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(fcb-help-recipe-template)=

Git recipe template

+++ 

:class: tip
This section is highly standardized and is relied upon by another component developed by FAIRplus to enhance search and presentation. It is therefore important to comply with the layout. 
The authors should therefore edit the all but the `recipe metadata`. 
For the `Intended Audience` section, the allowed values should be picked from the following list:

    - Funder
    - Procurement Officer
    - Principal Investigator
    - Data Curator
    - Data Manager
    - Data Scientist
        - Chemoinformatician
        - Bioinformatician
    - Software Engineer
    - System Administrator
    - Terminology Manager
    - Ontologist


For the `Recipe Type` section, the allowed values should be picked from the following list:

    - Background information (introductory material)
    - Survey / Review (state of the art material)
    - Guidance (documentation aimed at both technical and non-technical audience)
    - Technical Guidance (documentation aimed at a technical audience, without executable code examples)
    - Hands-on (documentation aimed at a technical audience, with executable code examples available as jupyter notebooks)




:identifier_text: RX.X
:identifier_link: http://example.com
:difficulty_level: 2
:recipe_type: background_information
:reading_time_minutes: 15
:intended_audience: principal_investigator, data_manager, data_scientist, funder
:has_executable_code: nope
:recipe_name: Recipe Template

Main Objectives

The main purpose of this recipe is:

Provid a summary statement about the purpose of the recipe.

Graphical Overview

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)


Do make sure to save the mermaid diagram in a separate file using the '.mmd' extension. This is required for building the book as the images are generated by the build process. 
All the images will be generated as png files.

Then reference the figure using the Alan Turing Institute style as shown below:

name: fcb-help-recipe-template-figure1
subtitle: C-3PO_droid

Requirements

  • technical requirements:
    • bash knowledge
    • ...
  • recipe dependency:
    • read Recipe 1 first!
  • knowledge requirement:
    • be sure to know what OBO is, or read it here: ...link to knowledge...

Capability & Maturity Table

:class: tip
this section is relied upon by another component developed by FAIRplus to enhance search and presentation. It is therefore important to comply with the layout.

This section is meant for authors to describe the specific capability which they aim to bring from one maturity level to the next. This is therefore to document the methods used to enable change at the level of information process The table is therefore structure to identify the capability, the initial maturity level it is estimated to be and the final maturity it has been brought to.

Capability Initial Maturity Level Final Maturity Level
Interoperability minimal repeatable

FAIRification Objectives, Inputs and Outputs

:class: tip
this section is relied upon by another component developed by FAIRplus to enhance search and presentation. It is therefore important to comply with the layout.
Actions.Objectives.Tasks Input Output
validation Structure Data File (SDF) report
calculation Structure Data File (SDF) InChi
calculation Structure Data File (SDF) SMILES
text annotation Human Phenotype Ontology annotated text

Table of Data Standards

:class: tip
this section is relied upon by another component developed by FAIRplus to enhance search and presentation. It is therefore important to comply with the layout.

Authors should list all the data standards, format specification, syntax and controlled terminologies used in the FAIRification process applied to the IMI project data. Ideally, authors should mark up the information using either EDAM Ontology URI or FAIRsharing identifiers (which are DOIs)

Data Formats Terminologies Models
FASTQ LOINC SRA XML
DICOM Human Phenotype Ontology OMOP

Main Content

This is the place for your actual content. You can also ...

... write executable code

import isatools
import json
import pandas as pd 
import holoview

...insert bibliographic references

:class: tip

If you need to include bibliograhic reference, use the following syntax: 

```md
{footcite}`Gu2020`
```

This style of referencing will show up in text like this {footcite}Gu2020, and clicking on the link will take you to the Referencesection at the bottom of the page.

... create workflow figures

If you want to include figures, please use the following

one may use the following mermaid syntax:

:container: container-lg pb-3
:column: col-lg-12 p-2
:card: rounded

```
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]
```

which is then rendered like this:

:container: container-lg pb-3
:column: col-lg-12 p-2
:card: rounded

<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>

Authors of graphical representations using the mermaid syntax can also style their graphs, as shown below

:container: container-lg pb-3
:column: col-lg-12 p-2
:card: rounded

<div class="mermaid">
graph TD;
    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>

Conclusion

Summerize Key Learnings of the recipe.

Suggest further reading using the following:

What should I read next?

References:

Authors

List the recipe contributors following the structure below and using the CASRAI credit vocabulary and do not change the structure of the table.
    - Conceptualization
    - Data curation
    - Formal Analysis
    - Funding acquisition
    - Investigation
    - Methodology
    - Project administration

    - Resources
    - Software
    - Supervision
    - Validation
    - Visualization
    - Writing - original draft
    - Writing - review & editing

:class: tip
this section is relied upon by another component developed by FAIRplus to enhance search and presentation. It is therefore important to comply with the layout.
Name Orcid Affiliation Type Elixir Node Credit Role
University of Oxford Writing - Review & Editing, Conceptualization

License

CC-BY-4.0