%20Code%20in%20Notebook)
7. [How to create workflow figures](#How%20to%20create%20workflow%20figures)
8. [License](#License)

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## Main Objectives

The main purpose of this recipe is:

> Making self describing tabular data using Frictionless tools instead of dumping Excel files.

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## Graphical Overview of the FAIRification Recipe Objectives

Note: use this section to provide a decision tree for the overall process described in the recipe
For more information about the syntax used to generate the diagram, please refer to the [following documentation](https://mermaid-js.github.io/mermaid/#/flowchart)

<div class="mermaid">
graph LR;
A[Data Acquisition] -->B(Raw Data)
B --> C{FAIR by Design}
C -->|Yes| D[Standard Compliant Data]
C -->|No| E[Vendor locked Data]
</div>

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## Capability & Maturity Table

| Capability | Initial Maturity Level | Final Maturity Level |
| :------------- | :------------- | :------------- |
| Interoperability | minimal | repeatable |

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## FAIRification Objectives, Inputs and Outputs

| Actions.Objectives.Tasks | Input | Output |
| :------------- | :------------- | :------------- |
| [validation](http://edamontology.org/operation_2428) | [Structure Data File (SDF)](https://fairsharing.org/FAIRsharing.ew26v7) | [report](http://edamontology.org/data_2048) |
| [calculation](http://edamontology.org/operation_3438) | [Structure Data File (SDF)](https://fairsharing.org/FAIRsharing.ew26v7) | [InChi](https://fairsharing.org/FAIRsharing.ddk9t9) |
| [calculation](http://edamontology.org/operation_3438) | [Structure Data File (SDF)](https://fairsharing.org/FAIRsharing.ew26v7) | [SMILES](https://fairsharing.org/FAIRsharing.qv4b3c) |
| [text annotation](http://edamontology.org/operation_3778) | [Human Phenotype Ontology](https://fairsharing.org/FAIRsharing.kbtt7f) | [annotated text](http://edamontology.org/data_3779) |

## Table of Data Standards

| Data Formats | Terminologies | Models |
| :------------- | :------------- | :------------- |
| [FASTQ](https://fairsharing.org/FAIRsharing.r2ts5t) | [LOINC](https://fairsharing.org/FAIRsharing.2mk2zb) | [SRA XML](https://fairsharing.org/FAIRsharing.q72e3w) |
| [DICOM](https://fairsharing.org/FAIRsharing.b7z8by) | [Human Phenotype Ontology](https://fairsharing.org/FAIRsharing.kbtt7f) | [OMOP](https://fairsharing.org/FAIRsharing.qk984b) |

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## Executable Code in Notebook

import isatools
import json
import pandas as pd 
import holoview

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## How to create workflow figures

one may use the following **[mermaid](https://mermaid-js.github.io/mermaid/#/)** syntax:

graph LR;
    A[Data Acquisition] -->B(Raw Data)
    B --> C{FAIR by Design}
    C -->|Yes| D[Standard Compliant Data]
    C -->|No| E[Vendor locked Data]

<div class="mermaid">
graph LR;
A["input data"]-->B["conversion to open format"];
A["input data"]-->C["automatic annotation"];
B["conversion to open format"]-->D(("output data"));
C["automatic annotation"]-->D(("output data"));

style A fill:#FF5733,stroke:#333,stroke-width:2px
style D fill:#0A749B,stroke:#333,stroke-width:2px
</div>

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## Authors:

| Name | Affiliation | orcid | CrediT role |
| :------------- | :------------- | :------------- |:------------- |
| Philippe Rocca-Serra | University of Oxford, Data Readiness Group| [0000-0001-9853-5668](https://orcid.org/orcid.org/0000-0001-9853-5668) | Writing - Original Draft |
| Susanna-Assunta Sansone | University of Oxford, Data Readiness Group | | Writing - Review & Editing, Funding acquisition |

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## License:

<a href="https://creativecommons.org/licenses/by/4.0/"><img src="https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png" height="20"/></a>