5. Git recipe template¶
Important
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)
5.1. Main Objectives¶
The main purpose of this recipe is:
Provid a summary statement about the purpose of the recipe.
5.2. Graphical Overview¶
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
Warning
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:
Fig. 5.20 C-3PO_droid¶
5.3. 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…
5.4. Capability & Maturity Table¶
Important
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 |
5.5. FAIRification Objectives, Inputs and Outputs¶
Important
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 |
|---|---|---|
5.6. Table of Data Standards¶
Important
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 |
|---|---|---|
5.7. Main Content¶
This is the place for your actual content. You can also …
5.7.1. … write executable code¶
import isatools
import json
import pandas as pd
import holoview
5.7.2. …insert bibliographic references¶
Tip
If you need to include bibliographic reference, use the following syntax:
{footcite}`Gu2020`
This style of referencing will show up in text like this 1, and clicking on the link will take you to
the Referencesection at the bottom of the page.
5.7.3. … create workflow figures¶
If you want to include figures, please use the following
one may use the following mermaid syntax:
````{panels}
: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:
Authors of graphical representations using the mermaid syntax can also style their graphs, as shown below:
````{panels}
: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>
````
5.8. Conclusion¶
Summerize Key Learnings of the recipe.
Suggest further reading using the following:
5.8.1. What should I read next?¶
using a reference tag affored by MyST markdown and sphinx with JupyterBook 0.7+. my-prefered-label
Note
To the Reviewers and Editors: The following panels show how to link with external resources such as :
The RDMtoolkit
The Pistoia Alliance
The Turing Way Book of Data Science
5.9. References:¶
References
- 1
W. Gu, S. Hasan, P. Rocca-Serra, and V. P. Satagopam. Road to effective data curation for translational research. Drug Discov Today, Dec 2020.
5.10. Authors¶
Note
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
Important
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.
Note
Consult the python file global_variables_fairplus.py
Authors
Name |
ORCID |
Affiliation |
Type |
ELIXIR Node |
Contribution |
|---|---|---|---|---|---|
University of Oxford |
|
Writing - Review & Editing |
|||
University of Luxembourg |
|
Writing - Review & Editing |
