04-data.knit

class: title-slide
count: false

.title[
  # 04 - Data
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella & Davide Massidda
]

.institute[

]

---
class: center, middle, inverse

# Step III: Sharing Data
---
# Data Structures

--
.pull-left-50[
- **Wide Format**

]
.pull-right-50[
- **Long Format.**

<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> Name </th>
   <th style="text-align:left;"> Sex </th>
   <th style="text-align:center;"> Age </th>
   <th style="text-align:left;"> Time </th>
   <th style="text-align:center;"> Value </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Alice </td>
   <td style="text-align:left;"> F </td>
   <td style="text-align:center;"> 24 </td>
   <td style="text-align:left;"> Pre </td>
   <td style="text-align:center;"> ... </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Alice </td>
   <td style="text-align:left;"> F </td>
   <td style="text-align:center;"> 24 </td>
   <td style="text-align:left;"> Post </td>
   <td style="text-align:center;"> ... </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Bob </td>
   <td style="text-align:left;"> M </td>
   <td style="text-align:center;"> 21 </td>
   <td style="text-align:left;"> Pre </td>
   <td style="text-align:center;"> ... </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Bob </td>
   <td style="text-align:left;"> M </td>
   <td style="text-align:center;"> 21 </td>
   <td style="text-align:left;"> Post </td>
   <td style="text-align:center;"> ... </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Carl </td>
   <td style="text-align:left;"> M </td>
   <td style="text-align:center;"> 23 </td>
   <td style="text-align:left;"> Pre </td>
   <td style="text-align:center;"> ... </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Carl </td>
   <td style="text-align:left;"> M </td>
   <td style="text-align:center;"> 23 </td>
   <td style="text-align:left;"> Post </td>
   <td style="text-align:center;"> ... </td>
  </tr>
</tbody>
</table>

]

---
# Data Structures

- **Relational Model**

.pull-left-50[

<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
    <caption>Subjects</caption>
     <thead>
      <tr>
       <th style="text-align:right;"> ID </th>
       <th style="text-align:left;"> Name </th>
       <th style="text-align:left;"> Sex </th>
       <th style="text-align:right;"> Age </th>
      </tr>
     </thead>
    <tbody>
      <tr>
       <td style="text-align:right;"> 1 </td>
       <td style="text-align:left;"> Alice </td>
       <td style="text-align:left;"> F </td>
       <td style="text-align:right;"> 24 </td>
      </tr>
      <tr>
       <td style="text-align:right;"> 2 </td>
       <td style="text-align:left;"> Bob </td>
       <td style="text-align:left;"> M </td>
       <td style="text-align:right;"> 21 </td>
      </tr>
      <tr>
       <td style="text-align:right;"> 3 </td>
       <td style="text-align:left;"> Carl </td>
       <td style="text-align:left;"> M </td>
       <td style="text-align:right;"> 23 </td>
      </tr>
    </tbody>
    </table>

]
.pull-right-50[

<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
    <caption>Study</caption>
     <thead>
      <tr>
       <th style="text-align:center;"> ID </th>
       <th style="text-align:center;"> Subject_ID </th>
       <th style="text-align:left;"> Time </th>
       <th style="text-align:center;"> Value </th>
      </tr>
     </thead>
    <tbody>
      <tr>
       <td style="text-align:center;"> 1 </td>
       <td style="text-align:center;"> 1 </td>
       <td style="text-align:left;"> Pre </td>
       <td style="text-align:center;"> ... </td>
      </tr>
      <tr>
       <td style="text-align:center;"> 2 </td>
       <td style="text-align:center;"> 1 </td>
       <td style="text-align:left;"> Post </td>
       <td style="text-align:center;"> ... </td>
      </tr>
      <tr>
       <td style="text-align:center;"> 3 </td>
       <td style="text-align:center;"> 2 </td>
       <td style="text-align:left;"> Pre </td>
       <td style="text-align:center;"> ... </td>
      </tr>
      <tr>
       <td style="text-align:center;"> 4 </td>
       <td style="text-align:center;"> 2 </td>
       <td style="text-align:left;"> Post </td>
       <td style="text-align:center;"> ... </td>
      </tr>
      <tr>
       <td style="text-align:center;"> 5 </td>
       <td style="text-align:center;"> 3 </td>
       <td style="text-align:left;"> Pre </td>
       <td style="text-align:center;"> ... </td>
      </tr>
      <tr>
       <td style="text-align:center;"> 6 </td>
       <td style="text-align:center;"> 3 </td>
       <td style="text-align:left;"> Post </td>
       <td style="text-align:center;"> ... </td>
      </tr>
    </tbody>
    </table>

]

---
# Data Structures

- **Relational Model**

---
# Data Structures

- **Join Operations**

.move-up-15[
<img src="images/04-data/join.svg" width="60%" style="display: block; margin: auto;" />
]

---
# Data Documentation

.pull-left-50[
.no-border[
#### `README-data.md`
]
]

---
# Data Documentation

.pull-left-50[
.no-border[
#### `README-data.md`
]

General info:

.li-small[
- Study/Project reference
- Authors (citation/contact information)
- License
- Data collection process
]

]
.pull-right-50[
]

---
# Data Documentation

.pull-left-50[
.no-border[
#### `README-data.md`
]

General info:

.li-small[
- Study/Project reference
- Authors (citation/contact information)
- License
- Data collection process
]

Data info:

.li-small[
- Variable name
- Variable type
- Unit of measure
- Values range or levels
- Missing/special values
]
]
.pull-right-50[
]
---
# Data Documentation

.pull-left-50[
.no-border[
#### `README-data.md`
]

General info:

.li-small[
- Study/Project reference
- Authors (citation/contact information)
- License
- Data collection process
]

Data info:

.li-small[
- Variable name
- Variable type
- Unit of measure
- Values range or levels
- Missing/special values
]
]
.pull-right-50[
.code-small[

```r
#-----     README-data.md    ----#

# Data README

## General Info

Details about the study/project, authors, License, 
or other relevant information.

Description of the data collection process or links 
to the paper/external documentation for further details.

## Details

The dataset `my-study.csv` is formed by n rows and k columns:

- `Name`. Character variable indicating the subject name
- `Sex`. Factor variable indicating the subject gender 
         (levels are `"F"` for females and `"M"` for males)
- `Age`. Numeric variable indicating subject age (in years)
- `Time`. Factor variable indicating measure time 
         (levels are `"Pre"` and `"Post"`)
- `Value`. Numeric variable indicating the outcome measure 
         [unit of measure]
- ...
```
]
]

---
# Data Good Practices

- File format - proprietary vs open

- Machine readable - no `.pdf`

- Indicate encoding - prefer `UTF-8`

- The rawer the better

.emoji-xl[
.center[
❤️ `.csv` ❤️
]
]

---
# Data Sharing

.pull-left-50[
<img src="images/04-data/kepler.jpeg" width="55%" style="display: block; margin: auto;" />

.center[Johannes Kepler (1571 - 1630)]
]
.pull-right-50[

]

---
# Data Sharing

.pull-left-50[
<img src="images/04-data/kepler.jpeg" width="55%" style="display: block; margin: auto;" />

.center[Johannes Kepler (1571 - 1630)]
]
.pull-right-50[
<img src="images/04-data/brahe.jpg" width="55%" style="display: block; margin: auto;" />

.center[Tycho Brahe (1546 - 1601)]
]

---
# Data Sharing

<br>

---
# Data Sharing

.pull-left-50[
#### Legal Aspects:

.li-small[
- GDPR (😭)
- Personal data and anonymization
- Geographical restrictions
]

]
.pull-right-50[

]
---
# Data Sharing

.pull-left-50[
#### Legal Aspects:

.li-small[
- GDPR (😭)
- Personal data and anonymization
- Geographical restrictions
]

.move-down-50[
#### LICENSE - Open Data Commons:
]

.li-small[
- **ODC-BY.** Attribution License
- **ODbL.** Open Database License  (BY-SA)
- **PDDL.** Public Domain (all rights waived)
- **DbCL.** Database Content License (BY-SA)
]

.center[https://opendatacommons.org/]
]
.pull-right-50[

]

---
# Data Sharing

.pull-left-50[
#### Legal Aspects:

.li-small[
- GDPR (😭)
- Personal data and anonymization
- Geographical restrictions
]

.move-down-50[
#### LICENSE - Open Data Commons:
]

.li-small[
- **ODC-BY.** Attribution License
- **ODbL.** Open Database License  (BY-SA)
- **PDDL.** Public Domain (all rights waived)
- **DbCL.** Database Content License (BY-SA)
]

.center[https://opendatacommons.org/]
]
.pull-right-50[
#### Where?

.li-small[
- <img style="height:2em" src="images/04-data/osf.png" class="inline-img"> (https://osf.io)
- <img style="height:2em" src="images/04-data/github.png" class="inline-img">(https://github.com)
- <img style="height:2em" src="images/04-data/gitlab.png" class="inline-img">(https://gitlab.com)
- <img style="height:2em" src="images/04-data/dataverse.png" class="inline-img">(https://dataverse.org)
- <img style="height:2em" src="images/04-data/databrary.png" class="inline-img">(https://nyu.databrary.org)
- <img style="height:2em" src="images/04-data/icpsr.png" class="inline-img">(https://www.icpsr.umich.edu)
]
]

---
# Metadata

.pull-left-50[
`CITATION.cff`

.code-small[
```
cff-version: 1.2.0
message: "For attribution, please cite it as below."
authors:
  - family-names: "Zandonella Callegher"
    given-names: "Claudio"
    orcid: "https://orcid.org/0000-0001-7721-6318"
  - family-names: "Massidda"
    given-names: "Davide"
title: "The Open Science Manual: Make Your Scientific
        Research Accessible and Reproducible"
version: 1.0.1
doi: 10.5281/zenodo.6521850
date-released: 2023-01-02
url: "https://github.com/arca-dpss/manual-open-science"
```
]
]
.pull-right-50[

.move-up-50[
{{content}}
]
]

--
<img src="images/04-data/citation.png" width="90%" style="display: block; margin: auto;" />

---
# Metadata

.pull-left-50[
`CITATION.cff`

.move-up-50[
<img src="images/04-data/citation.png" width="90%" style="display: block; margin: auto;" />
]

Documentation:

.li-small[
- https://citation-file-format.github.io/
- [About CITATION files](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files)
]

]

---
# Metadata

#### Schema.org

<br>

.center[
*“Schema.org is a collaborative, community activity with a mission to create,<br>maintain, and promote schemas for structured data on the Internet,<br>on web pages, in email messages, and beyond.”*
]

<br>

Documentation:

.li-small[
- https://schema.org/
- https://www.software.ac.uk/resources/guides/adding-schema-dot-org
]
---
class: inverse, center, middle

# Sharing is Caring!

## Moving to the next step...