Finding and obtaining open datasets

# Finding and obtaining open datasets

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## Where is Open Data in the Open Science Universe?

- Open data is only a small part of the open science movement

.footnote[Image source from Foster Open Science [(www.fosteropenscience.eu/resources)](https://www.fosteropenscience.eu/resources).]

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## Different types of open data

- Accessibility is only one part of Openness

]

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## Different types of open data

- Accessibility is only one part of Openness

- Open data should be FAIR[1]:
  - Findable
  - Accessible
  - Interoperable
  - Reusable
]

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## FAIR data[1]

- **Findable**:
  The first step in (re)using data is to find them. Metadata and data should be easy to find for both humans and computers.

- **Accessible**:
  Once the user finds the required data, she/he needs to know **how** can they be accessed, possibly including authentication and authorisation.

- **Interoperable**:
  The data usually need to interoperate with applications or workflows for analysis, storage, and processing. (Meta)data should use a formal, accessible, shared language or format

- **Reusable**:
  Data and metadata should be well-described so that they can be replicated and/or combined in different settings.

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## Finding Open data

- Starting points:
    - Data Resources known in your network
    - Publication with link to data source / repository
    - Search in public repositories

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## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed

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## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed
.pull-right[
<img src="../images/CPRD.png" width="90%" height="90%" />
]
    - Commercial / Paid access 
        - e.g. [(CPRD)](https://www.cprd.com/)

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## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed
    - Commercial / Paid access 
        - e.g. [(CPRD)](https://www.cprd.com/)
    - Data sharing within a project/collaboration (restricted)
    
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## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed
.pull-right[
<img src="../images/whitehall.png" width="90%" height="90%" />
]
    - Commercial / Paid access 
        - e.g. [(CPRD)](https://www.cprd.com/)
    - Data sharing within a project/collaboration (restricted)
    - Gated Data Sharing (Application + Evaluation of proposal, processing fee)
        - e.g. Whitehall II Study [(Whitehall II Study)](https://www.ucl.ac.uk/epidemiology-health-care/research/epidemiology-and-public-health/research/whitehall-ii/data-sharing)

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## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed
.pull-right[
<img src="../images/ELSA.png" width="90%" height="90%" />
]
    - Commercial / Paid access 
        - e.g. [(CPRD)](https://www.cprd.com/)
    - Data sharing within a project/collaboration (restricted)
    - Gated Data Sharing (Application + Evaluation of proposal, processing fee)
        - e.g. Whitehall II Study [(Whitehall II Study)](https://www.ucl.ac.uk/epidemiology-health-care/research/epidemiology-and-public-health/research/whitehall-ii/data-sharing)
    - Only registration required
        - e.g. English Longitudinal Study of Ageing [(ELSA)](https://www.elsa-project.ac.uk/data-and-documentation) accessible via the [(UK Data Service)](https://ukdataservice.ac.uk/)

---

## Known data resources

- Wide range of options between fully closed and fully open (FAIR)
    - Closed
.pull-right[
<img src="../images/NHANES.png" width="90%" height="90%" />
]
    - Commercial / Paid access 
        - e.g. [(CPRD)](https://www.cprd.com/)
    - Data sharing within a project/collaboration (restricted)
    - Gated Data Sharing (Application + Evaluation of proposal, processing fee)
        - e.g. Whitehall II Study [(Whitehall II Study)](https://www.ucl.ac.uk/epidemiology-health-care/research/epidemiology-and-public-health/research/whitehall-ii/data-sharing)
    - Only registration required
        - e.g. English Longitudinal Study of Ageing [(ELSA)](https://www.elsa-project.ac.uk/data-and-documentation) accessible via the [(UK Data Service)](https://ukdataservice.ac.uk/)
    - No registration required
        - e.g. [(NHANES)](https://wwwn.cdc.gov/nchs/nhanes/)

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## Finding Open data

- Starting points:
    - Data Resource known in your network
    - Publication with link to data source / repository
    - Search in public repositories

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## Publications with links to data

Journals increasingly encourage publication of (links to) data

Let's have a look at the PLOS journals:

- Policy requiring researchers to share the data underlying their results or to state why this is not possible
- But: Are authors complying with these requirements? [(PLOS Medicine: Diabetes)](https://journals.plos.org/plosmedicine/search?filterJournals=PLoSMedicine&filterSubjects=Medicine+and%20health%20sciences&filterArticleTypes=Research%20Article&q=diabetes&page=1)

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## Publications with links to data

Journals increasingly encourage publication of (links to) data

Let's have a look at the PLOS journals:

- Policy requiring researchers to share the data underlying their results or to state why this is not possible
- But: Are authors complying with these requirements? [(Review by Federer et al)](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194768)
.center[
<img src="../images/FedererPLOSONE.png" width="85%" height="85%" />
]

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## Review of PLOS data statements (Federer 2018)

.center[
![](https://journals.plos.org/plosone/article/figure/image?id=10.1371/journal.pone.0194768.t001&size=medium)
]

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## Finding Open data

- Starting points:
    - Data Resource known in your network
    - Publication with link to data source / repository
    - Search in public repositories

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## Figshare

[Figshare: Diabetes](https://figshare.com/search?q=diabetes&sortBy=posted_date&sortType=desc&licenses=1,2,47,52,3,40,49&itemTypes=3&categories=7,48)
.center[
<img src="../images/Figshare.png" width="90%" height="90%" />
]

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## Dryad

[Dryad: Diabetes](https://datadryad.org/search?utf8=%E2%9C%93&q=diabetes)
.center[
<img src="../images/Dryad.png" width="90%" height="90%" />
]

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## Github Collection

[Github: Awesome Public Datasets](https://github.com/awesomedata/awesome-public-datasets)
.center[
<img src="../images/Github.png" width="90%" height="90%" />
]

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## Rigsarkivet (Overview and access info)

[Rigsarkivet: Sundhed](https://www.sa.dk/da/forskning-rigsarkivet/rigsarkivet-sundhed/)
.center[
<img src="../images/Rigsarkivet.png" width="90%" height="90%" />
]

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## Open Neuro (MRI and fMRI images)

[Openneuro: Diabetes](https://openneuro.org/search/diabetes)
.center[
<img src="../images/OpenNeuro.png" width="90%" height="90%" />
]

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## How are you allowed to use data you find?

- First important step: know who 'owns' the data and what they allow you to do with it
    - Public Domain: There is no owner, you are allowed to use the data in any way
    - Data are protected by copyright: but the owner gives you a license to use it in a certain way
  
- Different Open Licenses

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## Different Open Licenses

- Creative Commons:
    - CC BY-NC (Attribution-NonCommercial)
    - CC BY-ND (Attribution-NoDerivatives)
    - CC BY-SA (Attribution-ShareAlike)
    - CC-BY (only Attribution required)
    - CC0 (= placing something in the public domain)
- Open Data Commons Licenses:
    - ODC-By (Attribution required)
    - PDDL (= placing a database in the public domain)
]
.pull-right[
Mostly for Open Source Software:

- GNU
- MIT
]

Finding a suitable license for your data: [(Choose a license)](https://choosealicense.com/) or [(Creative Commons Chooser)](https://chooser-beta.creativecommons.org/)

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## Summary

- Open Data is only a part of the Open Science Universe
- Open Data should be FAIR (but are often only in part)
- There are many different ways of finding Open Data, none are ideal (yet)
- Be mindful of the licence attached to a dataset

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## Links and references

.pull-left[
**General Resources**
- [Go Fair] (International initiative to promote FAIR data)
- [Foster Open Science] (EU project with general resources on Open Science)
- [Open Science Framework] (Resources for Open Science)
- [Center for Open Science] (Resources for Open Science)

]

.pull-right[
**Data Repositories**
- [Dryad] (Mostly Manuscript-linked)
- [Figshare] (Mostly Manuscript-linked)
- [European Data Portal] (Mostly high aggregation level)
- [NIH data repositories] (Links to topic specific repositories)
- [YODA project] (Request access to RCT data)
- [Project Datasphere] (Cancer Research databases)
- [Nature recommended data repositories]
- [ClinicalStudyDataRequest] (Request access to RCT data)
]

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# Thank you!

[Open Science Framework]: https://osf.io/
[European Data Portal]: https://www.europeandataportal.eu/
[GitHub]: https://github.com/
[Dryad]: https://datadryad.org/
[Figshare]: https://figshare.com/
[Center for Open Science]: https://cos.io/
[Choose a License]: https://choosealicense.com/
[Creative Commons]: https://creativecommons.org/
[Go Fair]: https://www.go-fair.org/fair-principles/
[EU Turning FAIR into reality]: https://ec.europa.eu/info/sites/info/files/turning_fair_into_reality_0.pdf
[Plan S]: https://www.coalition-s.org/
[Foster Open Science]: https://www.fosteropenscience.eu/
[NIH data repositories]: https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html
[UK Data Archive]: https://data-archive.ac.uk/find/archive-catalogue
[YODA project]: https://yoda.yale.edu/
[Project Datasphere]: https://www.projectdatasphere.org/projectdatasphere/html/home
[ClinicalStudyDataRequest]: https://www.clinicalstudydatarequest.com/
[Nature recommended data repositories]: https://www.nature.com/sdata/policies/repositories